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 Tirumala limniace (Lepidoptera: Nymphalidae: Danainae) Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia & Jiasheng Hao To cite this article: Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia & Jiasheng Hao (2014): The complete mitochondrial genome of Tirumala limniace (Lepidoptera: Nymphalidae: Danainae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.930839
Published online: 30 Jun 2014.
Submit your article to this journal
Article views: 14
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: [Australian National University]
Date: 05 November 2015, At: 20:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.930839
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tirumala limniace (Lepidoptera: Nymphalidae: Danainae) Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia, and Jiasheng Hao
Downloaded by [Australian National University] at 20:08 05 November 2015
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, People’s Republic of China
Abstract
Keywords
The complete mitochondrial nucleotide sequence of Tirumala limniace is 15,285 bp in size, containing typical metazoan 37 genes: 13 protein-coding genes (PCGs), 22tRNA genes, 2 ribosomal RNA genes and one noncoding AT-rich region. All the 13 PCGs initiated with ATN, except for COI gene which is started by CGA codon. Nine PCGs use the complete termination codon (TAA), whereas the COI, COII, ND4 and ND5 genes end with single T. A total of 132 bp intergenic spacers and a total of 37 bp overlapping sequences are interspersed throughout the whole genome. The two rRNA genes (rrnL and rrnS) are 1352 bp and 779 bp in size, with their AT contents of 84.6% and 85.5%, respectively. All tRNA genes display typical secondary cloverleaf structures except for trnS1 (AGN) which loses DHU arm. The 438 bp long AT-rich region contains several features common to the other lepidopterans, such as the ATAGA motif followed by a 18 bp poly-T stretch, a 9 bp poly-T stretch, a 10 bp poly-A stretch and some microsatellite-like (AT)n elements.
Danainae, mitochondrial genome, nymphalidae, tirumala limniace
Danainae is a butterfly subfamily of Nymphalidae, which includes about 185 species, with most of the species being found in the tropical areas. However, up to the present, there are a lot of controversy about the taxonomy and phylogeny of Danainae, and therefore more mtDNA sequence data are needed to clarify this problem. However, only four complete mitogenomes of Danainae species have been reported, including Euploea mulciber
History Received 30 May 2014 Accepted 1 June 2014 Published online 26 June 2014
(Hao et al., 2013), Danaus plexippus (Servı´n-Garciduen˜as & Martı´nez-Romero, 2013), Danaus chrysippus (Gan et al., 2014a), and Ideopsis similis (Gan et al., 2014b). In this article, we reported the complete mitochondrial genome of another species of Danainae, the Tirumala limniace, in order to provide more useful information for the future phylogenetic and systematic studies.
Table 1. Organization of the T. limniace mitochondrial genome. Gene tRNAMet tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg
Direction F F R F F R R F F F F F F F F F F F F
Nucleotide no. 1–67 69–132 130–198 274–1287 1286–1352 1345–1409 1410–1473 1482–3012 3013–3079 3080–3755 3755–3827 3826–3891 3892–4056 4050–4730 4730–5518 5521–5588 5586–5942 5945–6009 6009–6072
Size(bp)
Intergenic nucleotides
67 64 69 1014 67 65 64 1531 67 676 73 66 165 681 789 68 357 65 64
1 3 75 2 8 0 2 0 0 1 2 0 7 1 3 3 2 1
Start code
Stop code
ATT
TAA
CAG
T-tRNA
ATG
T-tRNA
ATT ATG ATG
TAA TAA TAA
ATA
TAA
(continued )
Correspondence: J.-S. Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, 241000, P.R. China. Tel: +86 553 3818721. E-mail: [email protected]
2
S. Gan et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued
Gene
Downloaded by [Australian National University] at 20:08 05 November 2015
Asn
tRNA tRNASer(AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer(UCN) ND1 tRNALeu(CUN) lrRNA tRNAVal srRNA A+T-rich region
Direction
Nucleotide no.
