Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea species complex (Cladoniaceae).

Accepted Manuscript Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea species complex (Cladoniaceae) Brinda A. Timsina, Georg Hausner, Michele D. Piercey-Normore PII:

S1878-6146(14)00121-4

DOI:

10.1016/j.funbio.2014.08.001

Reference:

FUNBIO 507

To appear in:

Fungal Biology

Received Date: 13 March 2014 Revised Date:

14 July 2014

Accepted Date: 4 August 2014

Please cite this article as: Timsina, B.A, Hausner, G., Piercey-Normore, M.D, Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea species complex (Cladoniaceae), Fungal Biology (2014), doi: 10.1016/j.funbio.2014.08.001. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Running title: PKS gene evolution in Cladonia

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Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea

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species complex (Cladoniaceae)

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BRINDA A TIMSINA, 2GEORG HAUSNER, AND 1MICHELE D PIERCEY-NORMORE

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Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada, R3T

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2N2, 2Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T

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Corresponding author: Michele D. Piercey-Normore

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Email: [email protected]

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Phone: (204) 474-9610; Fax: (204) 474-7588.

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ACCEPTED MANUSCRIPT 2 ABSTRACT

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Lichen-forming fungi synthesize a diversity of polyketides, but only a few non-reducing

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polyketide synthase (PKS) genes from a lichen-forming fungus have been linked with a specific

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polyketide. While it is a challenge to link the large number of PKS paralogs in fungi with specific

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products, it might be expected that the PKS paralogs from closely related species would be similar

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because of recent evolutionary divergence. The objectives of this study were to reconstruct a PKS

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gene phylogeny of the C. chlorophaea species complex based on the ketosynthase domain, a

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species phylogeny of the complex, and to explore the presence of PKS gene paralogs among

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members of the species complex. DNA was isolated from 51 individuals of Cladonia chlorophaea,

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C. coccifera, C. grayi, C. fimbriata, C. magyarica, C. merochlorophaea, C. pocillum, and C.

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pyxidata to screen for the presence of 13 PKS paralogs. A 128 sequence PKS gene phylogeny

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using deduced amino acid sequences estimated from the 13 PKS paralogs and sequences subjected

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to BLASTx comparisons showed losses of each of two PKS domains (ketosynthase and

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methylation). The species relationships were consistent with previous studies where incomplete

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lineage sorting was inferred. This research provided insight into the evolution of PKS genes in the

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C. chlorophaea group, species evolution in the group, and it identified potential directions for

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further investigation of polyketide synthesis in the C. chlorophaea species complex.

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Key words: Cladonia chlorophaea complex; gene phylogeny; ITS rDNA species phylogeny,

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polyketide synthases; PKS paralogs.

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Introduction The Cladonia chlorophaea species complex is a group of closely related lichen-forming fungi in the large and diverse genus Cladonia (Ahti 2000). Within the C. chlorophaea species

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complex there are 13 chemical variants known to produce 14 secondary metabolic products

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(Culberson & Kristinsson 1969). Genetic variability within C. chlorophaea was first reported by

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DePriest (1993) and subsequently the C. chlorophaea species complex was shown to be

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polymorphic (DePriest 1994; Beiggi & Piercey-Normore 2007; Kotelko & Piercey-Normore 2010)

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but the species within the complex may be restricted to different habitats (Wetherbee 1969;

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Hennings 1983; Oksanen 1987). Three habitats in North Carolina, from coastal to mountainous

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regions, were shown to correspond with the amount of fumarprotocetraric acid produced by

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members of the C. chlorophaea species complex (Culberson et al. 1977). Fumarprotocetraric acid

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is one of hundreds of polyketides produced by lichen-forming fungi (Huneck & Yoshimura 1996)

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and the roles of these products are varied including allelopathic, light screening, hydrophobic, and

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antimicrobial or antiherbivory properties (Huneck 1999).

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Fungal polyketide synthesis (PKS) is catalysed by iterative Type I PKSs, multidomain

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proteins (Keller et al. 2005) with the following ketosynthase (KS), acyl transferase (AT), acyl

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carrier protein (ACP or PPb), three reducing (dehydratase [DH], enoyl reductase [ER],

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ketoreductase [KR]), and thioesterase (Th) domains (Graziani et al. 2004). The KS, AT, and

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ACP/PPb domains comprise the simplest fungal PKSs, which are required for carboxylic acid

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condensation (Hopwood 1997) but they lack any reduction in their chemical structure (Bingle et

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al. 1999). The fungal PKSs that include KR, DH and ER domains, produce polyketides with

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varying degrees of chemical reduction in structure. The ME domain is sometimes present and is

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responsible for methylation of the third carbon producing ß-orcinol depsides and depsidones.

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ACCEPTED MANUSCRIPT 4 Orcinol products do not require the ME domain. The Cladonia species produce a mix of orcinol

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and b-orcinol products. While the link between many polyketides and PKS genes is becoming

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known in fungi that do not form lichens, only a few non-reducing PKS genes from lichen-forming

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fungi, e. g. Cladonia grayi and C. macilenta, have been closely linked to a specific lichen

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polyketide (Armaleo et al. 2011; Jeong et al. 2014).

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The large number of PKS gene paralogs (Kroken et al. 2003; Nierman et al. 2005;

Opanowicz et al. 2006; Hoffmeister & Keller 2007; Sanchez et al. 2008; Schmitt et al. 2008;

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Schmitt & Lumbsch 2009; Armaleo et al. 2011) may facilitate adaptation to changing

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environments (Fitzgerald et al. 2011). They are thought to arise through gene duplication events,

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gene decay, mobile genetic elements, gene fusion, or other mechanisms (reviewed by Long et al.

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2003) within a genome and the DNA sequence and gene function may diverge through subsequent

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generations. Alternative explanations include horizontal gene transfer from bacteria to fungi

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(Schmitt & Lumbsch 2009), or between fungi (Khaldi et al. 2008), which may have resulted in

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gains and losses of genes through evolution (Koonin 2005; Blanco et al. 2006). The evolution of

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typical lichen compounds was hypothesized to be facilitated by the horizontal transfer of an

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actinobacterial PKS gene (Schmitt & Lumbsch 2009), producing multiple paralogs. Knowledge of

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the large numbers of paralogs reported for non-lichenized (Sanchez et al., 2008) and lichenized

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fungi (Opanowicz et al. 2006) and those available in the publicly accessible Cladonia grayi

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genome (Armaleo et al. 2011), may suggest that PKS gene paralogs should be the same within

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closely related species. While it is expected that the PKS paralog sequences from closely related

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species would be similar because of a recent evolutionary divergence, it is not clear whether the

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sharing of few PKS genes by fungi of the same genus (Kroken et al. 2003) was a result of the

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broad overview of PKS gene evolution. The comparative analysis of PKS gene paralogs from

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ACCEPTED MANUSCRIPT 5 multiple individuals within one species, through DNA sequence comparison and by screening for

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their presence in individuals, would allow novel insights into the evolution of the PKS genes

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within a closely related group of species.

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The goals of this study were to reconstruct the PKS gene phylogeny of closely related species in the C. chlorophaea species complex, to estimate a species phylogeny, and to explore the

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presence and absence of PKS gene paralogs among closely related members of the Cladonia

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chlorophaea complex, specifically Cladonia chlorophaea s. s., C. grayi, C. fimbriata, C.

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magyarica, C. merochlorophaea, C. pocillum, C. pyxidata, and one ally outside the complex, C.

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coccifera.

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10 Materials and Methods

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Lichen material

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All samples used in this study are listed in Table 1 showing the source of collection, TLC results,

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and the purpose of the specimen in this study. Fifty-one DNA samples (37 from North America

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and 14 from Europe) that include representatives from seven species of the Cladonia chlorophaea

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species complex (C. chlorophaea s.s., C. fimbriata, C. grayi, C. magyarica, C. merochlorophaea,

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C. pocillum, and C. pyxidata; Huovinen & Ahti 1982) and one more distantly related species, C.

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coccifera, for a total of eight species were used for the PCR screening. The phylogenetic analyses

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included 128 sequences for the PKS gene phylogeny, which are listed in Table 2. In addition, 13

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concatenated PKS gene sequences and 36 ITS rDNA sequences representing 6 and 9 taxa,

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respectively, were used for the species phylogenies. The 13 PKS paralogs were also analysed as

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individual data sets (Supplementary Figure 1).

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Thin Layer Chromatography

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Thin Layer Chromatography (TLC) was performed on all samples collected in this study (Table 1)

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to confirm the major secondary metabolites present in each thallus. The TLC protocol was

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modified from Culberson (1972) and Orange et al. (2001) using solvent A (toluene 180mL:

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dioxane 45mL: glacial acetic acid 5mL). Spot characteristics of secondary metabolites outlined in

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Huovinen & Ahti (1982) and Orange et al. (2001) were consulted for polyketide identification.

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Positive controls were taken from herbarium samples of species that are known to contain large

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quantities of the metabolite such as merochlorophaeic acid in C. wainioi, grayanic acid in C. grayi,

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fumarprotocetraric acid in C. verruculosa, sekikaic acid in Cliostomum toensbergii, and

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homosekikaic acid in C. rei and Ramalina intermedia. All specimens have been deposited in the

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University of Manitoba herbarium (WIN).

12 DNA extraction and amplification

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Total DNA was extracted from 1-2 adjacent podetia from the same specimen (representing a

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sample) following a CTAB DNA extraction protocol (Grube et al. 1995). The amplification of

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PKS paralogs was done using a series of primers designed in this study (Table 3). These primers

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were designed from PKS sequence fragments (kindly provided by D. Armaleo, Duke University)

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from Cladonia grayi, each corresponding to a KS (Keto Synthase) domain (Supplementary Table

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1). The corresponding genome sequences can be found at http://genome.jgi-

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psf.org/Clagr3/Clagr3.home.html.

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Fragments were amplified from 51 specimens representing eight species using two primer

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sets for each of 13 PKS paralogs (Table 3), and the presence of the fragment indicated the primer

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sites were present in the template DNA. The absence of a fragment indicated that one or more

ACCEPTED MANUSCRIPT 7 primer sites were absent from the template DNA, but the gene was not necessarily absent. Three

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annealing temperatures were tested for the PKS genes including 52oC, 54 oC, and 56oC, but the

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best results were obtained using 58 oC. Two sets of primer pairs in four combinations were used to

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test for presence of PCR product for each KS domain. The 13 paralogs were labeled CgrPKS1 to

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CgrPKS16 (excluding 4, 6, 8, and 9) and CgrPKSMSAS to be consistent with those used in

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Armaleo et al. (2011).

