Genomics 104 (2014) 306–312
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The mitochondrial genome of Frankliniella intonsa: Insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera Dankan Yan a,b,1, Yunxia Tang a,1, Min Hu a, Fengquan Liu a, Dongfang Zhang b, Jiaqin Fan a,⁎ a b
College of Plant Protection, Nanjing Agricultural University and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Article history: Received 24 March 2014 Accepted 6 August 2014 Available online 14 August 2014 Keywords: Mitochondrial genomes evolution Frankliniella intonsa Thysanoptera Strand asymmetry Lower taxonomic levels
a b s t r a c t Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215 bp in length with an A + T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A + T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. © 2014 Elsevier Inc. All rights reserved.
1. Introduction The mitochondrial (mt) genomes of most bilateral animals are a single circular chromosome, about 16 kb long and have 37 genes (13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes), and one control region (CR) [1,2]. However, more and more special mt genomes have been known in the last decades. It involves primarily the following aspects: the variation of CR, gene rearrangements and multiple chromosomes. The CR is essential for the initiation of transcription and replication in the mt genomes. Generally it is a major non-region, but two or more CRs have been reported [3–16]. While the arrangement of mt genomes is conserved in most bilateral animals, it is variable at many different taxonomic levels in insect [17]. Multipartite mt genomes have been found in mesozoa [18], nematodes [19,20], rotifers [21], lice [13,24–25] and booklice [15]. The number of chromosomes in a multipartite mt genome varies from 2 in Liposcelis ⁎ Corresponding author. E-mail address: [email protected] (J. Fan). 1 The first two authors contribute equally to this research.
http://dx.doi.org/10.1016/j.ygeno.2014.08.003 0888-7543/© 2014 Elsevier Inc. All rights reserved.
bostrychophila [15] to 18 in Pediculus humanus [13]. Intriguingly, the above phenomenon happened in Paraneoptera. Paraneoptera is a monophyletic superorder of insects which includes three orders, the Hemiptera (bugs, cicadas, whiteflies, aphids, etc.), the Thysanoptera (thrips) and the Psocodea (barklice and true lice) [26]. The abundance and diversities of CRs presented in this assemblage. One CR has been found in Hemiptera, the duplicate and triplicate CRs have been reported in Thysanoptera [16,27] and 20 CRs have been found in human lice [13]. In contrast to other hexapods, they have various gene rearrangements relative to the putative ancestral arrangement. Most of the hemipteran mt genomes possess the ancestral gene order except the whiteflies [28] and the unique headed bug [29]. Both of the known thrips were highly rearrangement relative to the ancestral insect mt genomes, but they were similar to each other [9,16]. Some special rearrangements have been found in the barklouse [15,27]. Louse mt genomes show few ancestral boundaries and share only 11 arrangements between any two louse species [22]. Moreover, minicircular mt genomes were also identified as several types of louse and booklice. Various changes of mt genomes in Paraneoptera make it an excellent model for studying the evolution of mt genomes. Compared to other
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two orders, Thysanoptera has special rearrangements which differ massively from the ancestral insect mt genomes, and similar mt gene arrangements between the two known thrips [9,16,17]. It is neither ultra-conservation like Hemiptera nor higher evolution in Psocodea (Psocoptera and Phthiraptera), which provide more concrete information for insight into the mt genome evolution. However, the related research has been hampered by the lack of mt genomes from Thysanoptera. Presently, only 2 whole mt genomes of thrips have been known [9,16]. Here the entire nucleotide sequence of mt genome of the flower thrips, Frankliniella intonsa (Thysanoptera) was presented and the analyses of the nucleotide composition, codon usage, amino acid usage and compositional biases were provided. The possible mechanisms of evolution of control regions and gene rearrangements in F. intonsa were discussed. The evolutionary characteristics of the mt genomes were revealed in Thysanoptera. 2. Results 2.1. Genome organization and structure The mt genome of F. intonsa was a single circular of 15,215 bp in length (GenBank accession numbers: JQ917403), and contained 37 genes usually present in most animal mt genomes, and the triplicate CRs were found (Fig. 1; Supplementary Table S1). Two gene blocks (trnP-trnY and nad5-trnH-nad4-nad4L) were transcribed on the minority strand, whereas the others were oriented on the majority strand. Gene overlaps were found at six pairs of neighboring genes. In addition to triplicate putative CRs, there were 151 nucleotides dispersed in 14 intergenic spacers, ranging in size from 1 to 33 bp. The longest spacer sequence was located between trnY and nad2. 2.2. Nucleotide composition and codon usage The nucleotide composition of the majority-strand of F. intonsa mt genome was 6275 A (41.24%), 1980 C (13.01%), 5277 T (34.68%) and 1683 G (11.06%). The AT skew and GC skew of the majority strand were 0.086 and −0.081 each. The total length of all 13 protein-coding genes (PCGs) was 11,005 bp, and accounted for 72.33% of the entire length of F. intonsa mt genome. Analysis of base composition at each codon position of the concatenated 13 PCGs showed that A + T content in the third codon position (82.5%) was higher than that in the first
