Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) Yong-Liang Zhang & An-Quan Wu To cite this article: Yong-Liang Zhang & An-Quan Wu (2015): The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003854
Published online: 28 Jan 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Otago]
Date: 25 October 2015, At: 06:55
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003854
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) Yong-Liang Zhang and An-Quan Wu
Downloaded by [University of Otago] at 06:55 25 October 2015
College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China
Abstract
Keywords
In this study, the complete mitochondrial genome sequence of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) has been reported for the first time. The total length of the mitogenome was 15,659 bp with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with CGA codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as some structures of repeated motifs and microsatellite-like elements and a poly-A element upstream of transfer RNA M (trnM) gene.
Bombyx mori Chunyun, insect, mitogenome, silkworm
In the past several decades, mitochondrial DNA has been widely used as an informative molecular marker in diverse evolutionary study areas, including molecular phylogenetics and evolution, molecular ecology, comparative and evolutionary genomics (Caterino et al., 2000; Krzywinski et al., 2006). Although the lepidoptera is one of the largest groups of insects, only about more than 30 complete or near-complete mitogenomes are currently available in GenBank. Currently, only four complete mitogenomes of species of Bombycidae have been reported, including Bombyx mori Xiafang (Lu et al., 2002), Bombyx mori C108 (Yukuhiro et al., 2002), Bombyx mori Dazao (Liu et al., 2013), Bombyx mori strain H9 (Dai et al., 2013). In this article, we determined the complete mitogenome sequence of Bombyx mori strain Chunyun, in order to provide more useful information for the taxonomic and phylogenetic studies of Bombyx mori. The new sequence of this whole mtDNA genome has been deposited in GenBank with the accession number KP192478. The complete mitogenome of Bombyx mori strain Chunyun is a circular molecule of 15,659 bp in length, containing typical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rrnL and rrnS) and 1 major noncoding AT-rich region (Table 1). Its gene order and orientation are identical to those of sequenced lepidopteran mitogenomes (Liu et al., 2012; Yukuhiro et al., 2002). Besides the AT-rich region, 20 intergenic
History Received 26 November 2014 Accepted 5 December 2014 Published online 28 January 2015
spacers (377 bp in total) and 5 overlapping regions (20 bp in total) are dispersed throughout the whole genome. The nucleotide compositions of the genome are significantly biased toward AT(81.35%), which is well within the range of other sequenced lepidopteran, from 79.7% in Pieris rapae (Mao et al., 2010) to 82.2% in Drosophila melanogaster (de Bruijn, 1983). All PCGs are initiated by a typical ATN codon, except for the COI gene, which uses CGA codon as observed in the sequenced Bombycidae (Lu et al., 2002). Eleven PCGs have a complete termination codon TAA and the other two genes end with a single nucleotide T (Table 1). All tRNAs displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes from several lepidopteran and metazoan insects (Dai et al., 2013; Wolstenholme, 1992). Furthermore, the two rRNAs (1378 bp rrnL and 783 bp rrnS) are also significantly biased towards AT nucleotides (84.41% for rrnL and 85.57% for rrnS, respectively). The 494 bp AT-rich region is located between the rrnS and trnM genes, with the AT content (94.93%) in the mitogenome, which is within the range reported for other lepidopteran insects (Cameron et al., 2008; Pan et al., 2008; Yang et al., 2009; Yukuhiro et al., 2002), and contains several structures characteristic of lepidopterans, such as the ATAGA motif followed by an 18 bp poly-T stretch and two microsatellite-like (AT)8 and (AT)8 element and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.
Correspondence: Yong-Liang Zhang, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China. E-mail: [email protected]
2
Y.-L. Zhang & A.-Q. Wu
Mitochondrial DNA, Early Online: 1–2
Table 1. Summary of the mitogenome of Bombyx mori strain Chunyun.