Size(bp)
Intergenic nucleotides
F F F R R R R R F R F F F R R R R R F
6075–6140 6139–6198 6200–6264 6263–6326 6327–8046 8064–8125 8126–9464 9464–9751 9754–9817 9818–9882 9885–10,406 10,410–11,558 11,557–11,622 11,643–12,581 12,583–12,649 12,650–14,001 14,002–14,068 14,069–14,847 14,848–15,285
66 60 65 64 1720 64 1339 288 64 65 522 1149 72 939 67 1352 67 779 438
2 2 1 2 0 19 0 1 3 0 2 3 2 20 1 0 0 0 0
Start code
Stop code
ATC
T-tRNA
ATG ATG
T-tRNA TAA
ATC ATG
TAA TAA
ATG
TAA
In the column intergenic length, the positive number indicates interval base pairs between genes, while the negative number indicates the overlapping base pairs between genes.
The complete mitogenome of Tirumala limniace was a circular molecule of 15,285 bp in length, containing typical insect 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 other butterflies determined to date (Chen et al., 2014; Gan et al., 2014; Hao et al., 2013; Shi et al., 2012; Wang et al., 2011). Besides the AT-rich region, 12 intergenic spacers (132 bp in total) and 14 overlapping regions (37 bp in total) are dispersed throughout the whole genome. The mitogenome nucleotide skewness analysis (AT-skew ¼ 0.062, GC-skew ¼ 0.219) indicates a slight level of T and C skews. The total 13 PCGs was 11 170 bp long and all of them start with a typical ATN codon, except for the COI which uses CGA as its start codons (Table 1); nine PCGs stop with codon TAA, while the COI, COII, ND5, ND4 genes stop with the single nucleotide T (Table 1). This case was also frequently found in most insect mitogenomes sequenced to date (Cheng et al., 2014; Gan et al., 2014; Zhang et al., 2014). Like those of all other determined butterflies, All the Tirumala limniace tRNAs harbor the typical predicted secondary cloverleaf structures except for trnS1(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop (Chen et al., 2014; Servı´n-Garciduen˜as & Martı´nez-Romero, 2013; Shi et al., 2012, 2013; Shao et al., 2014). The two rRNAs (rrnL and rrnS) are 1318 bp and 786 bp long, with their AT contents of 84.6% and 85.5%, respectively. The T. limniace A+T-rich region is 438 bp long located between srRNA and Met-Ile-Gln tRNA cluster, exhibiting the highest A+T content (93.4%) of any region of the whole genome. Several short sequence repeats characteristic of lepidopterans are scattered throughout the whole region, such as a 18-bp poly T stretch preceded by the ATAGA motif, a microsatellite-like (AT)10 element. Additionally, some single nucleotides repeats which are frequently found in some other insect species, such as (T)2–9, (A)2–10, are also detected in the region (Chen et al., 2014; Cheng et al., 2014; Hao et al., 2012, 2013).
Nucleotide sequence accession number The complete genome sequence of T. limniace has been assigned GenBank accession number KJ784473.