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(71.6%) and second (69.6%) codon positions (Supplementary Table S2). The nucleotide bias was reflected in the codon usage (Supplementary Table S3; Fig. 2). All codons presented in the PCGs of this genome, but UAG occurred only once. Four most frequently used codon, TTA (leucine), ATT (isoleucine), TTT (phenylalanine) and ATA (methionine), were all composed wholly of A and/or T (Fig. 2). Six A + T-rich codons (encoding amino acids Asn, Ile, Lys, Met, Phe, and Tyr) appeared 1648 times (45.03%), whereas four C + G-rich codons (encoding amino acids Ala, Arg, Gly, and Pro) appeared 454 times (12.40%) (Fig. 3). 2.3. Protein-coding genes All of the typical protein-coding genes except nad4L were identified by BLAST searches of NCBI database. The gene nad4L was identified by comparison of the amino acid sequence to those of the other two thrips (Thrips imaginis and Frankliniella occidentalis) (Supplementary Fig. S1). Start and stop codons were determined based on alignments with corresponding genes of other thrips. All of PCGs initiated with ATN (three with ATG, five with ATA and five with ATT). Eight genes employed a complete translation termination codon, either TAG (nad5) or TAA (cox1, nad3, cox2, cox3, cob, atp6 and nad6), whereas the remaining five genes had incomplete stop codon T. 2.4. Transfer RNA genes and ribosomal RNA genes The entire complement of 22 tRNA genes was found in F. intonsa, and 15 of them were determined using tRNAscane-SE. The other seven tRNA genes were determined by the anti-codon sequences and secondary structures. The A + T content of the tRNA genes was 79.29%, which was higher than the overall A + T composition of the mtDNA. Most of the tRNA genes could fold into the typical clover-leaf structure except for trnV, which lost D-arm (Fig. 4). This phenomenon was a common theme in the thrips mt genomes. The anti-codon nucleotides for the corresponding tRNA genes were identical to those commonly found in typical arthropod mt genomes. The boundaries of rRNA genes were determined through comparison with the Thysanoptera mt genomes published previously. The small ribosomal RNA (rrnS) was located between trnF and atp8, then the large ribosomal RNAs (rrnL) was found between trnV and trnS. The length of rrnL and rrnS was determined to be 1, 077 bp and 622 bp, respectively. The two rRNA genes were distant from putative CRs and encoded by the majority strand. 2.5. Control regions Three large non-coding regions (452 bp, 236 bp and 254 bp) were highly enriched in AT (80.75%, 80.93% and 77.56%). Nucleotide sequences of them had 165 bp in common. Based on the specific unique patterns (T-stretch, A + T-rich segment, stem-loop, and G[A]nT), they possibly function as control regions. The identified patterns in these regions are shown in Figs. 5 and 6. As in F. occidentalis mt genome, tandem repeat sequences were not found. The flanking sequences of three CRs were blasted. About 50 bp from CR1 and CR3 was identity, presumably derived from trnQ which was located on the upstream of CR2 (Fig. 7). We failed to find the similar sequence with the downstream sequences of CR1 and CR2. 2.6. Gene rearrangements
Fig. 1. The gene map for mitochondrial genome of Frankliniella intonsa. DNA strands are shown as two thick-line circles. Genes are represented as boxes. Protein-coding genes and ribosomal RNA genes are shown with standard abbreviations. Transfer RNA genes (tRNA) are named with single-letter amino acid abbreviations except for those coding for leucine and serine, which are named as L1 (tag), L2 (taa), S1 (tct), and S2 (tga). CR is the abbreviation for the control region.
Compared to F. occidentalis, three tRNA genes (trnI, trnQ and trnT) in the mt genome of F. intonsa have been translocations. Beside these tRNA genes, the other five tRNA genes (trnD, trnR, trnN, trnE and trnS2) have moved compared with T. imaginis. Numerous gene rearrangements have apparently occurred in the mt genome between F. intonsa and the inferred gene arrangement of the ancestral insect (Fig. 8). Six PCGs, sixteen tRNA genes and two rRNA genes have been rearranged.
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Fig. 2. Relative synonymous codon usage (RSCU) in the mitochondrial genome of Frankliniella intonsa. Codon families are provided on the x-axis. RSCU are present on the y-axis. The amino acids are named with single-letter abbreviations.
Furthermore, five tRNA genes, two rRNA genes, and one PCG have been inverted. Compared to the ancestral insect, neither of CRs appeared in the original location. 3. Discussion 3.1. Base composition, strand asymmetry and gene arrangements Nucleotide composition of the available thrips mt genomes is stably A + T biased (76.6% in T. imaginis, 77.6% in F. occidentalis and 75.9% in F. intonsa). Positive AT-skew and negative GC-skew for the majority
strand of three thrips mt genomes are consistent with the usual strand biases of metazoan mtDNA. It shows normal strand asymmetry in mt genomes of thrips. The reversal of strand asymmetry over the entire mt genome was found to have accelerated gene rearrangement rates in louse [30]. As the gene arrangements of the three thrips mt genomes are very similar, the evolution might be very little among them. It is suggested that the low rearrangement rates may be contributed to the usual strand asymmetry within the thrips mt genomes. However, the massive gene rearrangements appear not to affect the base composition in the mt genomes of thrips. So the relationship between the gene rearrangement and strand asymmetry still needs further study.
Fig. 3. The amino acid usage of the mitochondrial genome of Frankliniella intonsa. Six A + T-rich codons (encoding amino acids Asn, Ile, Lys, Met, Phe and Tyr) were present in a small circle.
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Fig. 4. Inferred secondary structures of the 22 tRNAs encoded by the mitochondrial genome of Frankliniella intonsa. Nucleotide sequences are from 5′ to 3′, as indicated for trnR. Each arm and loop is illustrated as for trnR, AA-arm for amino acid acceptor arm, T-arm for TΨC arm, V-loop for variable loop, AC-arm for anticodon arm, and D-arm for dihydrouridine arm.
3.2. Control regions and gene rearrangements Three control regions are identical nucleotide sequences about 165 bp and could form a stable stem-loop secondary structure which may play a role in regulating replication and transcription. The up and downstream sequences of CRs have been detected. The upstream sequence of CR1 and CR3 may be derived from trnQ which located upstream of CR2. About 70 bp downstream sequences of the putative origin of replication are the same in CR1 and CR2. The high degree of
sequence conservation within the CRs is likely due to concerted evolution among them. This approach has previously been used to discuss the duplicated CR elements in termites [31,32]. Because CR2 has a functional trnQ and the other two CRs (CR1 and CR3) only contain partial sequence of trnQ, it can be concluded that CR2 must be the ancestral CR while CR1 and CR 3 might be duplicated from CR2. The three CRs are in the same spot in each of the three thrips, suggesting that the duplication might occur in the most recent common ancestor of the three thrips.
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Fig. 5. Comparison of the nucleotide sequences of the three putative control regions of the mitochondrial genome of Frankliniella intonsa. Dashes (−) indicate indels. Four types of sequences were recognized in the control regions: T-stretch (double line), A + T-rich sequences (thin line), stem-loops (thick line), and G(A)nT(dashed line) (see also Fig. 6).