Downloaded by [University of Otago] at 06:55 25 October 2015
Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2 (UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1 (AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 (UCN) nad1 trnL1 (CUN) rrnL trnV rrnS Control region
Direction
Location
Size
Anticodon
Start codon
Stop codon
F F R F F R R F F F F F F F F F F F F F F F R R R R R F R F F F R R R R R
1–64 65–130 128–196 263–1267 1273–1342 1336–1400 1410–1471 1489–3019 3020–3086 3087–3768 3769–3839 3838–3905 3906–4067 4061–4738 4753–5541 5544–5609 5613–5963 6011–6078 6115–6178 6180–6246 6247–6313 6331–6396 6397–6461 6467–8185 8207–8273 8321–9673 9673–9963 9968–10,032 10,033–10,098 10,101–10,631 10,680–11,831 11,835–11,900 11,926–12,858 12,865–12,935 12,936–14,314 14,315–14,382 14,383–15,165 15,166–15,659
64 66 69 1005 70 65 62 1531 67 682 71 68 162 678 789 66 351 68 64 67 67 66 65 1719 67 1353 291 65 66 531 1152 66 933 71 1378 68 783 494
CAT30–32 GAT94–96 TTG164–166 — TCA1304–1306 TGC1371–1373 GTA1440–1442 — TAA3050–3052 — CTT3799–3801 GTC3870–3872 — — — TCC5574–5576 — TGC6043–6045 TCG6144–6146 GTT6211–6213 GCT6273–6275 TTC6361–6363 GAA6427–6429 — GTG8241–8243 — — TGT9999–10001 TGG10066–10068 — — TGA11865–11867 — TAG12903–12905 — TAC14349–14351 — —
— — — ATA — — — ATA — ATG — — ATA ATG ATG — ATA — — — — — — ATT — ATG ATG — — ATT ATA — ATT — — — — —
— — — TAA — — — T — T — — TAA TAA TAA — TAA — — — — — — TAA — TAA TAA — — TAA TAA — TAA — — — — —
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This work was supported by the National Natural Science Fundation of China (31271627) and the Key Discipline Construction Fund Project of Zhoukou Normal University.
References Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–13. Caterino MS, Cho S, Sperling FAH. (2000). The current state of insect molecular systematics: A thriving tower of babel. Ann Rev Entomol 45:1–54. Dai LS, Zhu BJ, Liu QN, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae). Gene 519:326–34. de Bruijn MH. (1983). Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature 304:234–41. Krzywinski J, Grushko OG, Besansky NJ. (2006). Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39:417–23.
Liu QN, Zhu BJ, Dai LS, Liu CL. (2013). The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects. Genomics 101:64–7. Liu QN, Zhu BJ, Dai LS, Wei GQ, Liu CL. (2012). The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene 505:291–9. Lu C, Liu YQ, Liao SY, Li B, Xiang ZH, Han H, Xue XG. (2002). Complete sequence determination and analysis of Bombyx mori mitochondrial genome. J Agric Biotechnol 10:163–70. Mao ZH, Hao JS, Zhu GP, Hu J, Si MM, Zhu CD. (2010). Sequencing and analysis of the complete mitochondrial genome of Pieris rapae Linnaeus (Lepidoptera: Pieridae). Acta Entomol Sinica 5:1295–304. Pan MH, Yu QY, Xia YL, Dai FY, Liu YQ, Lu C, Zhang Z, Xiang ZH. (2008). Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae). Sci China C Life Sci 51:693–701. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Yang L, Wei ZJ, Hong GY, Jiang ST, Wen LP. (2009). The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep 36:1441–9. Yukuhiro K, Sezutsu H, Itoh M, Shimizu K, Banno Y. (2002). Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth. Bombyx mori. Mol Biol Evol 19:1385–9.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) Yong-Liang Zhang & An-Quan Wu To cite this article: Yong-Liang Zhang & An-Quan Wu (2015): The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003854
Published online: 28 Jan 2015.