Amplification of the PKS genes and the mtSSU region was done with initial denaturing at

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94oC for 5 min, then 33 cycles of denaturing at 94oC for 1 min, annealing at 58oC for 1 min,

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extension at 72oC for 1.5 min. All amplifications were performed in a thermal cycler (Biometra T-

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Gradient; Tampa, FL, USA) in 20 µL reaction volumes with 1X buffer (200 mM Tris-HCl, 500

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mM KCl) with 1.25 units GO Taq (Go Taq ® Hot Start polymerase, Promega), 3.125 mM MgCl2

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1.25 mM of each dNTP, 1.0 M of each primer, and about 50 ng of DNA. The mtSSU was used as

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a positive control to confirm the presence of DNA. The mitochondrial small subunit gene (mtSSU)

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was amplified with mrSSU1 and mrSSU2R primers (mrSSU1: AGCAGTGAGGAATATTGGTC;

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Zoller et al. 1999) and mrSSU2R; CCTTCGTCCTTCAACGTCAG; Zoller et al. 1999).

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Amplifications were performed in a thermal cycler (Biometra T-Gradient; Tampa, FL, USA) in 20

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µL reaction volumes with 1X buffer (200 mM Tris-HCl, 500 mM KCl), 1.25 units GO Taq (Go

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Taq ® Hot Start polymerase, Promega), 3.125 mM MgCl2 1.25 mM of each dNTP, 1.0 M of each

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primer, and 40 to 60 ng of DNA. The Internal Transcribed Spacers (ITS) of the nuclear ribosomal

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DNA (rDNA) were also amplified using the primer pair ITS1F (Gardes & Bruns 1993) and ITS2

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(White et al. 1990). A touchdown PCR cycle consisted of initial denaturing at 94oC for 5 min, then

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30 cycles of denaturing at 94oC for 1 min, annealing at 60oC, 58oC, 56oC, and 54oC each for 2

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cycles and 45 sec, then 52oC for 45 sec for the remaining 22 cycles, and extension at 72oC for 1

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min. The ITS rDNA was used to examine species phylogeny.

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A volume of 200-300 µL PCR product for each sample was precipitated by adding 2.5 volumes of

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100% ethanol and 0.2 volumes of 5M NaCl and centrifuged at 13000 rpm for 10 min. The DNA

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pellet was dissolved in 20 µL sterile distilled water, and gel purified by excising the band from 1%

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agarose gel and purified using the Wizard ® SV Gel and PCR Clean-Up System (Promega,

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Madison, WI, USA) following the manufacturer’s instructions. Cycle sequencing reaction volumes

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were 20 µL, which contained about 50 ng of purified DNA. BigDye V3.1 (Applied Biosystem,

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Foster City, CA, USA) and the PCR primers (Table 3) were used for sequencing. Post reaction

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clean up followed the manufacturer’s instructions for the ethylene diamine tetraacetic acid

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(EDTA) and ethanol precipitation method. The dried product was dissolved in 20 µL formamide,

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denatured at 95oC for 5 min, placed on ice, and loaded into a 96-well plate for sequencing on a

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3130 Genetic Analyser (Applied Biosystems, Foster City, CA, USA).

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Data analysis

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For the PKS phylogenetic analysis, 128 sequences were aligned consisting of a partial KS domain

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for 115 sequences generated in this study and 13 sequences from GenBank BLAST searches. A

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BLASTx search was performed using each of the 13 PKS paralogs as queries in NCBI GenBank.

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The results indicated best matches with the KS domains in other GenBank accessions. The 13

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sequences from the NCBI search representing the best matches were combined with the PKS gene

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alignment and were used to infer the domain structure in Fig. 1. All nucleotide sequences

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generated in this study have been deposited in NCBI GenBank (Table 2). Amino acid sequences

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for the PKS paralogs were aligned using ClustalX 2.1 (Thompson et al. 1997). The 128-gene PKS alignment was subjected to phylogenetic analyses using Maximum

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Parsimony (MP) in PAUP* 4.0b10 (Swofford 2003) and Bayesian analysis in MrBayes v3.2.1

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(Huelsenbeck & Ronquist 2001) as both parsimony and likelihood based methods offer advantages

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(Penny and Steel 2000; Kolaczkowski and Thornton 2004). The options for the MP analyses were

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tree bisection and reconnection (TBR) branch swapping, heuristic searches using 1000 random

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addition replicates, and bootstrap searches of 500 resamplings (Felsenstein 1985). Bootstrap

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values greater than 70 are reported in the phylogenies. For Bayesian analysis, a six parameter

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hLRTs (Hierarchial Likelihood Ratio Tests) model was applied with a gamma shaped parameter

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and proportion of invariable sites uniformly distributed under the AIC criterion. This model was

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the best model estimated with Modeltest 3.7 (Posada & Crandall 1998) for the 128-gene PKS and

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the ITS rDNA analyses. Bayesian analyses were performed using 5,000,000 generations for the

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PKS gene phylogeny. All runs converged on similar likelihood values and were terminated when

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the standard deviation of split frequencies fell below 0.01. Every 500th tree was sampled, and the

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first 25% of trees were discarded as burn-in for the analyses. Posterior probability values greater

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than 95 are reported on the phylogenies. The Aspergillus clavatus (XM001268489) sequence was

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assigned as an outgroup, as a reference sequence to the phylogeny in Kroken et al. (2003). We also

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included a second sequence of PKS reducing clade IV (from Kroken et al. 2003). The ITS rDNA

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and the concatenated PKS analyses were analysed by MP and Maximum Likelihood (ML) in

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PAUP* using the same MP criteria as above. The ML criteria were ten heuristic searches using

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HKY85, a transition/transversion ratio of 2.0, and kappa = 4.00. The individual PKS alignments

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were analysed using MP in PAUP* and unrooted bootstrap trees were presented (Supplementary

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Fig. 1). All trees were visualized using a MP tree from PAUP* and the support values and clade

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labels were added using Microsoft powerpoint. Ancestral state character evolution was estimated for the reducing/non-reducing domains

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and the presence and absence of the ME domain using Mesquite ver 2.75 (Maddison and

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Maddison 2011). A maximum parsimony approach was used to trace the character evolution in the

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128 sequence PKS gene phylogeny. The option "trace character over trees" was used to determine

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uncertainty as equivocal results in tree topology. This was implemented for the 73 parsimony trees

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imported from the phylogenetic analysis in PAUP*.

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Scoring PKS paralogs

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Two different sets of 13 paralog-specific primer pairs (Table 3) in four combinations were used to

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determine the presence or absence of PKS paralogs in 51 samples belonging to eight species of

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Cladonia. Since three species, C. coccifera, C. magyarica, and C. fimbriata, were represented by

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two, one, and two specimens respectively, five species with three or more specimens each, were

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screened for PCR products. The presence or absence of PCR product was recorded from gel

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electrophoresis. Amplification of the ITS rDNA and the mitochondrial small subunit (mtSSU)

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rDNA primers were used as positive controls to ensure the presence of DNA even when no PKS

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fragments were amplified. Sixteen representatives of the ITS rDNA were sequenced to ensure the

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correct species, and thereafter the fragment lengths were used for confirmation of species.

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Results

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Confirmation of polyketides and PKS gene sequences

ACCEPTED MANUSCRIPT 11 Fumarprotocetraric acid was detected in all individuals of all species examined, except for two

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individuals of C. coccifera, which produced usnic acid and zeorin. Many individuals contained at

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least one additional major metabolite and some contained trace amounts of other metabolites

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(Table 1). Polyketides are not listed for those species whose sequences were obtained from

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GenBank.

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The top hits of the 13 Cladonia PKS sequence fragments in the NCBI database confirmed that they represented KS domains of fungal PKSs (Supplementary Table 1). The samples of C.

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chlorophaea (N8787 and N8792) were used as queries against the C. grayi genome

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(http://genome.jgi-psf.org/Clagr3/Clagr3.home.html), and all produced perfect matches, except for

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paralog CgrPKS12, which resulted in no match, indicating missing sequences in the current

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assembly.

12 PKS gene phylogeny

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The 128-gene PKS gene phylogeny was inferred from the amino acid sequences belonging to 13

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PKS paralogs (Fig. 1). The PKS alignment for the MP tree contains 447 total characters with 279

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parsimoniously informative characters and the length of the tree is 3391 steps. The Consistency

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and Retention Indices of the phylogenetic tree are 0.6868 and 0.9239, respectively. All 13 paralogs

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formed highly supported monophyletic clades with greater than 95% bootstrap and 95% posterior

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probability support. Six major clades (A to F) are indicated in the PKS gene tree, where clade A

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represents CgrPKS2 and one sequence from GenBank. Clade B represents CgrPKS1, CgrPKS13,

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CgrPKS14 and three sequences from GenBank, which is supported by 89% bootstrap and greater

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than 95% posterior probability. Clade C has low support and contains CgrPKS3, CgrPKS5,

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CgrPKS7, CgrPKS10, and five sequences from GenBank. Clade C showed topological and

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ACCEPTED MANUSCRIPT 12 support discrepancies between Bayesian and MP analyses where Giberella moniliformis was basal

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to CgrPKS3, CgrPKS7, CgrPKS10, CgrPKS5, CgrPKS1, CgrPKS13 and CgrPKS14 in Bayesian

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analysis but it was clustered with CgrPKS3, CgrPKS7 and CgrPKS10 in the MP analysis. Even

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though the posterior probability was 100 for the lineage leading to CgrPKS7, CgrPKS10,

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Zymoseptoria tritici, and Aspergillus clavatus (Fig.1), the bootstrap support for the lineage was

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only 60%. Clade D contains sequences representing CgrPKS15 and one GenBank sequence. Clade

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E has low support with posterior probability of 77 and less than 50% bootstrap support and

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contains CgrPKS11, CgrPKS12, CgrPKSMSAS, and one sequence from GenBank. The lineage in

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clade E which leads to CgrPKS11 and CgrPKS12 (asterisk) had only 78% bootstrap support and

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less than 60% posterior probability and collapsed in the Bayesian analysis. Similarly, the lineage

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leading to CgrPKSMSAS and Aspergillus niger (asterisk) had 100% bootstrap support and less

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than 60% posterior probability and also collapsed in the Bayesian analysis. Clade F contains

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sequences representing CgrPKS16. CgrPKS15 and CgrPKS16 clustered together in the Bayesian

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analysis with 96% posterior probability but were separated as clades D and F in the MP analysis.