With a few notable exceptions, the numerous gene rearrangements have been found in the mt genome of F. intonsa. However, only three and eight tRNA genes translocate in the genus Frankliniella and the family Thripidae, respectively. So we propose that the mt genomes of thrips remain stable through a certain evolutionary process after some early numerous rearrangements [17]. Based on the great changes of gene arrangement, tandem duplication random loss (TDRL) [33,34] has happened several times in the ancestral mt genomes of the thrips. The translocated tRNA genes among the thrips are transcribed from the same strand and near to the CRs. This phenomenon can be also explained by TDRL, as both of the strand slippage and imprecise termination are probably included surrounding the CRs in the duplicated gene block [17]. As all the inverted genes are the same in the mt genomes of the three thrips, the identical inverted genes might be originated from the common ancestral mt genomes of the three thrips. We assume that they were translocated to a block in the early rearrangement and inverted together by intramitochondrial recombination [35].
3.3. Evolution of mitochondrial genomes in Thysanoptera In this study, we found some details to understand the evolutionary process of mt genomes at lower taxonomic levels in Thysanoptera and several tRNA genes translocated within the genus and family. We confirm that the three thrips mt genomes have a low rate of rearrangement among them and a single massive rearrangement between the order and other Paraneoptera. These rearrangements may be originated from the most recent common ancestor of the three thrips. It would be interesting to know why the large rearrangement occurred in Thysanoptera and when this happened. So we assume that a study of the complete mt genomes within the order (Thysanoptera) and suborders (Tubulifera and Terebrantia) could contribute to understanding this unique phenomenon. 4. Materials and methods 4.1. Sample collection, DNA extraction and PCR amplification Specimens were collected from the campus of Nanjing Agricultural University and identified as F. intonsa by morphology [36]. Living thrips were snap frozen in liquid nitrogen and stored at − 70 °C. Total DNA was extracted from one thrips using the Universal Genomic DNA Extraction Kit Ver. 3.0 (TaKaRa, Shiga, Japan). Two pairs of primers were designed, based upon the cox1 (GenBank accession numbers: FN 546000.1) and Cytb (GenBank accession numbers: EU 327340.1) sequences for F. intonsa. The entire mt genome of F. intonsa was amplified in these overlapping fragments by long polymerase chain reaction (PCR) with two pairs of primers:
Fig. 6. Inferred stem-loops in the control regions of the mitochondrial genome of F. intonsa. Nucleotides of the stem-loops are in bold font, whereas those flanking the stem-loops are in regular font. Inferred Watson–Crick bonds are illustrated by lines, TG bonds by dots.
1. C1-1-F 5′-CAGCAATCCTACTTCTTTTATCCTTACCAG-3′ cob-1-R 5′-GCGTTGTCTACTGAAAATCCTCCTCAAAT-3′ 2. cob-2-F 5′-ATCTTTTATCAGCGGTTCCCTATCTAGG-3′ C1-2-R 5′-ACCCGAATGATAGAATGTTGATAATGGTGG-3′
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Fig. 7. The up and downstream sequences of the control regions in the mitochondrial genome of Frankliniella intonsa. Dashes (−) indicate indels. The control region flanking genes trnQ and nad5 are represented. Abbreviations of the control regions and genes are defined in the legend of Fig. 1. The lengths of regions are present inside the box.
The names of the primers indicate the target gene (C1 for cox1 and cob for Cytb). Premix LA Taq Hot Start Version (TaKaRa, Shiga, Japan) was used for long PCR amplification. The cycling conditions of the short PCR were 1 min at 94 °C followed by 35 cycles of 30 s at 94 °C, 30 s at 50 °C, and 5 min at 68 °C, and then 10 min at 68 °C for C1-1-F and cob-1-R. The long PCR was performed under the following cycling conditions: 1 cycle (2 min at 92 °C), 10 cycles (10 s at 92 °C, 30 s at 58 °C, and 10 min at 68 °C), 20 cycles (10 s at 92 °C, 30 s at 58 °C, and 12 min at 68 °C with 1 cycle of elongation of 20 s for each cycle), and
1 cycle (a prolonged elongation for 8 min at 68 °C) for cob-2-F and C1-2-R.
4.2. Sequencing and analysis The short fragment was cloned into a pMD19-T vector (TaKaRa, Shiga, Japan) and sequenced with the PCR primers and internal primers. The long fragment was sequenced by shotgun sequencing method as
Fig. 8. Comparison of mitochondrial gene arrangements among Frankliniella intonsa, Frankliniella occidentalis, Thrips imaginis and the ancestral insect Drosophila yakuba. The circular genomes were linearized at the 5′ end of cox1. Genes are transcribed from left to right except yellow boxes, which are transcribed from right to left. Blue boxes represent genes with the different position between F. intonsa and F. occidentalis; red boxes represent gene clusters that changed positions among F. intonsa, F. occidentalis and T. imaginis. Protein-coding genes and ribosomal RNA genes are shown with standard abbreviations. Abbreviations of tRNA genes and the control regions are defined in the legend of Fig. 1. Lines with arrows indicate translocations of genes from their ancestral positions to the current positions in F. intonsa.
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previously described [16] (Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China). Raw sequence files were proof-read and aligned into contigs in BioEdit version 7.0.5.3 [37]. Base compositions, codon and amino acid usage were conducted with MEGA 5.0 [38]. Strand asymmetry was calculated using the formulae: AT skew = [A − T] / [A + T] and GC skew = [G − C] / [G + C] [39] for the strand encoding the majority of the protein-coding genes. The rRNA genes were identified by BLAST searches of NCBI database [40]. The tRNA genes were identified by tRNAscan-SE [41]. Some tRNA genes that could not be found by tRNAscan-SE were identified from the anti-codon sequences and secondary structures [42]. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.ygeno.2014.08.003. Acknowledgment We thank Dr. Yu Chen (Anhui Academy of Agricultural Sciences) and Dr. Ian Riley (University of Adelaide) for their valuable comments and suggestions. This work was supported by the Project of the National Science and Technology Support Program of China (Grant No. 2012BAD19B06), the Special Fund for Agro-scientific Research in the Public Interest of China (Grant No. 201103026), Innovation Team of Anhui Academy of Agricultural Sciences (Grant No. 12C1105) and the 2014 Innovation Fund of Anhui Academy of Agricultural Sciences for Outstanding Youth (14B1110).
