http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003838
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Graphium chironides (Lepidoptera: Papilionidae: Papilioninae) Xiao Chen and Jiasheng Hao
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu 241000, People’s Republic of China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Graphium chironides is a circular molecule of 15,235 bp in length, containing 37 typical animal mitochondrial genes: 13 proteincoding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a non-coding AT-rich region. All PCGs start with a typical ATN initiation codon, except for COI, which is initiated with the CGA codon as observed in other butterfly species. Eleven PCGs terminate in the complete stop codon TAA or TAG, whereas the COI and COII genes end with single T. Twelve intergenic spacers (79 bp in total) and 15 overlapping regions (42 bp in total) are dispersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1343 bp and 778 bp in size, with the AT contents of 84.2% and 85.3%, respectively. All tRNA genes display typical secondary cloverleaf structures except for tRNASer(AGN) which loses the DHU arm. The 419 bp long AT-rich region contains several features common to the other lepidopterans, such as the ATAGA motif followed by a 12 bp poly-T stretch, two microsatellite-likes (TA)7 and (TA)9 preceded by the ATTTA motif.
Graphium chironides, mitochondrial genome, Papilionidae, Papilioninae
The Papilioninae includes about 480 species and occurs worldwide, with most of the species being found in the tropical and subtropical areas. However, current knowledge about Papilioninae mitochondrial genomes is still limited. Till date, only 12 complete mitogenomes of Papilioninae have been reported, including
History Received 18 November 2014 Accepted 5 December 2014 Published online 20 January 2015
Papilio maraho (Wu et al., 2010), Teinopalpus aureus (Qin et al., 2012), Papilio maackii (Dong et al., 2013), Papilio bianor (Hou et al., 2014), Graphium timur (Chen et al., 2014a), Papilio polytes (Wang et al., 2014), Papilio syfanius (Dong et al., 2014), Byasa alcinous (Chen et al., 2014b), Lamproptera curius
Table 1. Organization of the complete mitochondrial genome in Graphium chironides.
Met
tRNA tRNAlle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu (UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg
Direction
Position
Size(bp)
Intergenic length
Start codon
Stop codon
F F R F F R R F F F F F F F F F F F F
1–67 68–131 129–197 236–1250 1248–1313 1306–1371 1368–1432 1435–2965 2966–3032 3033–3717 3718–3788 3788–3856 3854–4018 4012–4689 4689–5477 5481–5546 5547–5900 5899–5962 5962–6025
67 64 69 1015 66 66 65 1531 67 685 71 69 165 678 789 66 354 64 64
0 3 38 3 8 4 2 0 0 0 1 3 7 1 3 0 2 1 0
– – – ATT – – – CGA – ATG – – ATT ATG ATG – ATC – –
– – – TAA – – – T-tRNA – T-tRNA – – TAA TAA TAA – TAG – – (continued )
Correspondence: J.-S. Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Science, Anhui Normal University, Wuhu 241000, P.R. China. Tel: + 86 553 3818721. E-mail: [email protected]
2
X. Chen & J. Hao
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
Asn
tRNA tRNASer(AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer(UCN) ND1 tRNALeu(CUN) lrRNA tRNAVal srRNA AT-rich region
Direction
Position
Size(bp)
Intergenic length
Start codon
Stop codon
F F F R R R R R F R F F F R R R R R R
6026–6090 6091–6150 6154–6220 6218–6283 6283–8031 8029–8095 8097–9437 9437–9727 9730–9793 9794–9859 9861–10,391 10,401–11,552 11,551–11,616 11,633–12,571 12,573–12,640 12,642–13,984 13,975–14,038 14,039–14,816 14,817–15,235
65 60 67 66 1749 67 1341 291 64 66 531 1152 66 939 68 1343 64 778 419
0 3 3 1 3 1 1 2 0 1 1 1 16 1 1 10 0 0
– – – – ATT – ATG ATG – – ATT ATG – ATG – – – – –
– – – – TAA – TAA TAA – – TAA TAA – TAG – – – – –
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.