Declaration of interest This work was supported by the National Science Foundation of China (Grant No. 41172004) and the Opening Funds from the State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (Grant No. 104143). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Chen YH, Gan SS, Shao LL, Cheng CH, Hao JS. (2014). The complete mitochondrial genome of the Pazala timur (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA 1–2. Cheng CH, Xiaoyan Sun, Gai YH, Hao JS, Yang Q. (2014). The complete mitochondrial genome of the Epacanthaclisis banksi Krivokhatsky, 1998 (Neuroptera: Myrmeleontidae). Mitochondrial DNA 1–2. Hao JS, Sun QQ, Zhao HB, Sun XY, Gai YH, Yang Q. (2012). The complete mitochondrial genome of the Tawny Angle Ctenoptilum vasava Moore (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genom 2012:1–13. Hao JS, Sun ME, Shi QH, Sun XY, Shao LL, Yang Q. (2013). Complete mitogenomes of Euploea mulciber (Nymphalidae: Danainae) and Libythea celtis (Nymphalidae: Libytheinae) and their phylogenetic implications. ISRN Genomics 491636:1–14. Gan SS, Sun XY, Gai YH, Hao JS. (2014a). The complete mitochondrial genome of Danaus chrysippus (Lepidoptera: Nymphalidae: Danainae). Mitochondrial DNA 1–2. Gan SS, Chen YH, Zuo N, Zhang W, Hao JS. (2014b). The complete mitochondrial genome of Ideopsis similis (Lepidoptera: Nymphalidae: Danainae). Mitochondrial DNA 1–2. Servı´n-Garciduen˜as LE, Martı´nez-Romero E. (2013). Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae). Mitochondrial DNA 1–2. Shao LL, Sun QQ, Hao JS. (2014). The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae). Mitochondrial DNA 1–2. Shi QH, Xia J, Sun XY, Hao JS, Yang Q. (2012). Complete mitogenome of the Painted Jezebel, Delias hyparete Linnaeus (Lepidoptera: Pieridae) and its comparison with other butterfly species. Zool Res 33:111–20. Shi QH, Zhao F, Hao JS, Yang Q. (2013). Complete mitochondrial genome of the common evening brown, Melanitis leda Linnaeus (Lepidoptera: Nymphalidae: Satyrinae). Mitochondrial DNA 24: 492–4.
DOI: 10.3109/19401736.2014.930839
Downloaded by [Australian National University] at 20:08 05 November 2015
Wang XC, Sun XY, Sun QQ, Zhang DX, Hu J, Yang Q, Hao JS. (2011). The complete mitochondrial genome of the laced fritillary Argyreus hyperbius (Lepidoptera: Nymphalidae). Zool Res 32:465–75.
Mitogenome of T. limniace
3
Zhang W, Gan SS, Zuo N, Cheng CH, Wang Y, Hao JS. (2014). The complete mitochondrial genome of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae). Mitochondrial DNA1–2.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Tirumala limniace (Lepidoptera: Nymphalidae: Danainae) Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia & Jiasheng Hao To cite this article: Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia & Jiasheng Hao (2014): The complete mitochondrial genome of Tirumala limniace (Lepidoptera: Nymphalidae: Danainae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.930839
Published online: 30 Jun 2014.
Submit your article to this journal
Article views: 14
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: [Australian National University]
Date: 05 November 2015, At: 20:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.930839
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Tirumala limniace (Lepidoptera: Nymphalidae: Danainae) Shanshan Gan, Yanhong Chen, Ni Zuo, Chenchen Xia, and Jiasheng Hao
Downloaded by [Australian National University] at 20:08 05 November 2015
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, People’s Republic of China
Abstract
Keywords
The complete mitochondrial nucleotide sequence of Tirumala limniace is 15,285 bp in size, containing typical metazoan 37 genes: 13 protein-coding genes (PCGs), 22tRNA genes, 2 ribosomal RNA genes and one noncoding AT-rich region. All the 13 PCGs initiated with ATN, except for COI gene which is started by CGA codon. Nine PCGs use the complete termination codon (TAA), whereas the COI, COII, ND4 and ND5 genes end with single T. A total of 132 bp intergenic spacers and a total of 37 bp overlapping sequences are interspersed throughout the whole genome. The two rRNA genes (rrnL and rrnS) are 1352 bp and 779 bp in size, with their AT contents of 84.6% and 85.5%, respectively. All tRNA genes display typical secondary cloverleaf structures except for trnS1 (AGN) which loses DHU arm. The 438 bp long AT-rich region contains several features common to the other lepidopterans, such as the ATAGA motif followed by a 18 bp poly-T stretch, a 9 bp poly-T stretch, a 10 bp poly-A stretch and some microsatellite-like (AT)n elements.