[15]
[16]
[17] [18]
[19] [20]
[21]
[22]
[23]
[24]
[25]
[26] [27]
References [28] [1] J.L. Boore, Animal mitochondrial genomes, Nucleic Acids Res. 27 (1999) 1767–1780. [2] D.R. Wolstenholme, Animal mitochondrial DNA: structure and evolution, Int. Rev. Cytol. 141 (1992) 173–216. [3] Y. Kumazawa, H. Ota, M. Nishida, T. Ozawa, Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster, Mol. Biol. Evol. 13 (1996) 1242–1254. [4] A. Arndt, M. Smith, Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria, Mol. Biol. Evol. 15 (1998) 1009–1016. [5] W. Black, R.L. Roehrdanz, Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes, Mol. Biol. Evol. 15 (1998) 1772–1785. [6] N. Campbell, S.C. Barker, The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region, Mol. Biol. Evol. 16 (1999) 732–740. [7] J.R. Eberhard, T.F. Wright, E. Bermingham, Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona, Mol. Biol. Evol. 18 (2001) 1330–1342. [8] J.-S. Lee, M. Miya, Y.-S. Lee, C.G. Kim, E.-H. Park, et al., The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish, Gene 280 (2001) 1–7. [9] R. Shao, S.C. Barker, The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes, Mol. Biol. Evol. 20 (2003) 362–370. [10] K. Ogoh, Y. Ohmiya, Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions, Gene 327 (2004) 131–139. [11] R. Shao, S.C. Barker, H. Mitani, Y. Aoki, M. Fukunaga, Evolution of duplicate control regions in the mitochondrial genomes of metazoa: a case study with Australasian Ixodes ticks, Mol. Biol. Evol. 22 (2005) 620–629. [12] R. Shao, S.C. Barker, H. Mitani, M. Takahashi, M. Fukunaga, Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes), J. Mol. Evol. 63 (2006) 251–261. [13] R. Shao, E.F. Kirkness, S.C. Barker, The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus, Genome Res. 19 (2009) 904–912. [14] A. Braband, L. Podsiadlowski, S.L. Cameron, S. Daniels, G. Mayer, Extensive duplication events account for multiple control regions and pseudo-genes in the
[29]
[30]
[31]
[32]
[33]
[34] [35] [36]
[37] [38]
[39] [40]
[41] [42]
mitochondrial genome of the velvet worm Metaperipatus inae (Onychophora, Peripatopsidae), Mol. Phylogenet. Evol. 57 (2010) 293–300. D.-D. Wei, R. Shao, M.-L. Yuan, W. Dou, S.C. Barker, et al., The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genomes in bilateral animals, PLoS One 7 (2012) e33973. D. Yan, Y. Tang, X. Xue, M. Wang, F. Liu, et al., The complete mitochondrial genome sequence of the western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) contains triplicate putative control regions, Gene 506 (2012) 117–124. S.L. Cameron, Insect mitochondrial genomics: implications for evolution and phylogeny, Annu. Rev. Entomol. 59 (2014) 95–117. K.I. Watanabe, Y. Bessho, M. Kawasaki, H. Hori, Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema, J. Mol. Biol. 286 (1999) 645–650. M.R. Armstrong, V.C. Blok, M.S. Phillips, A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida, Genetics 154 (2000) 181–192. T. Gibson, V.C. Blok, M. Dowton, Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives, J. Mol. Evol. 65 (2007) 308–315. K. Suga, D.B.M. Welch, Y. Tanaka, Y. Sakakura, A. Hagiwara, Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis, Mol. Biol. Evol. 25 (2008) 1129–1137. S.L. Cameron, K. Yoshizawa, A. Mizukoshi, M.F. Whiting, K.P. Johnson, Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera), BMC Genomics 12 (2011) 394. R. Shao, X.-Q. Zhu, S.C. Barker, K. Herd, Evolution of extensively fragmented mitochondrial genomes in the lice of humans, Genome Biol. Evol. 4 (2012) 1088–1101. H. Jiang, S.C. Barker, R. Shao, Substantial variation in the extent of mitochondrial genome fragmentation among blood-sucking lice of mammals, Genome Biol. Evol. 5 (2013) 1298–1308. W.-G. Dong, S. Song, D.-C. Jin, X.-G. Guo, R. Shao, Fragmented mitochondrial genomes of the rat lice, Polyplax asiatica and Polyplax spinulosa: intra-genus variation in fragmentation pattern and a possible link between the extent of fragmentation and the length of life cycle, BMC Genomics 15 (2014) 44. D. Grimaldi, Evolution of the Insects, Cambridge University Press, 2005. R. Shao, M. Dowton, A. Murrell, S.C. Barker, Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects, Mol. Biol. Evol. 20 (2003) 1612–1619. M.L. Thao, L. Baumann, P. Baumann, Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha), BMC Evol. Biol. 4 (2004) 25. H. Li, H. Liu, A. Shi, P. Štys, X. Zhou, et al., The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae), PLoS One 7 (2012) e29419. S.L. Cameron, K.P. Johnson, M.F. Whiting, The mitochondrial genome of the screamer louse Bothriometopus (Phthiraptera: Ischnocera): effects of extensive gene rearrangements on the evolution of the genome, J. Mol. Evol. 65 (2007) 589–604. S.L. Cameron, N. Lo, T. Bourguignon, G.J. Svenson, T.A. Evans, A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): robust support for interfamilial relationships and molecular synapomorphies define major clades, Mol. Phylogenet. Evol. 65 (2012) 163–173. S.L. Cameron, M.F. Whiting, Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae), Genome 50 (2007) 188–202. J.L. Boore, The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals, Comparative Genomics, Springer, 2000. 133–147. C. Moritz, T. Dowling, W. Brown, Evolution of animal mitochondrial DNA: relevance for population biology and systematics, Annu. Rev. Ecol. Syst. 18 (1987) 269–292. M. Dowton, N.J. Campbell, Intramitochondrial recombination—is it why some mitochondrial genes sleep around? Trends Ecol. Evol. 16 (2001) 269–271. M. Hoddle, L. Mound, PARIS D, Thrips of California 2012, CBIT Publishing, Queensland, 2012. (http://keys.lucidcentral.org/keys/v3/thrips_of_california/identifythrips/key/california-thysanoptera-2012/Media/Html/browse_species/ Frankliniella_intonsa.htm ). T.A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, 1999. 95–98. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol. 28 (2011) 2731–2739. N.T. Perna, T.D. Kocher, Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Evol. 41 (1995) 353–358. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25 (1997) 3389–3402. T.M. Lowe, S.R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res. 25 (1997) 0955–0964. Y. Kumazawa, M. Nishida, Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics, J. Mol. Evol. 37 (1993) 380–398.