(KJ141168), Papilio machaon (HM243594), Papilio dardanus (JX313686) and Troides aeacus (EU625344). Here, we present the complete mitogenome sequence of Graphium chironides, one representative species of Papilioninae, with the aim of providing more molecular data for the taxonomic and phylogenetic studies of Papilioninae. The whole mitogenome is a circular molecule of 15,234 bp in length, containing typical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (lrRNA and srRNA) and a non-coding AT-rich region (Table 1). Similar to the majority of other insect groups, the nucleotide composition of the Graphium chironides mitogenome is significantly biased toward AT (80.4%). Besides the AT-rich region, 12 intergenic spacers (79 bp in total) and 15 overlapping regions (42 bp in total) are dispersed throughout the whole genome. Nucleotide skewness analysis of the whole mitogenome (AT-skew ¼ 0.014, GC-skew ¼ 0.216) indicates a slight level of T and C skews. The 13 PCGs are 11,220 bp in total encoding 3728 amino acid residues, with the AT content of 78.9%. All PCGs are initiated by typical ATN codons (seven ATG codons, four ATT codons and one ATC codon), with the exception of COI gene that uses CGA as its start codon (Table 1). This unconventional start codon is also reported in other available lepidopteran mitogenomes (Chen et al., 2014a,b; Hao et al., 2013; Hou et al., 2014). Eleven PCGs use TAA or TAG as their stop codons, while the COI and COII stop with single nucleotide T (Table 1). This case was also frequently found in most insect mitogenomes sequenced to date (Chen et al., 2014a,b; Cheng et al., 2014; Hao et al., 2013). All tRNAs can be folded into the typical cloverleaf secondary structures except for tRNASer(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop, as seen in all other determined butterfly species (Park et al., 2012; Chen et al., 2014a,b; Hao et al., 2013). The two rRNAs (lrRNA and srRNA) genes are 1343 bp and 778 bp, with their AT contents of 84.2% and 85.3%, respectively. The 419 bp AT-rich region is located between the srRNA gene and the tRNAMet–tRNAIle–tRNAGln (M–I–Q) gene cluster, with the highest AT content (95.7%) of any region of the whole genome, and contains several structures characteristic of lepidopterans, such as the motif ATAGA followed by a 12-bp poly-T stretch, two microsatellite-likes (TA)7 and (TA)9 preceded by the
ATTTA motif. Additionally, some single nucleotide repeats which are frequently found in some other butterfly species, such as (T)2-11, (A)2-10, are detected in the region. Nucleotide sequence accession number. The complete genome sequence of Graphium chironides has been assigned GenBank accession number KP159289.
Declaration of interest This work was supported by the National Science Foundation of China (Grant No. 41172004). 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. (2014a). The complete mitochondrial genome of the Pazala timur (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.905843. Chen YH, Gan SS, Wang YL, Wang Y, Zuo N, Hao JS. (2014b). The complete mitochondrial genome of the Byasa alcinous (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.919472. Cheng CH, Sun XY, Gai YH, Hao JS, Yang Q. (2014). The complete mitochondrial genome of the Epacanthaclisis banksi Krivokhatsky, 1998 (Neuroptera: Myrmeleontidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.855910. Dong Y, Zhu LX, Wu YF, Wu XB. (2013). The complete mitochondrial genome of the Alpine Black Swallowtail, Papilio maackii (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:639–41. Dong Y, Zhu LX, Ding MJ, Wang JJ, Luo LG, Liu Y, Ou YY. (2014). Complete mitochondrial genome of Papilio syfanius (Lepidoptera: Papilionidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.898278. 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. Hou LX, Ying S, Yang XW, Yu Z, Li HM, Qin XM. (2014). The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.873923. Park JS, Cho Y, Kim MJ, Nam SH, Kim I. (2012). Description of complete mitochondrial genome of the black-veined white, Aporia
DOI: 10.3109/19401736.2014.1003838
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species. J Asia Pac Entomol 15:331–41. Qin F, Jiang GF, Zhou SY. (2012). Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mitochondrial DNA 23:123–5. Wang L, Du XJ, Li XF. (2014). The complete mitogenome of the Common Mormon Papilio polytes (Insecta: Lepidoptera:
Mitogenome of G. chironides
3
Papilionoidea). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.945550. Wu LW, Lees DC, Yen SH, Hsu YF. (2010). The Complete mitochondrial genome of the near–threatened swallowtail, Agehana maraho (Lepidoptera: Papilionidae): Evaluating sequence variability and suitable markers for conservation genetic studies. Entomol News 121:267–80.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Graphium chironides (Lepidoptera: Papilionidae: Papilioninae) Xiao Chen and Jiasheng Hao
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
Laboratory of Molecular Evolution and Biodiversity, College of Life Sciences, Anhui Normal University, Wuhu 241000, People’s Republic of China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of Graphium chironides is a circular molecule of 15,235 bp in length, containing 37 typical animal mitochondrial genes: 13 proteincoding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a non-coding AT-rich region. All PCGs start with a typical ATN initiation codon, except for COI, which is initiated with the CGA codon as observed in other butterfly species. Eleven PCGs terminate in the complete stop codon TAA or TAG, whereas the COI and COII genes end with single T. Twelve intergenic spacers (79 bp in total) and 15 overlapping regions (42 bp in total) are dispersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1343 bp and 778 bp in size, with the AT contents of 84.2% and 85.3%, respectively. All tRNA genes display typical secondary cloverleaf structures except for tRNASer(AGN) which loses the DHU arm. The 419 bp long AT-rich region contains several features common to the other lepidopterans, such as the ATAGA motif followed by a 12 bp poly-T stretch, two microsatellite-likes (TA)7 and (TA)9 preceded by the ATTTA motif.
Graphium chironides, mitochondrial genome, Papilionidae, Papilioninae
The Papilioninae includes about 480 species and occurs worldwide, with most of the species being found in the tropical and subtropical areas. However, current knowledge about Papilioninae mitochondrial genomes is still limited. Till date, only 12 complete mitogenomes of Papilioninae have been reported, including
History Received 18 November 2014 Accepted 5 December 2014 Published online 20 January 2015
Papilio maraho (Wu et al., 2010), Teinopalpus aureus (Qin et al., 2012), Papilio maackii (Dong et al., 2013), Papilio bianor (Hou et al., 2014), Graphium timur (Chen et al., 2014a), Papilio polytes (Wang et al., 2014), Papilio syfanius (Dong et al., 2014), Byasa alcinous (Chen et al., 2014b), Lamproptera curius
Table 1. Organization of the complete mitochondrial genome in Graphium chironides.
Met
tRNA tRNAlle tRNAGln ND2 tRNATrp tRNACys tRNATyr COI tRNALeu (UUR) COII tRNALys tRNAAsp ATP8 ATP6 COIII tRNAGly ND3 tRNAAla tRNAArg
Direction
Position
Size(bp)
Intergenic length
Start codon
Stop codon
F F R F F R R F F F F F F F F F F F F
1–67 68–131 129–197 236–1250 1248–1313 1306–1371 1368–1432 1435–2965 2966–3032 3033–3717 3718–3788 3788–3856 3854–4018 4012–4689 4689–5477 5481–5546 5547–5900 5899–5962 5962–6025
67 64 69 1015 66 66 65 1531 67 685 71 69 165 678 789 66 354 64 64
0 3 38 3 8 4 2 0 0 0 1 3 7 1 3 0 2 1 0
– – – ATT – – – CGA – ATG – – ATT ATG ATG – ATC – –
– – – TAA – – – T-tRNA – T-tRNA – – TAA TAA TAA – TAG – – (continued )
Correspondence: J.-S. Hao, Laboratory of Molecular Evolution and Biodiversity, College of Life Science, Anhui Normal University, Wuhu 241000, P.R. China. Tel: + 86 553 3818721. E-mail: [email protected]
2
X. Chen & J. Hao
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
Asn
tRNA tRNASer(AGN) tRNAGlu tRNAPhe ND5 tRNAHis ND4 ND4L tRNAThr tRNAPro ND6 Cytb tRNASer(UCN) ND1 tRNALeu(CUN) lrRNA tRNAVal srRNA AT-rich region
Direction
Position
Size(bp)
Intergenic length
Start codon
Stop codon
F F F R R R R R F R F F F R R R R R R
6026–6090 6091–6150 6154–6220 6218–6283 6283–8031 8029–8095 8097–9437 9437–9727 9730–9793 9794–9859 9861–10,391 10,401–11,552 11,551–11,616 11,633–12,571 12,573–12,640 12,642–13,984 13,975–14,038 14,039–14,816 14,817–15,235
65 60 67 66 1749 67 1341 291 64 66 531 1152 66 939 68 1343 64 778 419
0 3 3 1 3 1 1 2 0 1 1 1 16 1 1 10 0 0
– – – – ATT – ATG ATG – – ATT ATG – ATG – – – – –
– – – – TAA – TAA TAA – – TAA TAA – TAG – – – – –
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.