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The outgroup sequence, Aspergillus clavatus (XM001268489) is present in Clade IV sensu

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Kroken et al. (2003) to place this tree into perspective with a larger phylogenetic pattern of PKS

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genes. The MP bootstrap consensus tree (insert in Fig. 1) shows the collapsing of the backbone but

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it supported all six clades. Putative reducing and non-reducing lineages are indicated on the tree

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and were deduced from the BLASTx results with the assigned ancestral sequence containing

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reducing (R) and methylation (ME) domains. The ancestral state reconstruction showed a

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difference between the methylation and the reducing domains (Supplementary Fig. 2) in the trees,

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which is consistent with Fig. 1. The reconstruction also shows the backbone to be equivocal

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among the 73 MP trees supporting the collapse in the consensus tree (Fig. 1 insert).

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ACCEPTED MANUSCRIPT 13 1 PKS paralog screening

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Fifty-one samples representing eight species of Cladonia exhibited variable numbers of the 13

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possible PKS paralogs based on PCR screening, but only five species are shown in Fig. 2 which

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contained three or more samples each. The mtSSU rDNA was used a DNA control for this

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screening and produced bands in all 51 samples tested (not shown). Two sets of primers in four

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combinations and four annealing temperatures were used to amplify DNA from each of the 13

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paralogs which demonstrated the presence or absence of the primer sequence within the gene

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paralog. The internal primers were intended to partially address the issue of false negatives. All

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paralogs were amplified from each of five species (C. chlorophaea [7 specimens], C. grayi [3

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specimens], C. merochlorophaea [5 specimens], C. pocillum [14 specimens] and C. pyxidata [18

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specimens]) except CgrPKS12, which was not amplified from C. chlorophaea s.s. Three additional

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species did not produce PCR product from all paralogs (C. coccifera, C. fimbriata and C.

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magyarica) and were represented by only five individuals. Two samples of C. coccifera produced

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bands for CgrPKS1, CgrPKS2, CgrPKS3, CgrPKS7, CgrPKS12, CgrPKS13, CgrPKS15, and

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CgrPKS16. Two samples of C. fimbriata produced bands for all paralogs except CgrPKS12 and

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CgrPKS16. One sample of C. magyarica produced bands for CgrPKS1, CgrPKS2, CgrPKS3, and

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CgrPKS12.

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C. chlorophaea species phylogeny

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The species tree from the ITS rDNA is the bootstrap tree that represents 401 MP trees from 551

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aligned characters of 215 steps and was produced from 36 sequences (16 from this study; Table 1)

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representing nine species. Twenty sequences were obtained from GenBank. There were 78

ACCEPTED MANUSCRIPT 14 informative characters, the CI was 0.8372, and the RI was 0.8763 (Fig. 3A). The ML analysis of

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the ITS rDNA alignment produced one tree with -Ln=2102.2934 and the topology was consistent

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the maximum parsimony bootstrap tree. C. fimbriata and C. novochlorophaea formed

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monophyletic clades supported by 98% and 65% bootstrap in the ITS rDNA tree. None of the

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other taxa were monophyletic. The species tree from the 12 concatenated PKS genes represents

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one of three MP trees from 7998 aligned characters of 1425 steps. There were 438 informative

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characters, the CI was 0.7979, and the RI was 0.6175 (Fig. 3B). The tree shows the clustering of

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C. pocillum and C. pyxidata with 63% bootstrap support. While C. fimbriata also falls within the

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highly supported clade of 95%, a sequence of C. chlorophaea also falls within this clade. The ML

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tree of the concatenated PKS sequences is -Ln=19598.368 (Fig. 3C) and it had a similar topology

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to that of the MP tree but the C. pyxidata-C. pocillum group was separated (shaded boxes). The

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analyses of the 12 separate PKS paralog alignments showed no monophyletic species. The

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numbers of sequences for each tree ranged from five to 13 sequences (Supplementary Fig. 1).

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Three trees from CgrPKS2, CgrPKS5, and CgrPKS12 showed a highly supported separation of C.

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pyxidata-C. pocillum from C. chlorophaea s. l. chemospecies by 77%, 100%, and 100% bootstrap

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support, respectively.

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17 Discussion

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Origins of two PKS domains in the C. chlorophaea group

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This study shows that the presence of the ME and R domains in the PKS gene is polyphyletic

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among this group of taxa (Fig. 1). Polyphyly is evident even in the low resolution of the MP

22

bootstrap consensus tree (Fig. 1 insert). Since the assigned outgroup contains both ME and R

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domains, the hypothesized ME losses must have resulted in at least one ME gain to explain the

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ACCEPTED MANUSCRIPT 15 presence of ME domain in CgrPKS7 and CgrPKS10. However, the five losses of R domains have

2

not resulted in any secondary gains of reducing domains. These multiple domain losses are

3

supported by a broader range of taxa in Kroken et al. (2003) where one of the members of Clade

4

IV was assigned as the outgroup in this study to establish that the basal condition may be the

5

presence of the ME and the R domains in the PKS gene for the taxa selected in this analysis. The

6

loss of the R and ME domains may result from accumulation of large numbers of genes through

7

duplication and divergence (Long et al. 2003). However, the less common gain of domains has

8

been hypothesized to occur through horizontal gene transfer (Kroken et al. 2003; Schmitt &

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Lumbsch 2009; Khaldi et al. 2008), by domain skipping during modular polyketide synthesis

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(Beck et al. 2002), or by mechanisms reviewed in Long et al. (2003). Multiple losses or gains of

11

the domains would facilitate the adaptive potential of the species by allowing functional gene

12

divergence. Divergence between orcinol and b-orcinol producers would be expected to have a ME

13

domain in some PKS genes but not others. While the backbone in the tree has low support, the

14

divergence in clades B and C together, and to some extent clade E, represent multiple lineages and

15

have moderate to high support suggesting a radiation of gene evolution containing 10 of the 13

16

paralogs. If this rapid evolution is associated with gene function (Alba et al. 2000), and driven by

17

adaptation to environmental conditions, the large number of paralogs reported for fungi (Kroken et

18

al. 2003; Nierman et al. 2005; Opanowicz et al. 2006; Hoffmeister & Keller 2007; Sanchez et al.

19

2008; Schmitt et al. 2008; Schmitt & Lumbsch 2009; Armaleo et al. 2011) is conceivable.

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The loss and gain of domains hypothesized in this study may also be interpreted through

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selection of taxa or gene paralogs. Taxon selection is an important consideration for accuracy of

22

phylogenetic estimation in every study (Heath et al. 2008). Generally, as the number of taxa

23

increases, the phylogenetic error decreases. Density of taxon selection is another consideration

ACCEPTED MANUSCRIPT 16 where dense clustering may result in long branches such as between some of the GenBank

2

accessions and the Cladonia taxa used in this study. Since the domain structure was based on

3

GenBank database matches where closely related species with the same gene are usually absent,

4

there is a large evolutionary distance between some Cladonia clades and the GenBank accessions

5

resulting in long branches. The long branches allow for possibile evolutionary changes that may

6

affect the presence of the R or ME domains in the Cladonia ancestor of each clade. One clade in

7

particular, clade C, contains discrepancies in support between Bayesian and MP analyses, which

8

may have resulted from large evolutionary distances of the five GenBank taxa or genes with long

9

branches included in the clade. Long branches have been used to explain discrepancies between

10

nonparametric bootstrap and posterior probability (Huelsenbeck et al. 2002; Douady et al. 2003).

11

Even if clade C collapsed because of low support, the presence and absence of the ME domain

12

within the clade cannot be refuted (based on the structures provided), but the origin of ME

13

evolution would be in question. Similarly, clade A includes the long branch of the more distant

14

Botryotinia sequence but the large distance between Botryotinia and Cladonia may allow for

15

evolutionary changes in domain structure which is also supported by the equivocal nature of the

16

lineage in the ancestral state reconstruction (Supplementary Fig. 2). Even though the possibility of

17

discrepancies in domain structure is recognized, the inferred domain structure is consistent with

18

those of Armaleo et al. (2011). While the early evolution of the PKS genes in this group of

19

Cladonia is not resolved, the relationships among some groups of PKS genes can be discerned

20

from this study.

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DNA variation in the C. chlorophaea group

ACCEPTED MANUSCRIPT 17 Variation in polyketide products may be explained by differential expression of a PKS gene to

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allow for acclimation to external environmental conditions (Schlichting & Smith 2002; Sumner et

3

al. 2006) leading to fewer metabolic products than there are genes present. One to three secondary

4

metabolites were detected in all the samples examined in this study (Table 1) but a small

5

proportion of individuals in any one of the species may have no detectable compounds or a species

6

such as C. merochlorophaea may have up to six polyketides (Culberson & Kristinsson 1969). In

7

general, the numbers of gene paralogs encoding PKS enzymes is much higher than the number of

8

polyketides produced (Hoffmeister & Keller 2007; Sanchez et al. 2008; Gilsenan et al. 2009) and

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large numbers of PKS genes are expected in the C. grayi genome (JGI).

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The presence of PCR products from all 13 paralogs distributed among five species and 51

11

specimens of the Cladonia chlorophaea species complex (except CgrPKS12) in Fig. 2, supports a

12

role of these PKS genes in adaptive evolution (Schmidt et al. 2003; Ghalambor et al. 2007).

13

However, even though PCR screening of the paralogs is subject to false negatives because of

14

potential primer - template mismatching, these results illustrate the high level of variability of the

15

most conserved PKS domain, i.e. the KS domain, within this closely related group of species.

16

Primer - template mismatching may be the most likely explanation for the variability in presence

17

of genes where the implication is that a mismatch results in the absence of PCR product. However,

18

another explanation is the selection on the gene product resulting in some paralogs having stronger

19

selection than others. False negatives would result in an underestimation of the presence of

20

paralogs. One scenario is that the 13 paralogs detected in this study are all present within this

21

group of closely related species. In this case, some genes may be difficult to amplify because of

22

high GC content in the template DNA (McDowell et al. 1998), secondary structure (Henke et al.

