http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.878912
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of the common bean anthracnose pathogen Colletotrichum lindemuthianum Pablo Gutie´rrez1, Juan Alzate2, Mauricio Salazar Yepes3, and Mauricio Marı´n1 1
Laboratorio de Microbiologı´a Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellı´n, Medellı´n, Colombia, Centro Nacional de Secuenciacio´n Geno´mica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellı´n, Colombia, and 3 Museo Micolo´gico Universidad Nacional de Colombia, Sede Medellı´n-MMUNM, Universidad Nacional de Colombia Sede Medellı´n, Medellı´n, Colombia
Mitochondrial DNA Downloaded from informahealthcare.com by University of Melbourne on 10/30/14 For personal use only.
2
Abstract
Keywords
Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean (Phaseolus vulgaris), one of the most limiting factors for this crop in South and Central America. In this work, the mitochondrial sequence of a Colombian isolate of C. lindemuthianum obtained from a common bean plant (var. Cargamanto) with anthracnose symptoms is presented. The mtDNA codes for 13 proteins of the respiratory chain, 1 ribosomal protein, 2 homing endonucleases, 2 ribosomal RNAs and 28 tRNAs. This is the first report of a complete mtDNA genome sequence from C. lindemuthianum
Ascomycota, Glomerellaceae, mitogenome, Phaseolus vulgaris
Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara (Fungi, Ascomycota, Sordariomycetes, Glomerellaceae), the causal agent of anthracnose in common bean (Phaseolus vulgaris L.), is one of the most limiting factors for this crop in the mountainous regions of South and Central America (Mahuku & Riascos, 2004). Early severe anthracnose can result in severe defoliation and cause reductions in yield up to 95% in regions with high humidity, moderate temperatures and high precipitation frequency (Schwartz et al., 2005). This disease affects the quality of pods by inducing black, sunken cankers containing a salmon-colored ooze centre consisting of millions of conidia. Colletotrichum lindemuthianum can also affect petioles, leaf veins and stems where it induces the typical anthracnose sunken lesions (Schwartz et al., 2005). The genomes of Colletotrichum orbiculare, C. gloeosporioides, C. graminicola and C. higginsianum have been sequenced recently (Gan et al., 2013; O’Connell et al., 2012); however, there are no genome
Correspondence: Pablo Gutie´rrez, Laboratorio de Microbiologı´a Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellı´n, Calle 59A No 63-20, Medellı´n, Colombia. Fax: +57-44309332. E-mail: [email protected]
History Received 11 December 2013 Accepted 18 December 2013 Published online 22 January 2014
projects focused on C. lindemuthianum. Here, we present the complete mitochondrial sequence of a C. lindemuthianum isolate obtained from leaflet and pod tissues of a common bean plant (var. Cargamanto) with anthracnose symptoms collected in the province of Antioquia (Colombia; 04 340 5100 N 74 080 2000 W, 2150 MASL) and identified using morphological analysis and ITS sequencing. The DNA library was sequenced on a GS FLX 454 Life Sciences System (Roche, Basel, Switzerland) and assembled with Newbler (Roche). The C. lindemuthianum mtDNA sequence has been deposited in GenBank under accession: KF953885. The length of sequenced mitochondria of C. lindemuthianum was 36,957 bp with a mean GC content of 30.9% consisting of 34.4% A, 34.7% T, 16.9% G and 14.0% C. All protein-coding genes started with the standard ATG start codon and terminated at either TAA or TAG; as observed in other fungi, the UGA triplet was used as a Trp codon. Interestingly, all protein-coding genes seem to be transcribed with the same polarity. Sixteen ORFs were identified in the mitogenome of C. lindemuthianum; 13 of them code for proteins involved in respiration and oxidative phosphorylation: cob, cox1, cox2, cox3, nad1, nad2, nad4, nad4L, nad5, nad6, atp6, atp8 and atp9. Only one ribosomal protein, rps3, was encoded in the mitogenome of C. lindemuthianum. Two homing endonucleases, LAGLIDADG and GIY, normally associated with intron processing, were identified (Sethuraman et al., 2009). The LAGLIDADG endonuclease was encoded within an IA intron splitting the cob gene while the GIY endonuclease maps 282 bp upstream of the cox1 gene separated by an intervening intron IIB signature. The gene coding for cox1 contained a single ID-type intron while ribosomal protein S3 (rps3) was encoded within a group IA intron as observed in other fungi (Sethuraman et al., 2009). Twent-eight tRNA coding genes were identified in the C. lindemuthianum mtDNA ranging from 70 to 86 nt in size. Two copies were found for trnS (GCT, TGA) and trnT (TGT, TAG) and three for trnR (TCT(2), ACG), trnK (TTT) and trnM
Mitochondrial DNA Downloaded from informahealthcare.com by University of Melbourne on 10/30/14 For personal use only.