Submit your article to this journal
Article views: 4
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Otago]
Date: 25 October 2015, At: 06:55
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003854
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) Yong-Liang Zhang and An-Quan Wu
Downloaded by [University of Otago] at 06:55 25 October 2015
College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China
Abstract
Keywords
In this study, the complete mitochondrial genome sequence of Bombyx mori strain Chunyun (Lepidoptera: Bombycidae) has been reported for the first time. The total length of the mitogenome was 15,659 bp with 37 typical animal mitochondrial genes and 1 non-coding A + T-rich region. Its gene content and order were identical to those of other lepidopteran mitochondrial genomes. All protein-coding genes (PCGs) were initiated by ATN codons except for the COI gene, which began with CGA codon. Eleven PCGs stopped with termination codon TAA, whereas the COI and COII genes ended with single T. All tRNAs have typical structures of insect mitochondrial tRNAs. The 494 bp AT-rich region contains several features common to other lepidopterans, such as some structures of repeated motifs and microsatellite-like elements and a poly-A element upstream of transfer RNA M (trnM) gene.
Bombyx mori Chunyun, insect, mitogenome, silkworm
In the past several decades, mitochondrial DNA has been widely used as an informative molecular marker in diverse evolutionary study areas, including molecular phylogenetics and evolution, molecular ecology, comparative and evolutionary genomics (Caterino et al., 2000; Krzywinski et al., 2006). Although the lepidoptera is one of the largest groups of insects, only about more than 30 complete or near-complete mitogenomes are currently available in GenBank. Currently, only four complete mitogenomes of species of Bombycidae have been reported, including Bombyx mori Xiafang (Lu et al., 2002), Bombyx mori C108 (Yukuhiro et al., 2002), Bombyx mori Dazao (Liu et al., 2013), Bombyx mori strain H9 (Dai et al., 2013). In this article, we determined the complete mitogenome sequence of Bombyx mori strain Chunyun, in order to provide more useful information for the taxonomic and phylogenetic studies of Bombyx mori. The new sequence of this whole mtDNA genome has been deposited in GenBank with the accession number KP192478. The complete mitogenome of Bombyx mori strain Chunyun is a circular molecule of 15,659 bp in length, containing typical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rrnL and rrnS) and 1 major noncoding AT-rich region (Table 1). Its gene order and orientation are identical to those of sequenced lepidopteran mitogenomes (Liu et al., 2012; Yukuhiro et al., 2002). Besides the AT-rich region, 20 intergenic
History Received 26 November 2014 Accepted 5 December 2014 Published online 28 January 2015
spacers (377 bp in total) and 5 overlapping regions (20 bp in total) are dispersed throughout the whole genome. The nucleotide compositions of the genome are significantly biased toward AT(81.35%), which is well within the range of other sequenced lepidopteran, from 79.7% in Pieris rapae (Mao et al., 2010) to 82.2% in Drosophila melanogaster (de Bruijn, 1983). All PCGs are initiated by a typical ATN codon, except for the COI gene, which uses CGA codon as observed in the sequenced Bombycidae (Lu et al., 2002). Eleven PCGs have a complete termination codon TAA and the other two genes end with a single nucleotide T (Table 1). All tRNAs displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes from several lepidopteran and metazoan insects (Dai et al., 2013; Wolstenholme, 1992). Furthermore, the two rRNAs (1378 bp rrnL and 783 bp rrnS) are also significantly biased towards AT nucleotides (84.41% for rrnL and 85.57% for rrnS, respectively). The 494 bp AT-rich region is located between the rrnS and trnM genes, with the AT content (94.93%) in the mitogenome, which is within the range reported for other lepidopteran insects (Cameron et al., 2008; Pan et al., 2008; Yang et al., 2009; Yukuhiro et al., 2002), and contains several structures characteristic of lepidopterans, such as the ATAGA motif followed by an 18 bp poly-T stretch and two microsatellite-like (AT)8 and (AT)8 element and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.
Correspondence: Yong-Liang Zhang, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China. E-mail: [email protected]
2
Y.-L. Zhang & A.-Q. Wu
Mitochondrial DNA, Early Online: 1–2
Table 1. Summary of the mitogenome of Bombyx mori strain Chunyun.