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1997), high levels of polysaccharides (Monteiro et al. 1997) or other inhibitors of PCR (Bickley et

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ACCEPTED MANUSCRIPT 18 al. 1996), or variation in the target DNA region. Variation in the target regions of the KS domain

2

of these PKS genes may prevent primer annealing and final PCR product. However, the absence of

3

the gene or presence of pseudogenes cannot be ruled out as another possible explanation for the

4

absence of PCR product, which might be further investigated using Southern blots or genome

5

sequence analysis.

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6 Phylogeny of the C. chlorophaea group

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The ITS rDNA divergence between C. pocillum-fimbriata group and the C. chorophaea-

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merochlorophaea-grayi group, with C. pyxidata present in both groups, (Fig. 3; Kotelko and

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Piercey-Normore 2010), may suggest incomplete lineage sorting, i.e. that the groups of species

11

have not had sufficient time since divergence to become reproductively isolated (Knowles &

12

Carstens 2007), or the sampling may include paralogous ITS regions that evolve separately (e. g.

13

Gulyás et al. 2005; Hartmann et al. 2001). Incomplete lineage sorting may be driven by ecological

14

conditions, such as soil pH in C. pyxidata and C. pocillum (Gilbert 1977). The ITS rDNA is one

15

gene of choice for barcoding to represent fungal species (Schoch et al. 2012; Pino-Bodas et al.

16

2013) but it showed polyphyly in previous studies of this taxonomic group (Beiggi and Piercey-

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Normore 2007; Kotelko & Piercey-Normore 2010).

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complex (C. chlorophaea s.s., C. merochlorophaea, C. grayi [in this study]) by morphological

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features (Ahti 2000) although some overlap in features may exist. C. fimbriata has morphological

21

features (Kowalewska et al. 2008) that distinguish it from both these groups, and its monophyly in

22

this study was also supported by Dolnick et al. (2010), where three samples (different from those

23

in this study) were also monophyletic suggesting that the species status of C. fimbriata is not

ACCEPTED MANUSCRIPT 19 controversial. C. pyxidata and C. pocillum could be separated using morphological features

2

(Kowalewska et al. 2008) but they overlap in ITS rDNA sequence similarity forming conspecifics

3

(Kotelko and Piercey-Normore 2010).

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The chemical species, C. chlorophaea, C. merochlorophaea and C. grayi fall within C. chlorophaea s. l., and share morphological features (Kowalewska et al. 2008) but differ in their

6

polyketide production, fumarprotocetraric acid alone, merochlorophaeic acid, and grayanic acid,

7

respectively (Culberson & Kristinsson 1969). High support for C. merochlorophaea (three

8

sequences) and C. novochlorophaea (two sequences) together, was shown by Dolnik et al. (2010)

9

but no other members of the species complex were examined. Chemospecies within the C.

10

chlorophaea s. l. were examined by Culberson et al. (1988), who showed that interbreeding

11

occurred among individuals of C. grayi and C. merochlorophaea based on shared polyketides,

12

which might explain the polyphyly between those species and C. chlorophaea. However, if

13

purifying selection is thought to drive evolution in the KS domain of PKS genes (Muggia et al.

14

2008) toward niche specialization in this group of species, then the ecological distributions or

15

habitats may reflect the distribution of chemotypes, especially where ecological differences were

16

found (Wetherbee 1969; Hennings 1983; Oksanen 1987). The geographic and chemospecies

17

distributions in the C. chlorophaea complex were not consistent with one another (Holien and

18

Tonsberg 1985), but the geographic and chemical distributions were consistent with two allied

19

species, C. conista and C. humilis (Pino-Bodas et al. 2012).

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If PKS genes evolve independently of species evolution or are undergoing purifying

21

selection which might be expected since they are thought to be influenced by environmental

22

conditions (Fox and Howlett 2008; Stocker-Worgotter 2001; Timsina et al. 2013), a PKS topology

23

different from an ITS topology would be expected. In this study the topology of the concatenated

ACCEPTED MANUSCRIPT 20 PKS genes showed no species monophyly even though it was limited by the number of samples

2

used in the analysis, which was similar to the ITS topology. However, the three individual PKS

3

gene analyses (CgrPKS2, CgrPKS5, and CgrPKS12) showed high support for separation between

4

the C. pyxidata-C. pocillum group and the C. chlorophaea s. l. chemospecies group (Suppl. Fig.

5

1), but the analysis was limited by the number of taxa. It is difficult to distinguish among these

6

processes because neither the concatenated PKS nor ITS rDNA topologies show monophyly. The

7

lack of ITS monophyly may indicate ITS rDNA paralogs (Gulyás et al. 2005) or incomplete

8

lineage sorting (Knowles and Carstens, 2007), while the PKS genes may reflect purifying selection

9

(Muggia et al. 2008) because of their functions influenced by environmental conditions.

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Studies on phylogenetic relationships within this species group are generally focused only on some species within the group and include some of the allied species, which impedes a

12

complete understanding of evolution in the group of species. In addition, the relationship among

13

these species may be complicated by the number of genes used and taxon sampling in the analysis.

14

Even though this study provides insights into the potential for incomplete lineage sorting and ITS

15

paralogs, the sampling issues must be addressed before evolutionary processes such as

16

hybridization, incomplete lineage sorting, and ITS rDNA paralogs can be inferred. Dense taxon

17

sampling has the potential to address these issues in this difficult group of species, but it also has

18

its challenges.

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In conclusion, this study provided some of the first insights into PKS gene evolution and

20

their variability among and within species of the C. chlorophaea species complex. The results

21

provide direction for further functional studies of these genes in this taxonomic group. There were

22

four interpretations in this study: 1) Six (CgrPKS1, CgrPKS2, CgrPKS13, CgrPKS14, CgrPKS15

23

and CgrPKS16) of the 13 PKS paralogs analyzed for selection in Cladonia chlorophaea complex

ACCEPTED MANUSCRIPT 21 encode putative non-reducing PKS enzymes while the others encode reducing enzymes. If genes

2

for reducing enzymes are present, further studies may investigate whether the species are able to

3

synthesize reduced polyketides. 2) Incomplete lineage sorting may account for the inability to

4

separate the species within this closely related group, but more complete taxon sampling and

5

genome coverage is needed to address the evolutionary processes involved. 3) The presence of

6

CgrPKS16 in C. pocillum, C. pyxidata, C. chlorophaea, and C. merochlorophaea, in addition to C.

7

grayi, deserves more study. If CgrPKS16 codes for a grayanic acid synthase, the other species

8

should also be able to produce grayanic acid if grown under the appropriate conditions. However,

9

questions on PKS functionality raised in this study are speculative and must involve further

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detailed functional approaches. 4) The PKS gene phylogeny and the screening study suggests that

11

domain structure may vary among closely related species which may represent multiple losses of

12

reducing and methylation domains in the C. chlorophaea complex. The loss of these domains in a

13

closely related group of fungi is consistent with high rates of evolution in these genes. These

14

insights offer valuable directions for further investigation to better understand PKS gene evolution

15

in the C. chlorophaea s. l. and allies, a ubiquitous and difficult group of fungi.

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Acknowledgements

The authors thank D. Armaleo (Duke University) for providing fragments of fungal PKS

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sequences and providing helpful comments on an early review of the manuscript, R. Yahr (Royal

20

Botanic Garden, Edinburgh) and R. Kotelko for providing lichen samples, and J. Doering for lab

21

assistance. Funding was provided by NSERC (GH and MPN) and a Faculty of Science Graduate

22

studentship (BT), University of Manitoba.

23


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Schmitt I, Lumbsch HT, 2009. Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi. PLoS ONE 4: e4437. Steel M, Penny D, 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17: 839–850.


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two- and tripartite symbioses. Symbiosis 30:207–227.

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2

Sumner S, Pereboom JJM, Jordan WC, 2006. Differential gene expression and phenotypic

5

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6

Proceedings of the Royal Society B 273: 19–26.

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8

Swofford DL, 2003. PAUP. Phylogenetic analysis using Parsimony, Version 4. Sunderland, M.S: Sinauer Associates.

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11

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12

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14

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17 18 19 20 21 22 23

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EP

16

Wetherbee R, 1969. Population studies in the chemical species of the Cladonia chlorophaea

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AC C

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TE D

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Zoller S, Scheidegger C, Sperisen C, 1999. PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31: 511-516.


Source of collection (BLAST accession no.)

TLC

Aspergillus clavatus Aspergillus clavatus Aspergillus flavus Aspergillus niger Aspergillus terreus Bipolaris maydis

nt nt nt nt nt nt

nt fu

PKS sequence PCR screening

Cladonia chlorophaea Cladonia chlorophaea

Submitted by Nierman (XP001273762) Submitted by Nierman (XM001268489) Submitted by Nierman (XP002381496) Pel et al. (2007) (XM001402371) Submitted by Nierman (XP001210231) Submitted by Kroken and Turgeon (AAR90276) Genoscope CEA (CCD56082) UK, Scotland, Aberdeenshire, Creg Choinnich Wood. Yahr 5307 UK, England, Northumbria. Yahr 5335 UK, Scotland, Aberdeenshire. Yahr 5346

Cladonia chlorophaea Cladonia chlorophaea

UK, Scotland, Aberdeenshire. Yahr 5347 UK, England, Lancashire. Yahr 5361

fu fu

Cladonia coccifera

Canada, Manitoba, Wapusk National Park, Noochewayum Creek. Normore 10134

us, ze

Cladonia coccifera

Canada, Ontario, east of Borups Corners. Normore 6592 Canada, Manitoba, Wapusk National Park. Normore 9932 Canada, Manitoba, north of Grand Rapids. Normore 5600 UK, England, Northumbria. Yahr 5328

us, ze

TE D

M AN U

Botryotinia fuckeliana Cladonia chlorophaea

Cladonia fimbriata Cladonia fimbriata

Cladonia grayi

EP

Cladonia fimbriata

Cladonia grayi

SC

Species

RI PT

Table 1 – List of species, source of collection (BLAST accession numbers or location and date of collection), polyketides detected (fu=fumarprotocetraric acid; prot=protocetraric acid; sek=sekaikaic acid; at=atranorin; hom=homosekaikaic acid; 4-0-me=4-0methylcryptochlorophaeic acid; us-usnic acid; ze=zeorin; gr=grayanic acid; mer=merochlorophaeic acid; and nt=not tested), and the test for which the specimen was used for all vouchers in this study. ITS accession numbers are indicated on Fig. 3)

