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 Jin6 (Lepidoptera: Bombycidae) Yong-Liang Zhang, Jin-Hui Zhao & Qi-Ming Zhou To cite this article: Yong-Liang Zhang, Jin-Hui Zhao & Qi-Ming Zhou (2015): The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003896
Published online: 20 Jan 2015.
Submit your article to this journal
Article views: 9
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 Lethbridge]
Date: 06 November 2015, At: 00:59
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003896
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) Yong-Liang Zhang1, Jin-Hui Zhao1, and Qi-Ming Zhou2 College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China and 2Sericultural Science Research Institute of Henan Province, Nanyang City, Henan Province, China
Downloaded by [University of Lethbridge] at 00:59 06 November 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) has been reported for the first time. It was a circular molecule of 15,648 bp in length, containing 37 typical coding genes and one non-coding AT-rich region. The overall composition of the mitogenome was A (43.05%), G (7.30%), C (11.35%), and T (38.29%). Its gene order and content were identical to the common type found in most insect mitogenomes. All protein coding genes (PCGs) started with a typical ATN initiation codon, except for the cox1 gene, which began with CGA codon. Eleven genes used standard complete termination codon TAA, whereas the cox1 and cox2 genes ended with single T. All tRNA genes displayed typical secondary cloverleaf structures as those of other insects. Additionally, the 494 bp long AT-rich region contained several structures common to the other lepidopterons, such as some structures of repeated motifs and microsatellite-like elements.
Bombyx mori Jin6, insect, mitogenome, silkworm
To date, more than 240 species of the complete or nearly complete mitogenome sequences from insects have been determined based on the GenBank database. Although the Lepidoptera is the second most numerous order of insects, only about more than 30 complete or near-complete mitogenomes are currently available in
History Received 10 December 2014 Accepted 19 December 2014 Published online 20 January 2015
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), and Bombyx mori strain H9 (Dai et al., 2013). In this article, we determined the
Table 1. Summary of the mitogenome of Bombyx mori strain Jin6. Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN
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
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 6008–6075 6108–6171 6173–6239
64 66 69 1005 70 65 62 1531 67 682 71 68 162 678 789 66 351 68 64 67
CAT30–32 GAT94–96 TTG164–166 — TCA1304–1306 TGC1371–1373 GTA1440–1442 — TAA3050–3052 — CTT3799–3801 GTC3870–3872 — — — TCC5574–5576 — ATA TGC6040–6042 TCG6137–6139 GTT6204–6206
— — — ATA — — — CGA — ATG — — ATA ATG ATG — TAA — — —
— — — TAA — — — T — T — — TAA TAA TAA — — — — (continued )
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 et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Downloaded by [University of Lethbridge] at 00:59 06 November 2015
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 R R R R F R F F F R R R R R
6240–6306 6324–6389 6390–6454 6460–8178 8206–8272 8311–9663 9663–9953 9958–10,022 10,023–10,088 10,091–10,621 10,670–11,821 11,825–11,890 11,915–12,847 12,854–12,924 12,925–14,303 14,304–14,371 14,372–15,154 15,155–15,648
67 66 65 1719 67 1353 291 65 66 531 1152 66 933 71 1379 68 783 494
GCT6266–6268 TTC6354–6356 GAA6420–6422 — TGA8240–8242 — — TGT9989–9991 TGG10056–10058 — — TGA11855–11857 — TAG12892–12894 — TAC14338–14340 — —
— — — ATT — ATG ATG — — ATT ATA — ATT — — — — —
— — — TAA — TAA TAA — — TAA TAA — TAA — — — — —
complete mitogenome sequence of Bombyx mori strain Jin6, in order to provide more useful information for the taxonomic and phylogenetic studies of Bombyx mori. The new sequence of this whole mtDNA genome was deposited in GenBank with the accession number KP244370. The circular genome of this species is 15,648 bp long and contains a typical gene complement: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes (rrnL and rrnS), and a 494 bp long non-coding AT-rich region (Table 1). Its gene order and orientation are identical to those of sequenced lepidopteran mitogenomes. Besides the AT-rich region, 20 intergenic spacers (367 bp in total) and five overlapping regions (20 bp in total) are dispersed throughout the whole genome. The base composition of the genome is A (43.05%) 4T (38.29%) 4C (11.35%) 4G (7.30%), and the A-T bias (81.35%) was detected, 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 cox1 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 incomplete stop codons (T–) are found in the other two genes (cox1 and cox2) (Table 1). The 22 tRNA genes ranging in size from 62 bp to 71 bp displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes from several lepidopteran and metazoan insects (Dai et al., 2013). The two rRNAs (1379 bp rrnL and 783 bp rrnS) are also significantly biased towards A and T nucleotides (84.41% for rrnL and 85.57% for rrnS, respectively). The 494 bp AT-rich region is located between the rrnS gene and the trnM gene cluster, and exhibits the highest AT content (95.55%) among the whole genome, 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). Several characteristic structures are also detected in the AT-rich region, such as the ATAGA motif followed by an 18 bp poly-T stretch and the ATTTA motif followed by two microsatellite-like (AT)8 and
(AT)8 element and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.
Declaration of interest The authors report that they have 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 Foundation 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. 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. 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. 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, et al. (2008). Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae). Sci China C Life Sci 51:693–701. 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 Jin6 (Lepidoptera: Bombycidae) Yong-Liang Zhang, Jin-Hui Zhao & Qi-Ming Zhou To cite this article: Yong-Liang Zhang, Jin-Hui Zhao & Qi-Ming Zhou (2015): The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003896
Published online: 20 Jan 2015.