Contents lists available at ScienceDirect
Genomics journal homepage: www.elsevier.com/locate/ygeno
The mitochondrial genome of Frankliniella intonsa: Insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera Dankan Yan a,b,1, Yunxia Tang a,1, Min Hu a, Fengquan Liu a, Dongfang Zhang b, Jiaqin Fan a,⁎ a b
College of Plant Protection, Nanjing Agricultural University and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Article history: Received 24 March 2014 Accepted 6 August 2014 Available online 14 August 2014 Keywords: Mitochondrial genomes evolution Frankliniella intonsa Thysanoptera Strand asymmetry Lower taxonomic levels
a b s t r a c t Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215 bp in length with an A + T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A + T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. © 2014 Elsevier Inc. All rights reserved.
1. Introduction The mitochondrial (mt) genomes of most bilateral animals are a single circular chromosome, about 16 kb long and have 37 genes (13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes), and one control region (CR) [1,2]. However, more and more special mt genomes have been known in the last decades. It involves primarily the following aspects: the variation of CR, gene rearrangements and multiple chromosomes. The CR is essential for the initiation of transcription and replication in the mt genomes. Generally it is a major non-region, but two or more CRs have been reported [3–16]. While the arrangement of mt genomes is conserved in most bilateral animals, it is variable at many different taxonomic levels in insect [17]. Multipartite mt genomes have been found in mesozoa [18], nematodes [19,20], rotifers [21], lice [13,24–25] and booklice [15]. The number of chromosomes in a multipartite mt genome varies from 2 in Liposcelis ⁎ Corresponding author. E-mail address: [email protected] (J. Fan). 1 The first two authors contribute equally to this research.
http://dx.doi.org/10.1016/j.ygeno.2014.08.003 0888-7543/© 2014 Elsevier Inc. All rights reserved.
bostrychophila [15] to 18 in Pediculus humanus [13]. Intriguingly, the above phenomenon happened in Paraneoptera. Paraneoptera is a monophyletic superorder of insects which includes three orders, the Hemiptera (bugs, cicadas, whiteflies, aphids, etc.), the Thysanoptera (thrips) and the Psocodea (barklice and true lice) [26]. The abundance and diversities of CRs presented in this assemblage. One CR has been found in Hemiptera, the duplicate and triplicate CRs have been reported in Thysanoptera [16,27] and 20 CRs have been found in human lice [13]. In contrast to other hexapods, they have various gene rearrangements relative to the putative ancestral arrangement. Most of the hemipteran mt genomes possess the ancestral gene order except the whiteflies [28] and the unique headed bug [29]. Both of the known thrips were highly rearrangement relative to the ancestral insect mt genomes, but they were similar to each other [9,16]. Some special rearrangements have been found in the barklouse [15,27]. Louse mt genomes show few ancestral boundaries and share only 11 arrangements between any two louse species [22]. Moreover, minicircular mt genomes were also identified as several types of louse and booklice. Various changes of mt genomes in Paraneoptera make it an excellent model for studying the evolution of mt genomes. Compared to other
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two orders, Thysanoptera has special rearrangements which differ massively from the ancestral insect mt genomes, and similar mt gene arrangements between the two known thrips [9,16,17]. It is neither ultra-conservation like Hemiptera nor higher evolution in Psocodea (Psocoptera and Phthiraptera), which provide more concrete information for insight into the mt genome evolution. However, the related research has been hampered by the lack of mt genomes from Thysanoptera. Presently, only 2 whole mt genomes of thrips have been known [9,16]. Here the entire nucleotide sequence of mt genome of the flower thrips, Frankliniella intonsa (Thysanoptera) was presented and the analyses of the nucleotide composition, codon usage, amino acid usage and compositional biases were provided. The possible mechanisms of evolution of control regions and gene rearrangements in F. intonsa were discussed. The evolutionary characteristics of the mt genomes were revealed in Thysanoptera. 2. Results 2.1. Genome organization and structure The mt genome of F. intonsa was a single circular of 15,215 bp in length (GenBank accession numbers: JQ917403), and contained 37 genes usually present in most animal mt genomes, and the triplicate CRs were found (Fig. 1; Supplementary Table S1). Two gene blocks (trnP-trnY and nad5-trnH-nad4-nad4L) were transcribed on the minority strand, whereas the others were oriented on the majority strand. Gene overlaps were found at six pairs of neighboring genes. In addition to triplicate putative CRs, there were 151 nucleotides dispersed in 14 intergenic spacers, ranging in size from 1 to 33 bp. The longest spacer sequence was located between trnY and nad2. 2.2. Nucleotide composition and codon usage The nucleotide composition of the majority-strand of F. intonsa mt genome was 6275 A (41.24%), 1980 C (13.01%), 5277 T (34.68%) and 1683 G (11.06%). The AT skew and GC skew of the majority strand were 0.086 and −0.081 each. The total length of all 13 protein-coding genes (PCGs) was 11,005 bp, and accounted for 72.33% of the entire length of F. intonsa mt genome. Analysis of base composition at each codon position of the concatenated 13 PCGs showed that A + T content in the third codon position (82.5%) was higher than that in the first