Danainae, mitochondrial genome, nymphalidae, tirumala limniace
Danainae is a butterfly subfamily of Nymphalidae, which includes about 185 species, with most of the species being found in the tropical areas. However, up to the present, there are a lot of controversy about the taxonomy and phylogeny of Danainae, and therefore more mtDNA sequence data are needed to clarify this problem. However, only four complete mitogenomes of Danainae species have been reported, including Euploea mulciber
History Received 30 May 2014 Accepted 1 June 2014 Published online 26 June 2014
(Hao et al., 2013), Danaus plexippus (Servı´n-Garciduen˜as & Martı´nez-Romero, 2013), Danaus chrysippus (Gan et al., 2014a), and Ideopsis similis (Gan et al., 2014b). In this article, we reported the complete mitochondrial genome of another species of Danainae, the Tirumala limniace, in order to provide more useful information for the future phylogenetic and systematic studies.
Table 1. Organization of the T. limniace mitochondrial genome. Gene tRNAMet tRNAIle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu(UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg
Direction F F R F F R R F F F F F F F F F F F F
Nucleotide no. 1–67 69–132 130–198 274–1287 1286–1352 1345–1409 1410–1473 1482–3012 3013–3079 3080–3755 3755–3827 3826–3891 3892–4056 4050–4730 4730–5518 5521–5588 5586–5942 5945–6009 6009–6072
Size(bp)
Intergenic nucleotides
67 64 69 1014 67 65 64 1531 67 676 73 66 165 681 789 68 357 65 64
1 3 75 2 8 0 2 0 0 1 2 0 7 1 3 3 2 1
Start code
Stop code
ATT
TAA
CAG
T-tRNA
ATG
T-tRNA
ATT ATG ATG
TAA TAA TAA
ATA
TAA
(continued )
Correspondence: J.-S. Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu, 241000, P.R. China. Tel: +86 553 3818721. E-mail: [email protected]
2
S. Gan et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued
Gene
Downloaded by [Australian National University] at 20:08 05 November 2015
Asn
tRNA tRNASer(AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer(UCN) ND1 tRNALeu(CUN) lrRNA tRNAVal srRNA A+T-rich region
Direction
Nucleotide no.
Size(bp)
Intergenic nucleotides
F F F R R R R R F R F F F R R R R R F
6075–6140 6139–6198 6200–6264 6263–6326 6327–8046 8064–8125 8126–9464 9464–9751 9754–9817 9818–9882 9885–10,406 10,410–11,558 11,557–11,622 11,643–12,581 12,583–12,649 12,650–14,001 14,002–14,068 14,069–14,847 14,848–15,285
66 60 65 64 1720 64 1339 288 64 65 522 1149 72 939 67 1352 67 779 438
2 2 1 2 0 19 0 1 3 0 2 3 2 20 1 0 0 0 0
Start code
Stop code
ATC
T-tRNA
ATG ATG
T-tRNA TAA
ATC ATG
TAA TAA
ATG
TAA
In the column intergenic length, the positive number indicates interval base pairs between genes, while the negative number indicates the overlapping base pairs between genes.
The complete mitogenome of Tirumala limniace was a circular molecule of 15,285 bp in length, containing typical insect 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 other butterflies determined to date (Chen et al., 2014; Gan et al., 2014; Hao et al., 2013; Shi et al., 2012; Wang et al., 2011). Besides the AT-rich region, 12 intergenic spacers (132 bp in total) and 14 overlapping regions (37 bp in total) are dispersed throughout the whole genome. The mitogenome nucleotide skewness analysis (AT-skew ¼ 0.062, GC-skew ¼ 0.219) indicates a slight level of T and C skews. The total 13 PCGs was 11 170 bp long and all of them start with a typical ATN codon, except for the COI which uses CGA as its start codons (Table 1); nine PCGs stop with codon TAA, while the COI, COII, ND5, ND4 genes stop with the single nucleotide T (Table 1). This case was also frequently found in most insect mitogenomes sequenced to date (Cheng et al., 2014; Gan et al., 2014; Zhang et al., 2014). Like those of all other determined butterflies, All the Tirumala limniace tRNAs harbor the typical predicted secondary cloverleaf structures except for trnS1(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop (Chen et al., 2014; Servı´n-Garciduen˜as & Martı´nez-Romero, 2013; Shi et al., 2012, 2013; Shao et al., 2014). The two rRNAs (rrnL and rrnS) are 1318 bp and 786 bp long, with their AT contents of 84.6% and 85.5%, respectively. The T. limniace A+T-rich region is 438 bp long located between srRNA and Met-Ile-Gln tRNA cluster, exhibiting the highest A+T content (93.4%) of any region of the whole genome. Several short sequence repeats characteristic of lepidopterans are scattered throughout the whole region, such as a 18-bp poly T stretch preceded by the ATAGA motif, a microsatellite-like (AT)10 element. Additionally, some single nucleotides repeats which are frequently found in some other insect species, such as (T)2–9, (A)2–10, are also detected in the region (Chen et al., 2014; Cheng et al., 2014; Hao et al., 2012, 2013).