2
P. Gutie´rrez et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Circular DNA map of the mitochondrial genome of Colletotrichum lindemuthianum. The outer circle shows the position of protein coding genes (see text for details). Introns are represented light grey. The inner circle depicts the position of structural RNAs (rRNA and tRNA) and type I introns (IA, IB and ID).
(CAT). The large subunit RNA, rnl, was located between rps3 and trnP while the small subunit RNA mapped between trnR and trnY.
Declaration of interest This work was supported by Vicerrectorı´a de Investigaciones de la Universidad Nacional de Colombia, Grant: 20101009932. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the manuscript.
References Gan P, Ikeda K, Irieda H, Narusaka M, O’Connell RJ, Narusaka Y, Kubo Y, Shirasu K. (2013). Comparative genomic and transcriptomic
analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol 197:1236–49. Mahuku SG, Riascos JJ. (2004). Virulence and molecular diversity within Colletotrichum lindemuthianum isolates from Andean and Mesoamerican bean varieties and regions. Eur J Plant Pathol 110: 253–63. O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, et al. (2012). Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 44:1060–5. Schwartz HF, Steadman JR, Hall R, Forster RL. (2005). Compendium of bean diseases. 2nd ed. St Paul, MN: APS Press. Sethuraman J, Majer A, Friedrich NC, Edgell DR, Hausn£er G. (2009). Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene-encoded within an rnl group I intron of Ophiostoma and related taxa. Mol Biol Evol 26:2299–315.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of the common bean anthracnose pathogen Colletotrichum lindemuthianum Pablo Gutie´rrez1, Juan Alzate2, Mauricio Salazar Yepes3, and Mauricio Marı´n1 1
Laboratorio de Microbiologı´a Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellı´n, Medellı´n, Colombia, Centro Nacional de Secuenciacio´n Geno´mica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellı´n, Colombia, and 3 Museo Micolo´gico Universidad Nacional de Colombia, Sede Medellı´n-MMUNM, Universidad Nacional de Colombia Sede Medellı´n, Medellı´n, Colombia
Mitochondrial DNA Downloaded from informahealthcare.com by University of Melbourne on 10/30/14 For personal use only.
2
Abstract
Keywords
Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean (Phaseolus vulgaris), one of the most limiting factors for this crop in South and Central America. In this work, the mitochondrial sequence of a Colombian isolate of C. lindemuthianum obtained from a common bean plant (var. Cargamanto) with anthracnose symptoms is presented. The mtDNA codes for 13 proteins of the respiratory chain, 1 ribosomal protein, 2 homing endonucleases, 2 ribosomal RNAs and 28 tRNAs. This is the first report of a complete mtDNA genome sequence from C. lindemuthianum
Ascomycota, Glomerellaceae, mitogenome, Phaseolus vulgaris
Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara (Fungi, Ascomycota, Sordariomycetes, Glomerellaceae), the causal agent of anthracnose in common bean (Phaseolus vulgaris L.), is one of the most limiting factors for this crop in the mountainous regions of South and Central America (Mahuku & Riascos, 2004). Early severe anthracnose can result in severe defoliation and cause reductions in yield up to 95% in regions with high humidity, moderate temperatures and high precipitation frequency (Schwartz et al., 2005). This disease affects the quality of pods by inducing black, sunken cankers containing a salmon-colored ooze centre consisting of millions of conidia. Colletotrichum lindemuthianum can also affect petioles, leaf veins and stems where it induces the typical anthracnose sunken lesions (Schwartz et al., 2005). The genomes of Colletotrichum orbiculare, C. gloeosporioides, C. graminicola and C. higginsianum have been sequenced recently (Gan et al., 2013; O’Connell et al., 2012); however, there are no genome