Downloaded by [University of Otago] at 06:55 25 October 2015
Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2 (UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1 (AGN) trnE trnF nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 (UCN) nad1 trnL1 (CUN) rrnL trnV rrnS Control region
Direction
Location
Size
Anticodon
Start codon
Stop codon
F F R F F R R F F F F F F F F F F F F F F F R R R R R F R F F F R R R R R
1–64 65–130 128–196 263–1267 1273–1342 1336–1400 1410–1471 1489–3019 3020–3086 3087–3768 3769–3839 3838–3905 3906–4067 4061–4738 4753–5541 5544–5609 5613–5963 6011–6078 6115–6178 6180–6246 6247–6313 6331–6396 6397–6461 6467–8185 8207–8273 8321–9673 9673–9963 9968–10,032 10,033–10,098 10,101–10,631 10,680–11,831 11,835–11,900 11,926–12,858 12,865–12,935 12,936–14,314 14,315–14,382 14,383–15,165 15,166–15,659
64 66 69 1005 70 65 62 1531 67 682 71 68 162 678 789 66 351 68 64 67 67 66 65 1719 67 1353 291 65 66 531 1152 66 933 71 1378 68 783 494
CAT30–32 GAT94–96 TTG164–166 — TCA1304–1306 TGC1371–1373 GTA1440–1442 — TAA3050–3052 — CTT3799–3801 GTC3870–3872 — — — TCC5574–5576 — TGC6043–6045 TCG6144–6146 GTT6211–6213 GCT6273–6275 TTC6361–6363 GAA6427–6429 — GTG8241–8243 — — TGT9999–10001 TGG10066–10068 — — TGA11865–11867 — TAG12903–12905 — TAC14349–14351 — —
— — — ATA — — — ATA — ATG — — ATA ATG ATG — ATA — — — — — — ATT — ATG ATG — — ATT ATA — ATT — — — — —
— — — TAA — — — T — T — — TAA TAA TAA — TAA — — — — — — TAA — TAA TAA — — TAA TAA — TAA — — — — —
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This work was supported by the National Natural Science Fundation of China (31271627) and the Key Discipline Construction Fund Project of Zhoukou Normal University.
References Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–13. Caterino MS, Cho S, Sperling FAH. (2000). The current state of insect molecular systematics: A thriving tower of babel. Ann Rev Entomol 45:1–54. Dai LS, Zhu BJ, Liu QN, Wei GQ, Liu CL. (2013). Characterization of the complete mitochondrial genome of Bombyx mori strain H9 (Lepidoptera: Bombycidae). Gene 519:326–34. de Bruijn MH. (1983). Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature 304:234–41. Krzywinski J, Grushko OG, Besansky NJ. (2006). Analysis of the complete mitochondrial DNA from Anopheles funestus: An improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39:417–23.
Liu QN, Zhu BJ, Dai LS, Liu CL. (2013). The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects. Genomics 101:64–7. Liu QN, Zhu BJ, Dai LS, Wei GQ, Liu CL. (2012). The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene 505:291–9. Lu C, Liu YQ, Liao SY, Li B, Xiang ZH, Han H, Xue XG. (2002). Complete sequence determination and analysis of Bombyx mori mitochondrial genome. J Agric Biotechnol 10:163–70. Mao ZH, Hao JS, Zhu GP, Hu J, Si MM, Zhu CD. (2010). Sequencing and analysis of the complete mitochondrial genome of Pieris rapae Linnaeus (Lepidoptera: Pieridae). Acta Entomol Sinica 5:1295–304. Pan MH, Yu QY, Xia YL, Dai FY, Liu YQ, Lu C, Zhang Z, Xiang ZH. (2008). Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae). Sci China C Life Sci 51:693–701. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. Int Rev Cytol 141:173–216. Yang L, Wei ZJ, Hong GY, Jiang ST, Wen LP. (2009). The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep 36:1441–9. Yukuhiro K, Sezutsu H, Itoh M, Shimizu K, Banno Y. (2002). Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth. Bombyx mori. Mol Biol Evol 19:1385–9.