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(71.6%) and second (69.6%) codon positions (Supplementary Table S2). The nucleotide bias was reflected in the codon usage (Supplementary Table S3; Fig. 2). All codons presented in the PCGs of this genome, but UAG occurred only once. Four most frequently used codon, TTA (leucine), ATT (isoleucine), TTT (phenylalanine) and ATA (methionine), were all composed wholly of A and/or T (Fig. 2). Six A + T-rich codons (encoding amino acids Asn, Ile, Lys, Met, Phe, and Tyr) appeared 1648 times (45.03%), whereas four C + G-rich codons (encoding amino acids Ala, Arg, Gly, and Pro) appeared 454 times (12.40%) (Fig. 3). 2.3. Protein-coding genes All of the typical protein-coding genes except nad4L were identified by BLAST searches of NCBI database. The gene nad4L was identified by comparison of the amino acid sequence to those of the other two thrips (Thrips imaginis and Frankliniella occidentalis) (Supplementary Fig. S1). Start and stop codons were determined based on alignments with corresponding genes of other thrips. All of PCGs initiated with ATN (three with ATG, five with ATA and five with ATT). Eight genes employed a complete translation termination codon, either TAG (nad5) or TAA (cox1, nad3, cox2, cox3, cob, atp6 and nad6), whereas the remaining five genes had incomplete stop codon T. 2.4. Transfer RNA genes and ribosomal RNA genes The entire complement of 22 tRNA genes was found in F. intonsa, and 15 of them were determined using tRNAscane-SE. The other seven tRNA genes were determined by the anti-codon sequences and secondary structures. The A + T content of the tRNA genes was 79.29%, which was higher than the overall A + T composition of the mtDNA. Most of the tRNA genes could fold into the typical clover-leaf structure except for trnV, which lost D-arm (Fig. 4). This phenomenon was a common theme in the thrips mt genomes. The anti-codon nucleotides for the corresponding tRNA genes were identical to those commonly found in typical arthropod mt genomes. The boundaries of rRNA genes were determined through comparison with the Thysanoptera mt genomes published previously. The small ribosomal RNA (rrnS) was located between trnF and atp8, then the large ribosomal RNAs (rrnL) was found between trnV and trnS. The length of rrnL and rrnS was determined to be 1, 077 bp and 622 bp, respectively. The two rRNA genes were distant from putative CRs and encoded by the majority strand. 2.5. Control regions Three large non-coding regions (452 bp, 236 bp and 254 bp) were highly enriched in AT (80.75%, 80.93% and 77.56%). Nucleotide sequences of them had 165 bp in common. Based on the specific unique patterns (T-stretch, A + T-rich segment, stem-loop, and G[A]nT), they possibly function as control regions. The identified patterns in these regions are shown in Figs. 5 and 6. As in F. occidentalis mt genome, tandem repeat sequences were not found. The flanking sequences of three CRs were blasted. About 50 bp from CR1 and CR3 was identity, presumably derived from trnQ which was located on the upstream of CR2 (Fig. 7). We failed to find the similar sequence with the downstream sequences of CR1 and CR2. 2.6. Gene rearrangements
Fig. 1. The gene map for mitochondrial genome of Frankliniella intonsa. DNA strands are shown as two thick-line circles. Genes are represented as boxes. Protein-coding genes and ribosomal RNA genes are shown with standard abbreviations. Transfer RNA genes (tRNA) are named with single-letter amino acid abbreviations except for those coding for leucine and serine, which are named as L1 (tag), L2 (taa), S1 (tct), and S2 (tga). CR is the abbreviation for the control region.
Compared to F. occidentalis, three tRNA genes (trnI, trnQ and trnT) in the mt genome of F. intonsa have been translocations. Beside these tRNA genes, the other five tRNA genes (trnD, trnR, trnN, trnE and trnS2) have moved compared with T. imaginis. Numerous gene rearrangements have apparently occurred in the mt genome between F. intonsa and the inferred gene arrangement of the ancestral insect (Fig. 8). Six PCGs, sixteen tRNA genes and two rRNA genes have been rearranged.
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Fig. 2. Relative synonymous codon usage (RSCU) in the mitochondrial genome of Frankliniella intonsa. Codon families are provided on the x-axis. RSCU are present on the y-axis. The amino acids are named with single-letter abbreviations.
Furthermore, five tRNA genes, two rRNA genes, and one PCG have been inverted. Compared to the ancestral insect, neither of CRs appeared in the original location. 3. Discussion 3.1. Base composition, strand asymmetry and gene arrangements Nucleotide composition of the available thrips mt genomes is stably A + T biased (76.6% in T. imaginis, 77.6% in F. occidentalis and 75.9% in F. intonsa). Positive AT-skew and negative GC-skew for the majority
strand of three thrips mt genomes are consistent with the usual strand biases of metazoan mtDNA. It shows normal strand asymmetry in mt genomes of thrips. The reversal of strand asymmetry over the entire mt genome was found to have accelerated gene rearrangement rates in louse [30]. As the gene arrangements of the three thrips mt genomes are very similar, the evolution might be very little among them. It is suggested that the low rearrangement rates may be contributed to the usual strand asymmetry within the thrips mt genomes. However, the massive gene rearrangements appear not to affect the base composition in the mt genomes of thrips. So the relationship between the gene rearrangement and strand asymmetry still needs further study.
Fig. 3. The amino acid usage of the mitochondrial genome of Frankliniella intonsa. Six A + T-rich codons (encoding amino acids Asn, Ile, Lys, Met, Phe and Tyr) were present in a small circle.
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Fig. 4. Inferred secondary structures of the 22 tRNAs encoded by the mitochondrial genome of Frankliniella intonsa. Nucleotide sequences are from 5′ to 3′, as indicated for trnR. Each arm and loop is illustrated as for trnR, AA-arm for amino acid acceptor arm, T-arm for TΨC arm, V-loop for variable loop, AC-arm for anticodon arm, and D-arm for dihydrouridine arm.
3.2. Control regions and gene rearrangements Three control regions are identical nucleotide sequences about 165 bp and could form a stable stem-loop secondary structure which may play a role in regulating replication and transcription. The up and downstream sequences of CRs have been detected. The upstream sequence of CR1 and CR3 may be derived from trnQ which located upstream of CR2. About 70 bp downstream sequences of the putative origin of replication are the same in CR1 and CR2. The high degree of
sequence conservation within the CRs is likely due to concerted evolution among them. This approach has previously been used to discuss the duplicated CR elements in termites [31,32]. Because CR2 has a functional trnQ and the other two CRs (CR1 and CR3) only contain partial sequence of trnQ, it can be concluded that CR2 must be the ancestral CR while CR1 and CR 3 might be duplicated from CR2. The three CRs are in the same spot in each of the three thrips, suggesting that the duplication might occur in the most recent common ancestor of the three thrips.
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Fig. 5. Comparison of the nucleotide sequences of the three putative control regions of the mitochondrial genome of Frankliniella intonsa. Dashes (−) indicate indels. Four types of sequences were recognized in the control regions: T-stretch (double line), A + T-rich sequences (thin line), stem-loops (thick line), and G(A)nT(dashed line) (see also Fig. 6).