Canada, Manitoba, Wapusk National Park, Noochewaywum Creek. Normore 10130 Canada, Manitoba, Sandilands Provincial Forest. Normore 9644

AC C

1 2 3 4 5 6

fu fu

fu fu fu

fu, gr fu, gr

Cladonia grayi

Canada, Ontario, west of Spanish. Normore 7209

fu, gr

Cladonia grayi

from D. Armaleo (Armaleo et al. 2011) GU930713 Iran, East Azerbaijan. Sohrabi 4553 Canada, Manitoba, Sandilands Provincial Forest. Normore 8787 Canada, Manitoba, Sandilands Provincial Forest. Normore 8792 Canada, Manitoba, Wapusk National Park. Normore 9914

nt

Cladonia magyarica Cladonia merochlorophaea Cladonia merochlorophaea Cladonia merochlorophaea

fu, at fu, mer fu, mer, 4-0me fu, mer

Purpose in this study PKS sequence PKS sequence PKS sequence PKS sequence PKS sequence PKS sequence

PCR screening PCR screening ITS: KF378718 PCR screening PKS sequence PCR screening ITS: KF378717 PKS sequence PCR screening ITS: KF378721 ITS: KF378722 PCR screening ITS: KF378724 ITS: KF378725 PKS sequence PCR screening ITS: KF378723 PCR screening ITS: KF378727 PKS sequence PCR screening ITS: KF378716 PKS sequence PCR screening ITS: KF378726 PKS sequence PCR screening PKS sequence PCR screening PKS sequence PCR screening PCR screening ITS: KF378720


Cladonia merochlorophaea

Canada, Manitoba, Wapusk National Park, Noochewaywum Creek. Normore 10138 Canada, Quebec, northwest of Le Domaine. Normore 6824 UK, England, Northumbria. Yahr 5336

fu, sek, mer


UK, Scotland, Mid Perthshire. Yahr 5342

fu, sek, mer

Cladonia pocillum

Canada, British Columbia, north of Buckinghorse River. Kotelko 870 Canada, Yukon, Destruction Bay. Kotelko 962 Canada, British Columbia, north of Buckinghorse River. Kotelko 869

fu, at

Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pocillum Cladonia pyxidata

Canada, Yukon, Takini burn. Kotelko 945 Canada, Yukon, Aishihik Lake Road. Kotelko 951 Canada, Yukon, Congdon Creek. Kotelko 966 Canada, Yukon, east of Aishihik Lake Rd. Kotelko 974 Canada, Manitoba, Long Point. Normore 5556 Canada, Manitoba, north of The Pas. Normore 6081 Canada, Manitoba, south of The Pas. Normore 6085 Canada, Manitoba, Wapusk National Park. Normore 9061 Canada, Manitoba, Hwy 391, Leaf Rapids. Normore 9460 Canada, Manitoba, Mossy Portage Road. Normore 6102 Canada, Manitoba, Highway 6. Normore 6112 Canada, Manitoba, Long Point. Normore 6118 Canada, British Columbia. Kotelko 726

Canada, Yukon, west of Johnsons Crossing,. Kotelko 905 Canada, Yukon, Fox Lake. Kotelko 938 Canada, Yukon, Aishihik Lake Road. Kotelko 950 Canada, Yukon, Mount. Goldenside. Kotelko 999 Canada, Manitoba, Leaf Rapids. Normore 9458 Canada, Manitoba, Wapusk National Park, Rupert Creek. Normore 9817 Canada, Manitoba, Wapusk National Park. Normore 9996 Canada, Manitoba, south of West Ray. Normore 6086 Canada, Manitoba, Long Point. Normore

AC C

Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata

Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata

fu fu

PCR screening ITS: KF378719 PKS sequence PCR screening PKS sequence PCR screening PKS sequence PCR screening ITS: KF378715 PKS sequence PCR screening ITS: KF378729

fu fu

PKS sequence PCR screening ITS: KF378728 PCR screening PCR screening

fu fu

PCR screening PCR screening

fu

PCR screening

fu

PCR screening

fu

PCR screening

fu

fu

PKS sequence PCR screening PKS sequence PCR screening PCR screening

fu

PCR screening

fu

PCR screening

fu, prot

fu fu

PKS sequence PCR screening PKS sequence PCR screening PCR screening PCR screening

fu, prot

PCR screening

fu fu

PKS sequence PCR screening PCR screening

fu, prot

PCR screening

fu

PCR screening

fu

PCR screening

M AN U

Cladonia pocillum Cladonia pocillum

TE D

Cladonia pocillum

EP

Cladonia pocillum

fu, mer, hom

SC


fu, mer

RI PT


fu

fu


UK, Scotland, Perthshire. Yahr 5343 UK, England, NW Yorkshire. Lusy s.n. Kroken et al. (2003) (AY495603) Kroken et al. (2003) (AY495595) Submitted by Nowrousian (XP003350625) Submitted by Brunauer (ACJ24814) Submitted by Wang et al. (AEM75019) Goodwin et al. (2011) (XP003849645)

2 3 4

10 11 12

PCR screening PCR screening PCR screening PKS sequence PCR screening ITS: KF378730 PCR screening PCR screening PKS sequence PKS sequence PKS sequence PKS sequence PKS sequence PKS sequence

fu fu nt nt nt nt nt nt

EP

9

fu fu fu, prot fu

AC C

8

PCR screening

TE D

5

7

fu

M AN U

1

6

PCR screening

RI PT

Cladonia pyxidata Cladonia pyxidata Gibberella moniliformis Gibberella moniliformis Sordaria macrospora Umbilicaria torrefacta Usnea longissima Zymoseptoria tritici

Cladonia pyxidata

fu

SC

Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata Cladonia pyxidata

6115 Canada, Ontario, east of Kenora. Normore 6576 Canada, Ontario, east of Kenora. Normore 6578 UK, Scotland, Perthshire. Yahr 4952 UK, Scotland, Perthshire. Yahr 4953 UK, Scotland, Midlothian. Yahr 5309b UK, Scotland, Perthshire. Yahr 5340

Cladonia pyxidata

13 14 15 16

Table 3 – List of PCR and internal PKS primers designed in this study showing primer names and primer sequences (5’to 3’). The internal primers designed from each of the PCR primer fragments

ACCEPTED MANUSCRIPT 33 are indicated with a “2” at the end of the name. Primer names refer to each of the PKS paralogs (CgrPKS1, CgrPKS2, CgrPKS3, CgrPKS5, CgrPKS7, CgrPKS10, CgrPKS11, CgrPKS12, CgrPKS13, CgrPKS14, CgrPKS15, CgrPKS16, and CgrPKSMSAS). Primer sequence (5’-3’)

Internal primer name

Internal primer sequence (5’-3’)

PKS-1-DA-F PKS-1-DA-R PKS-2-DA-F PKS-2-DA-R PKS-3-DA-F PKS-3-DA-R PKS-5-DA-F PKS-5-DA-R PKS-7-DA-F PKS-7-DA-R PKS-10-DA-F PKS-10-DA-R PKS-11-DA-F PKS-11-DA-R PKS-12-DA-F PKS-12-DA-R PKS-13-DA-F PKS-13-DA-R PKS-14-DA-F PKS-14-DA-R PKS-15-DA-F PKS-15-DA-R PKS-16-DA-F PKS-16-DA-R PKS-MSAS-DA-F PKS-MSAS-DA-R

TGCCTTTCAAGCGATGGACT CAGGAGAATGCGGAATCGTT ATAGCCACTCAGGGACAGAT TGTGTTTCGCATCAGGCACT GGTGAGCTATGAAGCGCT GGCATCGTAATACCAGCAGT CATCGTCCAACACTGAGTCT GCCAGCATTCTTGTAGGTCT AAGCCCTTGAGAATGCT AGAGTCTCCATCTCGGAT AAGTCACGTACGAAGCCGT TACGCCGTATCAGCCAGAT ATGCTTGGAAGGAGGTCT AGGCTTCCCGAATAAGGT ACGAGGCATTTGAGAACGGT GAACCTAGTCTCACTGGTGT GCAGCTGAAACTGATCCT GTGCATCTCGACATAGCT GATCGCAGAGACCAAAGT TGCGTGATAGACACTGCT CACCTCCAAACGGATTGAGT ATGGATGACGCTGGTCTTGA CGATGTGGAGAAGATCCTT CCAGCATGTGGATGCGTTAT ATGGATCCGCAGCAAAGACT GACCTCCACCAGCTTTCAAT

PKS-1DA-F2 PKS-1DA-R2 PKS-2DA-F2 PKS-2DA-R2 PKS-3DA-F2 PKS-3DA-R2 PKS-5DA-F2 PKS-5DA-R2 PKS-7DA-F2 PKS-7DA-R2 PKS-10DA-F2 PKS-10DA-R2 PKS-11DA-F2 PKS-11DA-R2 PKS-12DA-F2 PKS-12DA-R2 PKS-13DA-F2 PKS-13DA-R2 PKS-14DA-F2 PKS-14DA-R2 PKS-15DA-F2 PKS-15DA-R2 PKS-16DA-F2 PKS-16DA-R2 PKS-MSAS-DA-F2 PKS-MSAS-DA-R2

GCTAAGCTGTCTTGAAGC TTAGCGATCTCCTCCATC ATGTTTCATAGGCGCCAG TTGAGGAGCTTCAGAACG ATGCAGAGTATCGATCGC GTAAGATCTCCCATCTGG GATCTAGGCTACTATTCC AAGAAGCATCGGATCTTG TGACGATGTAACGACCTC TTGTGGTCATCTGATCGG AGATGTCGAGTCAAGTGC TATAGCGCGAATCCTGTC ATGCTGTCGAACCGATTG AATAGTGTCTCCGTCTCG TCCAGCAGTTTAACAGCG TATCCTCATGGGCTCTAC CGCAACCTACTTTATTCC CTTGAGAATAATGGAGCC GCATAACGATCCAACTGG AAGCTTGACGAACAAGCC AATCTGGTGAAGGAGACG ATCCGTAAGGCGTATGAC ATGTCCACGCCAGTAAGC CTCGAGATGGCAGGATAC CAATGTACTTGGTGGTCC GACATACAAGAGCCATCG

5 6 7 8 9 10 11

Figure captions:

SC

M AN U

TE D

AC C

4

RI PT

Primer name

EP

1 2 3

ACCEPTED MANUSCRIPT 34 Fig 1 – Phylogenetic relationship among 13 PKS gene paralogs from the Cladonia chlorophaea

2

species complex based on the amino acid sequence alignment deduced from the DNA sequence of

3

a portion of the KS domain. This is one of 11 most parsimonious trees, which is consistent with

4

the Bayesian tree (not shown; exceptions indicated in the text). Clades discussed in the text are

5

indicated by circled letters (A to F). The assigned outgroup is Aspergillus clavatus

6

(XM001268489). Numbers above branches represent bootstrap support values greater then 70%

7

based on maximum parsimony analysis, thickened black lines indicate posterior probabilities

8

greater than 95% based on Bayesian analysis, and the thickened gray lines indicate posterior

9

probabilities between 60 and 95% based on Bayesian analysis. The loss and gain of R and ME

10

domains are indicated by arrows. The gene structure based on the GenBank sequence included

11

within each clade is represented to the right of each clade along with the paralog name. The single

12

asterisk represents the collapse of the clade in the Bayesian analysis (see text for discussion).