Submit your article to this journal
Article views: 9
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 Lethbridge]
Date: 06 November 2015, At: 00:59
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003896
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) Yong-Liang Zhang1, Jin-Hui Zhao1, and Qi-Ming Zhou2 College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou City, Henan Province, China and 2Sericultural Science Research Institute of Henan Province, Nanyang City, Henan Province, China
Downloaded by [University of Lethbridge] at 00:59 06 November 2015
1
Abstract
Keywords
In this study, the complete mitochondrial genome of Bombyx mori strain Jin6 (Lepidoptera: Bombycidae) has been reported for the first time. It was a circular molecule of 15,648 bp in length, containing 37 typical coding genes and one non-coding AT-rich region. The overall composition of the mitogenome was A (43.05%), G (7.30%), C (11.35%), and T (38.29%). Its gene order and content were identical to the common type found in most insect mitogenomes. All protein coding genes (PCGs) started with a typical ATN initiation codon, except for the cox1 gene, which began with CGA codon. Eleven genes used standard complete termination codon TAA, whereas the cox1 and cox2 genes ended with single T. All tRNA genes displayed typical secondary cloverleaf structures as those of other insects. Additionally, the 494 bp long AT-rich region contained several structures common to the other lepidopterons, such as some structures of repeated motifs and microsatellite-like elements.
Bombyx mori Jin6, insect, mitogenome, silkworm
To date, more than 240 species of the complete or nearly complete mitogenome sequences from insects have been determined based on the GenBank database. Although the Lepidoptera is the second most numerous order of insects, only about more than 30 complete or near-complete mitogenomes are currently available in
History Received 10 December 2014 Accepted 19 December 2014 Published online 20 January 2015
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), and Bombyx mori strain H9 (Dai et al., 2013). In this article, we determined the
Table 1. Summary of the mitogenome of Bombyx mori strain Jin6. Gene trnM trnI trnQ nad2 trnW trnC trnY cox1 trnL2(UUR) cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN
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
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 6008–6075 6108–6171 6173–6239
64 66 69 1005 70 65 62 1531 67 682 71 68 162 678 789 66 351 68 64 67
CAT30–32 GAT94–96 TTG164–166 — TCA1304–1306 TGC1371–1373 GTA1440–1442 — TAA3050–3052 — CTT3799–3801 GTC3870–3872 — — — TCC5574–5576 — ATA TGC6040–6042 TCG6137–6139 GTT6204–6206
— — — ATA — — — CGA — ATG — — ATA ATG ATG — TAA — — —
— — — TAA — — — T — T — — TAA TAA TAA — — — — (continued )
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 et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Downloaded by [University of Lethbridge] at 00:59 06 November 2015
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 R R R R F R F F F R R R R R
6240–6306 6324–6389 6390–6454 6460–8178 8206–8272 8311–9663 9663–9953 9958–10,022 10,023–10,088 10,091–10,621 10,670–11,821 11,825–11,890 11,915–12,847 12,854–12,924 12,925–14,303 14,304–14,371 14,372–15,154 15,155–15,648
67 66 65 1719 67 1353 291 65 66 531 1152 66 933 71 1379 68 783 494
GCT6266–6268 TTC6354–6356 GAA6420–6422 — TGA8240–8242 — — TGT9989–9991 TGG10056–10058 — — TGA11855–11857 — TAG12892–12894 — TAC14338–14340 — —
— — — ATT — ATG ATG — — ATT ATA — ATT — — — — —
— — — TAA — TAA TAA — — TAA TAA — TAA — — — — —
complete mitogenome sequence of Bombyx mori strain Jin6, in order to provide more useful information for the taxonomic and phylogenetic studies of Bombyx mori. The new sequence of this whole mtDNA genome was deposited in GenBank with the accession number KP244370. The circular genome of this species is 15,648 bp long and contains a typical gene complement: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes (rrnL and rrnS), and a 494 bp long non-coding AT-rich region (Table 1). Its gene order and orientation are identical to those of sequenced lepidopteran mitogenomes. Besides the AT-rich region, 20 intergenic spacers (367 bp in total) and five overlapping regions (20 bp in total) are dispersed throughout the whole genome. The base composition of the genome is A (43.05%) 4T (38.29%) 4C (11.35%) 4G (7.30%), and the A-T bias (81.35%) was detected, 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 cox1 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 incomplete stop codons (T–) are found in the other two genes (cox1 and cox2) (Table 1). The 22 tRNA genes ranging in size from 62 bp to 71 bp displayed the typical clover-leaf secondary structure observed in mitochondrial tRNA genes from several lepidopteran and metazoan insects (Dai et al., 2013). The two rRNAs (1379 bp rrnL and 783 bp rrnS) are also significantly biased towards A and T nucleotides (84.41% for rrnL and 85.57% for rrnS, respectively). The 494 bp AT-rich region is located between the rrnS gene and the trnM gene cluster, and exhibits the highest AT content (95.55%) among the whole genome, 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). Several characteristic structures are also detected in the AT-rich region, such as the ATAGA motif followed by an 18 bp poly-T stretch and the ATTTA motif followed by two microsatellite-like (AT)8 and
(AT)8 element and an 11 bp poly-A element upstream of transfer RNA M (trnM) gene.
Declaration of interest The authors report that they have 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 Foundation 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. 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. 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. 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, et al. (2008). Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bombyx mandarina (Lepidoptera: Bombycidae). Sci China C Life Sci 51:693–701. 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.