Correspondence: Pablo Gutie´rrez, Laboratorio de Microbiologı´a Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellı´n, Calle 59A No 63-20, Medellı´n, Colombia. Fax: +57-44309332. E-mail: [email protected]
History Received 11 December 2013 Accepted 18 December 2013 Published online 22 January 2014
projects focused on C. lindemuthianum. Here, we present the complete mitochondrial sequence of a C. lindemuthianum isolate obtained from leaflet and pod tissues of a common bean plant (var. Cargamanto) with anthracnose symptoms collected in the province of Antioquia (Colombia; 04 340 5100 N 74 080 2000 W, 2150 MASL) and identified using morphological analysis and ITS sequencing. The DNA library was sequenced on a GS FLX 454 Life Sciences System (Roche, Basel, Switzerland) and assembled with Newbler (Roche). The C. lindemuthianum mtDNA sequence has been deposited in GenBank under accession: KF953885. The length of sequenced mitochondria of C. lindemuthianum was 36,957 bp with a mean GC content of 30.9% consisting of 34.4% A, 34.7% T, 16.9% G and 14.0% C. All protein-coding genes started with the standard ATG start codon and terminated at either TAA or TAG; as observed in other fungi, the UGA triplet was used as a Trp codon. Interestingly, all protein-coding genes seem to be transcribed with the same polarity. Sixteen ORFs were identified in the mitogenome of C. lindemuthianum; 13 of them code for proteins involved in respiration and oxidative phosphorylation: cob, cox1, cox2, cox3, nad1, nad2, nad4, nad4L, nad5, nad6, atp6, atp8 and atp9. Only one ribosomal protein, rps3, was encoded in the mitogenome of C. lindemuthianum. Two homing endonucleases, LAGLIDADG and GIY, normally associated with intron processing, were identified (Sethuraman et al., 2009). The LAGLIDADG endonuclease was encoded within an IA intron splitting the cob gene while the GIY endonuclease maps 282 bp upstream of the cox1 gene separated by an intervening intron IIB signature. The gene coding for cox1 contained a single ID-type intron while ribosomal protein S3 (rps3) was encoded within a group IA intron as observed in other fungi (Sethuraman et al., 2009). Twent-eight tRNA coding genes were identified in the C. lindemuthianum mtDNA ranging from 70 to 86 nt in size. Two copies were found for trnS (GCT, TGA) and trnT (TGT, TAG) and three for trnR (TCT(2), ACG), trnK (TTT) and trnM
Mitochondrial DNA Downloaded from informahealthcare.com by University of Melbourne on 10/30/14 For personal use only.
2
P. Gutie´rrez et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Circular DNA map of the mitochondrial genome of Colletotrichum lindemuthianum. The outer circle shows the position of protein coding genes (see text for details). Introns are represented light grey. The inner circle depicts the position of structural RNAs (rRNA and tRNA) and type I introns (IA, IB and ID).
(CAT). The large subunit RNA, rnl, was located between rps3 and trnP while the small subunit RNA mapped between trnR and trnY.
Declaration of interest This work was supported by Vicerrectorı´a de Investigaciones de la Universidad Nacional de Colombia, Grant: 20101009932. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the manuscript.
References Gan P, Ikeda K, Irieda H, Narusaka M, O’Connell RJ, Narusaka Y, Kubo Y, Shirasu K. (2013). Comparative genomic and transcriptomic
analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol 197:1236–49. Mahuku SG, Riascos JJ. (2004). Virulence and molecular diversity within Colletotrichum lindemuthianum isolates from Andean and Mesoamerican bean varieties and regions. Eur J Plant Pathol 110: 253–63. O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, et al. (2012). Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 44:1060–5. Schwartz HF, Steadman JR, Hall R, Forster RL. (2005). Compendium of bean diseases. 2nd ed. St Paul, MN: APS Press. Sethuraman J, Majer A, Friedrich NC, Edgell DR, Hausn£er G. (2009). Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene-encoded within an rnl group I intron of Ophiostoma and related taxa. Mol Biol Evol 26:2299–315.