Nucleotide sequence accession number The complete genome sequence of T. limniace has been assigned GenBank accession number KJ784473.
Declaration of interest This work was supported by the National Science Foundation of China (Grant No. 41172004) and the Opening Funds from the State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (Grant No. 104143). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Chen YH, Gan SS, Shao LL, Cheng CH, Hao JS. (2014). The complete mitochondrial genome of the Pazala timur (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA 1–2. Cheng CH, Xiaoyan Sun, Gai YH, Hao JS, Yang Q. (2014). The complete mitochondrial genome of the Epacanthaclisis banksi Krivokhatsky, 1998 (Neuroptera: Myrmeleontidae). Mitochondrial DNA 1–2. Hao JS, Sun QQ, Zhao HB, Sun XY, Gai YH, Yang Q. (2012). The complete mitochondrial genome of the Tawny Angle Ctenoptilum vasava Moore (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genom 2012:1–13. Hao JS, Sun ME, Shi QH, Sun XY, Shao LL, Yang Q. (2013). Complete mitogenomes of Euploea mulciber (Nymphalidae: Danainae) and Libythea celtis (Nymphalidae: Libytheinae) and their phylogenetic implications. ISRN Genomics 491636:1–14. Gan SS, Sun XY, Gai YH, Hao JS. (2014a). The complete mitochondrial genome of Danaus chrysippus (Lepidoptera: Nymphalidae: Danainae). Mitochondrial DNA 1–2. Gan SS, Chen YH, Zuo N, Zhang W, Hao JS. (2014b). The complete mitochondrial genome of Ideopsis similis (Lepidoptera: Nymphalidae: Danainae). Mitochondrial DNA 1–2. Servı´n-Garciduen˜as LE, Martı´nez-Romero E. (2013). Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae). Mitochondrial DNA 1–2. Shao LL, Sun QQ, Hao JS. (2014). The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae). Mitochondrial DNA 1–2. Shi QH, Xia J, Sun XY, Hao JS, Yang Q. (2012). Complete mitogenome of the Painted Jezebel, Delias hyparete Linnaeus (Lepidoptera: Pieridae) and its comparison with other butterfly species. Zool Res 33:111–20. Shi QH, Zhao F, Hao JS, Yang Q. (2013). Complete mitochondrial genome of the common evening brown, Melanitis leda Linnaeus (Lepidoptera: Nymphalidae: Satyrinae). Mitochondrial DNA 24: 492–4.
DOI: 10.3109/19401736.2014.930839
Downloaded by [Australian National University] at 20:08 05 November 2015
Wang XC, Sun XY, Sun QQ, Zhang DX, Hu J, Yang Q, Hao JS. (2011). The complete mitochondrial genome of the laced fritillary Argyreus hyperbius (Lepidoptera: Nymphalidae). Zool Res 32:465–75.
Mitogenome of T. limniace
3
Zhang W, Gan SS, Zuo N, Cheng CH, Wang Y, Hao JS. (2014). The complete mitochondrial genome of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae). Mitochondrial DNA1–2.