M AN U

SC

RI PT

1

TE D

13

Fig 2 – Results of PCR screening of 51 specimens of five species from the Cladonia chlorophaea

15

species complex using 26 PKS primer pairs (Table 2). The bars represent the percentage values of

16

successful amplifications of each PKS paralog for each of five species (Cchl is C. chlorophaea

17

[n=7], Cgra is C. grayi [n=3], Cmer is C. merochlorophaea [n=5], Cpoc is C. pocillum [n=14], and

18

Cpyx is C. pyxidata [n=18]). The PKS gene is indicated above each graph.

AC C

19

EP

14

20

Fig 3 – Species phylogeny of the C. chlorophaea complex showing A. strict consensus tree using

21

36 ITS rDNA sequences, B. one of 3 MP trees based on 12 concatenated PKS genes, and C. the

22

ML tree based on 12 concatenated PKS genes. Numbers above branches represent bootstrap

23

support values greater then 50% based on maximum parsimony analysis. The shaded boxes show


the difference in the C. pyxidata - C. pocillum group between the the MP and ML trees (discussed

2

in the text).

RI PT

3 4

Supplementary Figure 1 - Unrooted MP phylogenetic trees for each of 12 individual PKS

6

paralogs (except CgrPKS16 with only three taxa). Each tree is the bootstrap consensus tree

7

with all bootstrap values shown on the branches. The analysis was performed on the DNA

8

sequences using the options as for other MP analyses. Three trees show a separation

9

between C. pyxidata-pocillum and the C. chlorophaea-merochlorophaea-grayi clades, the

M AN U

SC

5

10

CgrPKS2, CgrPKS5, and the CgrPKS12 trees. All others show taxa scattered throughout the

11

tree.

Supplementary Figure 2 - Ancestral state reconstruction of the reducing and methylation domains

14

for the PKS phylogeny in species of Cladonia. The black lines represent the presence of the

15

domains, the green lines represent the absence of the domains and the gray lines represent lineages

16

of equivocal position. The PKS paralogs are listed between the trees to represent the clades. Refer

17

to Fig. 1 for details of the phylogeny.

18 19

EP

TE D

13

AC C

12

ACCEPTED MANUSCRIPT

Table 2 – Accession numbers of all PKS gene paralogs generated in this study showing species with collection number in parentheses. Refer to Table 1 for voucher information. N. S. is not sequenced. Cgr PKS1

Cgr PKS2

Cgr PKS3

Cgr PKS5

Cgr PKS7

Cgr PKS10

Cgr PKS11

Cgr PKS12

Cgr PKS13

Cgr PKS14

Cgr PKS15

Cgr PKS16

Cgr PKSMSAS

Cladonia chlorophaea (Y5361) Cladonia coccifera (N10134) Cladonia fimbriata (Y5328) Cladonia grayi (N9644) Cladonia grayi (7209) Cladonia grayi (from D. Armaleo) Cladonia merochlorophaea (N8787) Cladonia merochlorophaea (N8792) Cladonia merochlorophaea (N6824) Cladonia merochlorophaea (Y5336) Cladonia merochlorophaea (Y5342) Cladonia pocillum (K870) Cladonia pocillum (K869) Cladonia pocillum (N9061) Cladonia pocillum (N9460)

KF483881

KF483891

N. S.

N. S.

N. S.

N. S.

KF483935

N. S.

KF483948

N. S.

KJ082052

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082049

N. S.

N. S.

N. S.

KF483895

N. S.

N. S.

KF483926

N. S.

N. S.

N. S.

KF483957

N. S.

KJ082050

N. S.

KF483974

KF483898

KF483910

KF483920

KF483930

KF483937

KF483942

KF483951

KF483960

KJ082060

N. S.

KF483969

SC

M AN U

KF483883

RI PT

Species

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082054

N. S.

N. S.

KF483877

KF483888

KF483905

KF483916

KF483927

KF483932

KF483939

KF483945

KF483947

KF483966

KJ082061

GU930713

KF483975

KF483878

N. S.

KF483896

KF483906

KF483917

KF483928

KF483933

KF483940

KF483946

KF483958

N. S.

KF483976

KF483967

KF483882

N. S.

KF483897

KF483909

KF483919

KF483929

KF483936

KF483941

KF483950

KF483959

KJ082056

N. S.

KF483968

N. S.

N. S.

N. S.

N. S.

KF483879

N. S.

N. S.

KF483907

KF483880

KF483892

N. S.

KF483908

N. S.

N. S.

N. S.

N. S.

KF483893

KF483884 KF483885

TE D

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082053

N. S.

N. S.

N. S.

N. S.

KF483934

N. S.

KF483949

N. S.

N. S.

N. S.

N. S.

KF483918

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082051

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082055

N. S.

N. S.

KF483899

KF483911

KF483921

N. S.

N. S.

KF483943

KF483952

KF483961

N. S.

N. S.

KF483970

KF483894

KF483900

KF483913

KF483922

KF483931

KF483938

N. S.

KF483953

KF483962

N. S.

N. S.

KF483971

N. S.

KF483901

KF483912

KF483923

N. S.

N. S.

N. S.

KF483954

KF483963

KJ082059

KF483977

KF483972

AC C

EP

N. S.

ACCEPTED MANUSCRIPT

KF483889

KF483902

KF483914

KF483924

N. S.

N. S.

KF483944

KF483955

KF483964

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

KJ082057

N. S.

N. S.

KF483887

KF483890

KF483903

KF483915

KF483925

N. S.

N. S.

N. S.

KF483956

KF483965

KJ082058

N. S.

KF483973

N. S.

N. S.

KF483904

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

N. S.

EP

TE D

M AN U

SC

RI PT

KF483886

AC C

Cladonia pyxidata (K726) Cladonia pyxidata (K950) Cladonia pyxidata (N9458) Cladonia pyxidata (Y5340)

ACCEPTED MANUSCRIPT

Loss of R domain 100

Bootstrap 54

100 76

80

81

100 100 95

C 53

99 100

92

(KS-AT-DH-PPb-PPb-ME)

CgrPKS13 (no ME; NR)

B

*

EP

TE D

C

D

AC C

E 53

CgrPKS1 (ME; NR)

CgrPKS2 (KS-AT-ME)