With a few notable exceptions, the numerous gene rearrangements have been found in the mt genome of F. intonsa. However, only three and eight tRNA genes translocate in the genus Frankliniella and the family Thripidae, respectively. So we propose that the mt genomes of thrips remain stable through a certain evolutionary process after some early numerous rearrangements [17]. Based on the great changes of gene arrangement, tandem duplication random loss (TDRL) [33,34] has happened several times in the ancestral mt genomes of the thrips. The translocated tRNA genes among the thrips are transcribed from the same strand and near to the CRs. This phenomenon can be also explained by TDRL, as both of the strand slippage and imprecise termination are probably included surrounding the CRs in the duplicated gene block [17]. As all the inverted genes are the same in the mt genomes of the three thrips, the identical inverted genes might be originated from the common ancestral mt genomes of the three thrips. We assume that they were translocated to a block in the early rearrangement and inverted together by intramitochondrial recombination [35].
3.3. Evolution of mitochondrial genomes in Thysanoptera In this study, we found some details to understand the evolutionary process of mt genomes at lower taxonomic levels in Thysanoptera and several tRNA genes translocated within the genus and family. We confirm that the three thrips mt genomes have a low rate of rearrangement among them and a single massive rearrangement between the order and other Paraneoptera. These rearrangements may be originated from the most recent common ancestor of the three thrips. It would be interesting to know why the large rearrangement occurred in Thysanoptera and when this happened. So we assume that a study of the complete mt genomes within the order (Thysanoptera) and suborders (Tubulifera and Terebrantia) could contribute to understanding this unique phenomenon. 4. Materials and methods 4.1. Sample collection, DNA extraction and PCR amplification Specimens were collected from the campus of Nanjing Agricultural University and identified as F. intonsa by morphology [36]. Living thrips were snap frozen in liquid nitrogen and stored at − 70 °C. Total DNA was extracted from one thrips using the Universal Genomic DNA Extraction Kit Ver. 3.0 (TaKaRa, Shiga, Japan). Two pairs of primers were designed, based upon the cox1 (GenBank accession numbers: FN 546000.1) and Cytb (GenBank accession numbers: EU 327340.1) sequences for F. intonsa. The entire mt genome of F. intonsa was amplified in these overlapping fragments by long polymerase chain reaction (PCR) with two pairs of primers:
Fig. 6. Inferred stem-loops in the control regions of the mitochondrial genome of F. intonsa. Nucleotides of the stem-loops are in bold font, whereas those flanking the stem-loops are in regular font. Inferred Watson–Crick bonds are illustrated by lines, TG bonds by dots.
1. C1-1-F 5′-CAGCAATCCTACTTCTTTTATCCTTACCAG-3′ cob-1-R 5′-GCGTTGTCTACTGAAAATCCTCCTCAAAT-3′ 2. cob-2-F 5′-ATCTTTTATCAGCGGTTCCCTATCTAGG-3′ C1-2-R 5′-ACCCGAATGATAGAATGTTGATAATGGTGG-3′
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Fig. 7. The up and downstream sequences of the control regions in the mitochondrial genome of Frankliniella intonsa. Dashes (−) indicate indels. The control region flanking genes trnQ and nad5 are represented. Abbreviations of the control regions and genes are defined in the legend of Fig. 1. The lengths of regions are present inside the box.
The names of the primers indicate the target gene (C1 for cox1 and cob for Cytb). Premix LA Taq Hot Start Version (TaKaRa, Shiga, Japan) was used for long PCR amplification. The cycling conditions of the short PCR were 1 min at 94 °C followed by 35 cycles of 30 s at 94 °C, 30 s at 50 °C, and 5 min at 68 °C, and then 10 min at 68 °C for C1-1-F and cob-1-R. The long PCR was performed under the following cycling conditions: 1 cycle (2 min at 92 °C), 10 cycles (10 s at 92 °C, 30 s at 58 °C, and 10 min at 68 °C), 20 cycles (10 s at 92 °C, 30 s at 58 °C, and 12 min at 68 °C with 1 cycle of elongation of 20 s for each cycle), and
1 cycle (a prolonged elongation for 8 min at 68 °C) for cob-2-F and C1-2-R.
4.2. Sequencing and analysis The short fragment was cloned into a pMD19-T vector (TaKaRa, Shiga, Japan) and sequenced with the PCR primers and internal primers. The long fragment was sequenced by shotgun sequencing method as
Fig. 8. Comparison of mitochondrial gene arrangements among Frankliniella intonsa, Frankliniella occidentalis, Thrips imaginis and the ancestral insect Drosophila yakuba. The circular genomes were linearized at the 5′ end of cox1. Genes are transcribed from left to right except yellow boxes, which are transcribed from right to left. Blue boxes represent genes with the different position between F. intonsa and F. occidentalis; red boxes represent gene clusters that changed positions among F. intonsa, F. occidentalis and T. imaginis. Protein-coding genes and ribosomal RNA genes are shown with standard abbreviations. Abbreviations of tRNA genes and the control regions are defined in the legend of Fig. 1. Lines with arrows indicate translocations of genes from their ancestral positions to the current positions in F. intonsa.
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previously described [16] (Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China). Raw sequence files were proof-read and aligned into contigs in BioEdit version 7.0.5.3 [37]. Base compositions, codon and amino acid usage were conducted with MEGA 5.0 [38]. Strand asymmetry was calculated using the formulae: AT skew = [A − T] / [A + T] and GC skew = [G − C] / [G + C] [39] for the strand encoding the majority of the protein-coding genes. The rRNA genes were identified by BLAST searches of NCBI database [40]. The tRNA genes were identified by tRNAscan-SE [41]. Some tRNA genes that could not be found by tRNAscan-SE were identified from the anti-codon sequences and secondary structures [42]. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.ygeno.2014.08.003. Acknowledgment We thank Dr. Yu Chen (Anhui Academy of Agricultural Sciences) and Dr. Ian Riley (University of Adelaide) for their valuable comments and suggestions. This work was supported by the Project of the National Science and Technology Support Program of China (Grant No. 2012BAD19B06), the Special Fund for Agro-scientific Research in the Public Interest of China (Grant No. 201103026), Innovation Team of Anhui Academy of Agricultural Sciences (Grant No. 12C1105) and the 2014 Innovation Fund of Anhui Academy of Agricultural Sciences for Outstanding Youth (14B1110).