RI PT

96 96

100

C. pocillum (N9061) 79 C. pyxidata (N9458) 97 C. fimbriata (Y5328) CgrPKS1 81 Loss of R domain C. pyxidata (K726) 82 70 100 CgrPKS14 C. pocillum (K869) (KS-AT-PPb-PPb-ME) 50 51 50 98 C. merochlorophaea (Y5342) (no ME; NR) 100 C. chlorophaea (Y5361) C. grayi (KF483877) 53 Bipolaris maydis (AAR90276) (KS-AT-DH-PPb-PP-PP-ME) CgrPKS5 100 54 C. merochlorophaea (N8792) 100 (no ME; NR) grayi (KF483947) 93 C. C. merochlorophaea (N8787) 61 C. pocillum (N9460) CgrPKS3 C. grayi (N9644) 100 56 89 C. merochlorophaea (Y5336) (no ME; R) CgrPKS13 94 C. pocillum (K869) 99 C. pocillum (N9061) (KS-AT-ACP-Th) 92 86 86 100 C. pyxidata (K726) CgrPKS10 (ME; R) C. pyxidata (N9458) 79 60 84 67 C. chlorophaea (Y5361) CgrPKS7 C. fimbriata (Y5328) 100 72 83 Umbilicaria torrefacta (ACJ24814) (ME; R) 90 C. pyxidata (K726) C. pocillum (K869) 98 C. grayi (KF483966) 84 53 98 C. merochlorophaea (N8792) CgrPKS15 98 C. grayi (N9644) 87 CgrPKS14 90 (no ME; NR) 78 59 C. pocillum (N9061) 98 Loss of R and ME domains C. merochlorophaea (N8787) (KS-AT-PPb-PPb-Th) C. pocillum (N9460) 63 CgrPKS16 (no ME; NR) C. pyxidata (N9458) 59 Aspergillus terreus (XP001210231) 83 54 80 CgrPKS11 (ME; R) C. pyxidata (K726) 100 C. grayi (N9644) 99 66 C. pocillum (K869) CgrPKS12 (ME; R) 100 98 C. pyxidata (N9458) C. pocillum (N9460) CgrPKSMSAS CgrPKS5 100 92 C. grayi (KF483916) C. merochlorophaea (N8792) (no ME; R) 100 (KS-AT-DH-ER-KR-PPb) C. pocillum (N9061) 100 C. merochlorophaea (Y5342) Outgroup (ME; R) 99 C. merochlorophaea (Y5336) C. merochlorophaea (N8787) Aspergillus flavus (XP002381496) C. grayi (KF483905) C. pyxidata (Y5340) C. grayi (N9644) C. merochlorophaea (N8792) C. pocillum (N9061) CgrPKS3 100 C. pyxidata (K726) C. pocillum (N9460) (KS-AT-DH-ER-KR-PPb) C. pyxidata (N9458) 96 C. pocillum (K869) 57 C. merochlorophaea (N8787) Sordaria macrospora (XP003350625) 89 C. grayi (KF483932) 92 C. merochlorophaea (N8792) CgrPKS10 100 89 C. merochlorophaea (N8787) Loss of ME domain C. grayi (N9644) (KS-AT-DH-ME-ER-KR-PPb) C. pocillum (N9061) 81 C. merochlorophaea (Y5342) C. grayi (KF483927) C. grayi (N9644) C. merochlorophaea (N8792) 76 89 C. pocillum (N9460) CgrPKS7 C. pyxidata (N9458) 89 C. fimbriata (Y5328) (KS-AT-DH-ME-ER-KR-PPb) C. merochlorophaea (N8787) 100 C. pocillum (K869) C. pocillum (N9061) C. pyxidata (K726) Zymoseptoria tritici (XP003849645) Gain of ME domain Aspergillus clavatus (XP001273762) Gibberella moniliformis (AY495603) C. grayi (KJ082061) C. grayi (N9644) 82 C. merochlorophaea (N8792) C. merochlorophaea (Y5342) C. grayi (N7209) C. pyxidata (K905) CgrPKS15 C. pocillum (N9640) 89 C. pocillum(K870) (KS-AT-PPb-Th) C. pyxidata (N9458) 100 C. chlorophaea (Y5361) C. fimbriata (Y5328) 100 C. merochlorophaea (N6824) C. coccifera (N10134) Usnea longissima (AEM75019) (KS-AT-PPb-PPb) 81 C. merochlorophaea (Y5336) C. merochlorophaea (N8792) Loss of R and ME domains C. chlorophaea (Y5361) CgrPKS11 C. grayi (KF483939) 73 C. grayi (N9644) (KS-AT-DH-ME-ER-KR-PPb) 100 C. merochlorophaea (N8787) C. pocillum (N9061) 78 C. merochlorophaea (N8792) 97 C. grayi (N9644) C. merochlorophaea (N8787) CgrPKS12 C. grayi (KF483945) 100 (KS-AT-DH-ME-ER-KR-PPb) C. pocillum (K869) C. pyxidata (K726) C. pyxidata (N9458) C. pocillum (N9460) Loss of ME domain C. pocillum (K869) C. fimbriata (Y5328) CgrPKSMSAS C. pocillum (N9061) 100 grayi (N9644) (KS-AT-DH-KR-PPb) 96 C. C. merochlorophaea (N8792) 100 C. grayi (KF483975 ) C. merochlorophaea (N8787) R and ME Aspergillus niger (XM001402371) Gibberella moniliformis (AY495595) (KS-AT-DH-ME-ER-KR-PPb) C. grayi (GU930713) 100 C. pocillum (N9460) CgrPKS16 (KS-AT-PPb-PPb-Th) C. merochlorophaea (N8787) Loss of R and ME domains 99

100

A

CgrPKS2 (ME; NR)

SC

B 91

D100 F

70

C. chlorophaea (Y5361) C. pyxidata (N9458) C. pocillum (N9460) C. merochlorophaea (Y5336) 73 75 C. grayi (KF483888) C. merochlorophaea (Y5342) C. merochlorophaea (N8792) C. merochlorophaea (N8787) C. grayi (N9644) C. pyxidata (K726) C. pocillum (N9061) Botryotinia fuckeliana (CCD56082)

M AN U

A 100

Cchl 5361 Cpyx 94582DA 2DA Cpc 9460 2DA Cchl Cchl 5336 5342 2DA 2DA Cgr 2DA8792 2DA Cmero Cmero 8787 2DA Cgr 9644 Cpyx K7262DA 2DA 9061 2DA BCpc fucCCD56082 Cpc 9061 1DA 2DA Cfim 5328 1DA Cpyx 9458 1DA Cpc K869 1DA Cchl Cpyx5342 K7261DA 1DA Cchl 5361DA PKS1 BCGR mayAAR90276 1DA Cmero 8792 13DA Cgr 13DA Cmero 8787 13DA Cpc 9644 9460 13DA 13DA Cgr Cchl 5336 13DA Cpyx 9458 13DA Cpc 869 13DA Cpc 9061 13DA Cpyx5361 K72613DA 13DA Cchl Cfim 5328 13DA UmbilicariatorrefactaACJ24814 13DA Cpyx k726 14DA Cpc PKS k8691414DA Cgr Cmero 8792 14DA Cgr 9644 14DA Cpc 9460 14DA Cpyx 9458 14DA Cmero 8787 14DA Cpc 9061 14DA AterreusNIH2624 Cpyx K7265DA 5DA XP 001210231 14DA Cgr 9644 Cchl 5342 5DA Cmero 8792 5DA Cpc K869 5DA Cpyx 9458 5DA Cpc PKS 94605DA 5DA Cgr Cpc 9061 5DA Cmero 8787 5DA 5336 5DA 5DA ACchl flavusNRRL3357 Cgr PKS 3DA Cpyx9644 53403DA 3DA Cgr Cmero 8792 3DA Cpc Cpyx9460 94583DA 3DA Cpc K869 3DA Cpyx9061 K7263DA 3DA Cpc Cmero 8787 3DA SordariamacrosporaXP003350625 3DA Cgr PKS 10 Cmero 8792 10DA Cmero 8787 10DA Cgr 9644 10DA Cpc 9061 10DA A clavatusNRRL1XP 001273762 10DA Cchl 5342 7DA Cgr 9644 7DA7DA Cmero 8792 Cgr PKS Cpc 946077DA Cpyx 9458 7DA Cfim 5328 7DA Cpyx CmeroK726 87877DA 7DA Cpc K869 7DA Cpc 9061 7DA ZymoseptoriatriticiIPO323 7DA Gmon AY495603 13PKS Cgr 15DA 9644 15DA 15DA 8792 5342 15DA 7209 15DA 9640 9458 15DA 15DA 870 536115DA 15DA 5328 15DA 682415DA 15DA 905 10134 15DA Ul0ng AEM75019 15DA CladoniagrayiGU930713 16DA C poc 9460 16R Cmero 878711DA 16DA Cchl 5336 Cchl 5361 11DA Cmero Cgr PKS8792 11 11DA Cgr 9644 11DA Cmero 8787 11DA Cpc 9061 11DA Cmero 8792 12DA Cgr 9644 12DA Cmero 8787 12DA Cgr 1212DA CpyxPKS K726 Cpc K869 12DA Cpyx9061 9458RS RS Cpc Cgr orsellinic 9644 RS likePKS Cgr Cmero 8792 RS Cfim 5328 RS Cpc K869 RS Cpc 9460 RS Cmero 8787 RS88 XM 001402371 ORS AnigerCBS513 G monAY495595 11DA001268489 12DA AspergillusclavatusXM

E

*

*

F

Aspergillus clavatus (XM 001268489) 10 changes

Figure 1

(KS-AT-DH-ME-ER-KR-PPb)

ACCEPTED MANUSCRIPT

CgrPKS11

100

50

50

0 Cchl Cgra Cmer Cpoc Cpyx

CgrPKS2

100

0

Cchl Cgra Cmer Cpoc Cpyx

CgrPKS12

100

50

50


CgrPKS3

0


CgrPKS13

100

50

SC

100

50


CgrPKS5

0


CgrPKS14

100

M AN U

100 50

50

0


CgrPKS7

100 50

0


CgrPKS15

100 50

0


CgrPKS10

100 50

0


CgrPKS16

100 50

TE D

0

Cchl Cgra Cmer Cpoc Cpyx 100


CgrPKS-‐MSAS

50 0

EP


Figure 2

AC C

RI PT

CgrPKS1

100

56

65

100 72

92

AC C

60

EP

98

98

C. merochlorophaea (Y5342) C. grayi (N9644) DQ530201 C. grayi AF455226 C. grayi GU188415 C. novochlorophaea GU188414 C. novochlorophaea C. merochlorophaea (N9914) GU188416 C. merochlorophaea GU188417 C. merochlorophaea AF455227 C. merochlorophaea KC592272 C. grayi C. grayi (N7209) C. chlorophaea (Y5361) C. chlorophaea (Y5346) C. merochlorophaea (N10138) FJ756765 C. pyxidata FJ756739 C. pyxidata FJ756751 C. pyxidata AF455223 C. pyxidata DQ530199 C. pyxidata C. grayi (N10130) AF455228 C. grayi FR799155 C. chlorophaea C. fimbriata (Y5328) C. fimbriata (Y5600) C. fimbriata (N9932) C. pyxidata (Y5340) C. pocillum (K869) FJ756747 C. pocillum C. pocillum (K962) FJ756729 C. pocillum FJ756741 C. pocillum FJ756766 C. pocillum FJ756769 C. pocillum C. coccifera (N10134) C. coccifera (N6592)

Figure 3

B

C. merochlorophaea (N8787) C. merochlorophaea (N8792) C. merochlorophaea (Y5336) 83 C. merochlorophaea (Y5342) C. grayi (GU930713) C. chlorophaea (Y5361) 96 C. fimbriata (Y5328) 95 98 C. pocillum (N9061) C. pyxidata (K726) 63 C. pocillum (N9460) 84 77 C. pyxidata (N9458) C. pocillum (K869) 50

M AN U

100

TE D

A

SC

RI PT

ACCEPTED MANUSCRIPT

50 changes

C

C. merochlorophaea (Y8787) C. merochlorophaea (Y8792) 97 67 C. merochlorophaea (Y5336) 64 C. grayi (GU930713) C. merochlorophaea (Y5342) C. chlorophaea (Y5361) 99 C. fimbriata (Y5328) 83 C. pocillum (N9460) C. pyxidata (N9458) 99 83 C. pocillum (K869) 97 C. pocillum (N9061) C. pyxidata (K726) 0.01 substitutions/site

ACCEPTED MANUSCRIPT

Highlights for “Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea species complex (Cladoniaceae)” by Timsina et al.

RI PT

We reconstructed a 13-paralog PKS gene phylogeny of the Cladonia chlorophaea species complex. We explore the presence of PKS paralogs among 51 individuals representing five species of the C. chlorophaea complex.

SC

The PKS phylogeny showed multiple losses of reducing and methylation domains. Evolution of the species complex inferred incomplete lineage sorting.

AC C

EP

TE D

M AN U

All paralogs were not exclusively present in members of the C. chlorophaea complex.

ACCEPTED MANUSCRIPT

PKS-2

C. mero 5336 C. mero 5342

C. grayi

C. poc K869

100

C. poc 9061

77

69

C. pyx K726 C. poc 9061

95

C. pyx 9458

C. pyx K726

C. chl 5361

C. pyx K726 100

C. grayi

C. grayi

C. mero 8787

100

C. mero 8787 C. grayi 9644

CgrPKS13

C. fim 5328 C. chl C. poc 5361 K869 C. poc 9061

100

92

100

C. mero 8792

C. mero 5342

C. grayi 9644

97

C. grayi 9644

100 51 64

C. mero 8792

C. poc 9460

C. mero C. mero8787

C. poc 9460

C. pyx K726

C. mero 8787

C. pyx 9458 C. poc 9460

C. poc K869 81

C. mero 8787

68

99 64

100

C. grayi 9644

C. pyx K726 C. poc 9061

65

C. mero 8792

88

C. pyx K726

99

C. poc 9061

C. chl 8792

C. grayi

C. poc 9061

88

C. mero 8787

C. grayi 9644

C. chl 5342

CgrPKS15

CgrPKSMSAS

C. pyx C. poc 9640 9458 C. fim 5328 C. poc 870

91

C. chl 5361

C. grayi 9644

96

C. grayi 9644

52 91

C. mero 5342

C. chl 8792

C. mero 8787

C. grayi

86

100

C. mero 6824

91

C. coc 10134 C. grayi 7209

65

C. mero 8792

100

C. pyx 905

C. grayi C. grayi

100 83

50

C. mero 8792

C. mero 8787

81

C. mero 9644

C. mero 5336

C. mero 8792 C. grayi

C. poc K869

C. fim 5328

CgrPKS14

C. grayi

5336

87

C. grayi

C. pyx K726

88

AC C

93

C. mero 9644

C. mero 8792

C. mero 9644

C. pyx 9458

74

C. pyx K726

52

C. poc K869

C. poc K869

98

C. poc 9061

100 100

C. pyx 5340

CgrPKS12

C. mero 5336 52

C. fim 5328

C. poc 9061

93

EP

98

71

98

C. mero 8787

PKS-10

C. pyx 9458

SC

C. grayi 9644

85

M AN U

82

C. mero 8792

C. poc 9061

C. pyx 9458

PKS-7

C. poc 9460 C. poc C. pyx K869 9458

C. poc 9460

TE D

C. mero 8792

C. chl 5361

CgrPKS11

C. grayi

PKS-5

91

C. mero 8787

C. poc 9460 C. chl 5361

C. mero 5342

C. grayi 87

C. pyx 9458

PKS-3

RI PT

PKS-1

C. poc 9061

96

89

C. poc 9460

C. fim 5328 C. poc K869

C. pyx 9458

Supplementary Figure 1: Unrooted MP phylogenetic trees for each of 12 individual PKS paralogs (except CgrPKS16 with only three taxa). Each tree is the bootstrap consensus tree with all bootstrap values shown on the branches. The analysis was performed on the DNA sequences using the options as for other MP analyses. Three trees show a separation between C. pyxidata-pocillum and the C. chlorophaeamerochlorophaea-grayi clades, the CgrPKS2, CgrPKS5, and the CgrPKS12 trees. All others show taxa scattered throughout the tree.

ACCEPTED MANUSCRIPT Reducing states

Outgroup CgrPKS16

Methyla1on states

CgrPKS11 CgrPKS15

M AN U

CgrPKS2

SC

CgrPKS12

RI PT

CgrPKS-‐MSAS

CgrPKS1

CgrPKS14

TE D

CgrPKS13

AC C

EP

CgrPKS5

CgrPKS3

CgrPKS10 CgrPKS7

Supplementary Figure 2: Ancestral state reconstruction of the reducing and methylation domains for the PKS phylogeny in species of Cladonia. The black lines represent the presence of the domains, the green lines represent the absence of the domains and the gray lines represent lineages of equivocal position. The PKS paralogs are listed between the trees to represent the clades. Refer to Fig. 1 for details of the phylogeny.

ACCEPTED MANUSCRIPT

Supplementary Table 1 – Results of the best matches from NCBI BLAST searches of amino acid sequences for each of the 13 PKS paralogs. R = reducing, PR = partially reducing, NR = nonreducing PKS.

CgrPKS1

Cladonia grayi Bipolaris maydis Botryotinia fuckeliana

GenBank Accession number ADX36084 AAR90276 CCD56082

CgrPKS2

Cladonia grayi Botryotinia fuckeliana Cochliobolus heterostrophus

ADM79462 CCD56082 AAR90276

2.00E-119 2.00E-36 3.00E-35

CgrPKS3

Sordaria macrospora Glomerella graminicola Macrophomina phaseolina Colletotrichum gloeosporioides

XP_003350625 EFQ28216 EKG17457 ELA26923

5.00E-58 5.00E-58 4.00E-61 1.00E-57

KS KS KS Not available

54% 54% 53% 54%

R R R

CgrPKS5

Aspergillus flavus Glarea lozoyensis Aspergillus niger Aspergillus oryzae

XP_002381496 EHL00839 XP_001394029 XP_001824383

3.00E-85 7.00E-89 4.00E-85 5.00E-84

KS KS KS KS

66% 69% 67% 66%

R R R R

CgrPKS7

Zymoseptoria tritici Peyronellaea zeae-maydis Talaromyces marneffei

XP_003849645 AAR85531 XP_002146288

2.00E-25 1.00E-17 1.00E-15

KS KS KS

64% 59% 60%

R R R

CgrPKS10

Aspergillus clavatus Aspergillus fumigatus Neosartorya fischeri Colletotrichum higginsianum

XP_001273762 XP_748462 XP_001258783 CCF44055

1.00E-41 2.00E-43 1.00E-41 8.00E-45

KS KS KS KS

41% 42% 41% 38%

R R R -

CgrPKS11

Gibberella moniliformis Verticillium albo-atrum Peltigera membranacea

AY495595 XM003007480 HM180411

1.00E-87 2.00E-87 1.00E-73

KS Not available Not available

73% 78% 67%

R R R

EP

Max identity

Reducing designation

1.00E-96 2.00E-97 4.00E-100

KS KS Not available

91% 79% 80%

NR R R

Not available KS Not available

87% 43% 37%

NR R R

SC

RI PT

Domain

E value

M AN U

TE D

BLASTp match

AC C

PKS paralog

CgrPKS12

Aspergillus clavatus Verticillium albo-atrum Pyrenophors teres

XM001268489 XM003007480 XM003302099

1.00E-58 4.00E-57 6.00E-54

Not available KS Not available

56% 60% 59%

R R R

CgrPKS13

Cladonia grayi Umbilicaria torrefacta Lecanora muralis Pertusaria amara

ADX36085 ACJ24814 ACJ24817 AAY00077

7.00E-151 5.00E-133 3.00E-126 2.00E-123

FabB KS KS KS

100% 81% 78% 74%

NR -

CgrPKS14

Cladonia grayi Aspergillus terreus Ascochyta rabiei

ADX36086 XP_001210231 ACS74449

2.00E-179 3.00E-146 1.00E-132

KS KS KS

96% 89% 73%

NR NR -

ACCEPTED MANUSCRIPT

Cladonia macilenta Usnea longissima

AFB81352 AEM75019

3.00E-68 2.00E-35

KS KS

82% 53%

NR NR

CgrPKS16

Cladonia grayi Evernia prunastri Coccotrema cucurbitula

ADM79459 EF212820 AY918716

3.00E-39 1.00E-17 3.00E-13

KS KS Not available

83% 65% 44%

NR -

XM_001402371 EF192113 EF192114

1.00E-08 2.00E-05 8.00E-114

Not available Not available KS

EP

TE D

M AN U

SC

Aspergillus niger Pertusaria pustulata Pertusaria subfallens

AC C

CgrPKSMSAS

RI PT

CgrPKS15

37% 42% 83%

R -

Sharpening the species boundaries in the Cladonia mediterranea complex (Cladoniaceae, Ascomycota).

Roles of Conserved Active Site Residues in the Ketosynthase Domain of an Assembly Line Polyketide Synthase.

A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase.

Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase.

Characterization of the Ketosynthase and Acyl Carrier Protein Domains at the LnmI Nonribosomal Peptide Synthetase-Polyketide Synthase Interface for Leinamycin Biosynthesis.

Rational domain swaps reveal insights about chain length control by ketosynthase domains in fungal nonreducing polyketide synthases.

Bioinformatical analysis of the sequences, structures and functions of fungal polyketide synthase product template domains.

Modular organization of genes required for complex polyketide biosynthesis.

Organization of the enzymatic domains in the multifunctional polyketide synthase involved in erythromycin formation in Saccharopolyspora erythraea.

Characterisation of actI-homologous DNA encoding polyketide synthase genes from the monensin producer Streptomyces cinnamonensis.

Analysis of the vaccine potential of plasmid DNA encoding nine mycolactone polyketide synthase domains in Mycobacterium ulcerans infected mice.

Evolution of PAS domains and PAS-containing genes in eukaryotes.

Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis.

Quantification of polyketide synthase genes in tropical urban soils using real-time PCR.

Structure of a modular polyketide synthase.

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi.

Substrate controlled divergence in polyketide synthase catalysis.

Functional replacement of genes for individual polyketide synthase components in Streptomyces coelicolor A3(2) by heterologous genes from a different polyketide pathway.

Three New Non-reducing Polyketide Synthase Genes from the Lichen-Forming Fungus Usnea longissima.

Epimerase and Reductase Activities of Polyketide Synthase Ketoreductase Domains Utilize the Same Conserved Tyrosine and Serine Residues.

Macrodiolide formation by the thioesterase of a modular polyketide synthase.

Dissecting complex polyketide biosynthesis.

Iterative assembly of two separate polyketide chains by the same single-module bacterial polyketide synthase in the biosynthesis of HSAF.

Tylosin polyketide synthase module 3: stereospecificity, stereoselectivity and steady-state kinetic analysis of β-processing domains via diffusible, synthetic substrates.