[15]
[16]
[17] [18]
[19] [20]
[21]
[22]
[23]
[24]
[25]
[26] [27]
References [28] [1] J.L. Boore, Animal mitochondrial genomes, Nucleic Acids Res. 27 (1999) 1767–1780. [2] D.R. Wolstenholme, Animal mitochondrial DNA: structure and evolution, Int. Rev. Cytol. 141 (1992) 173–216. [3] Y. Kumazawa, H. Ota, M. Nishida, T. Ozawa, Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster, Mol. Biol. Evol. 13 (1996) 1242–1254. [4] A. Arndt, M. Smith, Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria, Mol. Biol. Evol. 15 (1998) 1009–1016. [5] W. Black, R.L. Roehrdanz, Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes, Mol. Biol. Evol. 15 (1998) 1772–1785. [6] N. Campbell, S.C. Barker, The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region, Mol. Biol. Evol. 16 (1999) 732–740. [7] J.R. Eberhard, T.F. Wright, E. Bermingham, Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona, Mol. Biol. Evol. 18 (2001) 1330–1342. [8] J.-S. Lee, M. Miya, Y.-S. Lee, C.G. Kim, E.-H. Park, et al., The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish, Gene 280 (2001) 1–7. [9] R. Shao, S.C. Barker, The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes, Mol. Biol. Evol. 20 (2003) 362–370. [10] K. Ogoh, Y. Ohmiya, Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions, Gene 327 (2004) 131–139. [11] R. Shao, S.C. Barker, H. Mitani, Y. Aoki, M. Fukunaga, Evolution of duplicate control regions in the mitochondrial genomes of metazoa: a case study with Australasian Ixodes ticks, Mol. Biol. Evol. 22 (2005) 620–629. [12] R. Shao, S.C. Barker, H. Mitani, M. Takahashi, M. Fukunaga, Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes), J. Mol. Evol. 63 (2006) 251–261. [13] R. Shao, E.F. Kirkness, S.C. Barker, The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus, Genome Res. 19 (2009) 904–912. [14] A. Braband, L. Podsiadlowski, S.L. Cameron, S. Daniels, G. Mayer, Extensive duplication events account for multiple control regions and pseudo-genes in the
[29]
[30]
[31]
[32]
[33]
[34] [35] [36]
[37] [38]
[39] [40]
[41] [42]
mitochondrial genome of the velvet worm Metaperipatus inae (Onychophora, Peripatopsidae), Mol. Phylogenet. Evol. 57 (2010) 293–300. D.-D. Wei, R. Shao, M.-L. Yuan, W. Dou, S.C. Barker, et al., The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genomes in bilateral animals, PLoS One 7 (2012) e33973. D. Yan, Y. Tang, X. Xue, M. Wang, F. Liu, et al., The complete mitochondrial genome sequence of the western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) contains triplicate putative control regions, Gene 506 (2012) 117–124. S.L. Cameron, Insect mitochondrial genomics: implications for evolution and phylogeny, Annu. Rev. Entomol. 59 (2014) 95–117. K.I. Watanabe, Y. Bessho, M. Kawasaki, H. Hori, Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema, J. Mol. Biol. 286 (1999) 645–650. M.R. Armstrong, V.C. Blok, M.S. Phillips, A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida, Genetics 154 (2000) 181–192. T. Gibson, V.C. Blok, M. Dowton, Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives, J. Mol. Evol. 65 (2007) 308–315. K. Suga, D.B.M. Welch, Y. Tanaka, Y. Sakakura, A. Hagiwara, Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis, Mol. Biol. Evol. 25 (2008) 1129–1137. S.L. Cameron, K. Yoshizawa, A. Mizukoshi, M.F. Whiting, K.P. Johnson, Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera), BMC Genomics 12 (2011) 394. R. Shao, X.-Q. Zhu, S.C. Barker, K. Herd, Evolution of extensively fragmented mitochondrial genomes in the lice of humans, Genome Biol. Evol. 4 (2012) 1088–1101. H. Jiang, S.C. Barker, R. Shao, Substantial variation in the extent of mitochondrial genome fragmentation among blood-sucking lice of mammals, Genome Biol. Evol. 5 (2013) 1298–1308. W.-G. Dong, S. Song, D.-C. Jin, X.-G. Guo, R. Shao, Fragmented mitochondrial genomes of the rat lice, Polyplax asiatica and Polyplax spinulosa: intra-genus variation in fragmentation pattern and a possible link between the extent of fragmentation and the length of life cycle, BMC Genomics 15 (2014) 44. D. Grimaldi, Evolution of the Insects, Cambridge University Press, 2005. R. Shao, M. Dowton, A. Murrell, S.C. Barker, Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects, Mol. Biol. Evol. 20 (2003) 1612–1619. M.L. Thao, L. Baumann, P. Baumann, Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha), BMC Evol. Biol. 4 (2004) 25. H. Li, H. Liu, A. Shi, P. Štys, X. Zhou, et al., The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae), PLoS One 7 (2012) e29419. S.L. Cameron, K.P. Johnson, M.F. Whiting, The mitochondrial genome of the screamer louse Bothriometopus (Phthiraptera: Ischnocera): effects of extensive gene rearrangements on the evolution of the genome, J. Mol. Evol. 65 (2007) 589–604. S.L. Cameron, N. Lo, T. Bourguignon, G.J. Svenson, T.A. Evans, A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): robust support for interfamilial relationships and molecular synapomorphies define major clades, Mol. Phylogenet. Evol. 65 (2012) 163–173. S.L. Cameron, M.F. Whiting, Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae), Genome 50 (2007) 188–202. J.L. Boore, The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals, Comparative Genomics, Springer, 2000. 133–147. C. Moritz, T. Dowling, W. Brown, Evolution of animal mitochondrial DNA: relevance for population biology and systematics, Annu. Rev. Ecol. Syst. 18 (1987) 269–292. M. Dowton, N.J. Campbell, Intramitochondrial recombination—is it why some mitochondrial genes sleep around? Trends Ecol. Evol. 16 (2001) 269–271. M. Hoddle, L. Mound, PARIS D, Thrips of California 2012, CBIT Publishing, Queensland, 2012. (http://keys.lucidcentral.org/keys/v3/thrips_of_california/identifythrips/key/california-thysanoptera-2012/Media/Html/browse_species/ Frankliniella_intonsa.htm ). T.A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, 1999. 95–98. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol. 28 (2011) 2731–2739. N.T. Perna, T.D. Kocher, Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Evol. 41 (1995) 353–358. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25 (1997) 3389–3402. T.M. Lowe, S.R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res. 25 (1997) 0955–0964. Y. Kumazawa, M. Nishida, Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics, J. Mol. Evol. 37 (1993) 380–398.