(KJ141168), Papilio machaon (HM243594), Papilio dardanus (JX313686) and Troides aeacus (EU625344). Here, we present the complete mitogenome sequence of Graphium chironides, one representative species of Papilioninae, with the aim of providing more molecular data for the taxonomic and phylogenetic studies of Papilioninae. The whole mitogenome is a circular molecule of 15,234 bp in length, containing typical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (lrRNA and srRNA) and a non-coding AT-rich region (Table 1). Similar to the majority of other insect groups, the nucleotide composition of the Graphium chironides mitogenome is significantly biased toward AT (80.4%). Besides the AT-rich region, 12 intergenic spacers (79 bp in total) and 15 overlapping regions (42 bp in total) are dispersed throughout the whole genome. Nucleotide skewness analysis of the whole mitogenome (AT-skew ¼ 0.014, GC-skew ¼ 0.216) indicates a slight level of T and C skews. The 13 PCGs are 11,220 bp in total encoding 3728 amino acid residues, with the AT content of 78.9%. All PCGs are initiated by typical ATN codons (seven ATG codons, four ATT codons and one ATC codon), with the exception of COI gene that uses CGA as its start codon (Table 1). This unconventional start codon is also reported in other available lepidopteran mitogenomes (Chen et al., 2014a,b; Hao et al., 2013; Hou et al., 2014). Eleven PCGs use TAA or TAG as their stop codons, while the COI and COII stop with single nucleotide T (Table 1). This case was also frequently found in most insect mitogenomes sequenced to date (Chen et al., 2014a,b; Cheng et al., 2014; Hao et al., 2013). All tRNAs can be folded into the typical cloverleaf secondary structures except for tRNASer(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop, as seen in all other determined butterfly species (Park et al., 2012; Chen et al., 2014a,b; Hao et al., 2013). The two rRNAs (lrRNA and srRNA) genes are 1343 bp and 778 bp, with their AT contents of 84.2% and 85.3%, respectively. The 419 bp AT-rich region is located between the srRNA gene and the tRNAMet–tRNAIle–tRNAGln (M–I–Q) gene cluster, with the highest AT content (95.7%) of any region of the whole genome, and contains several structures characteristic of lepidopterans, such as the motif ATAGA followed by a 12-bp poly-T stretch, two microsatellite-likes (TA)7 and (TA)9 preceded by the
ATTTA motif. Additionally, some single nucleotide repeats which are frequently found in some other butterfly species, such as (T)2-11, (A)2-10, are detected in the region. Nucleotide sequence accession number. The complete genome sequence of Graphium chironides has been assigned GenBank accession number KP159289.
Declaration of interest This work was supported by the National Science Foundation of China (Grant No. 41172004). 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. (2014a). The complete mitochondrial genome of the Pazala timur (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.905843. Chen YH, Gan SS, Wang YL, Wang Y, Zuo N, Hao JS. (2014b). The complete mitochondrial genome of the Byasa alcinous (Lepidoptera: Papilionidae: Papilioninae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.919472. Cheng CH, Sun XY, Gai YH, Hao JS, Yang Q. (2014). The complete mitochondrial genome of the Epacanthaclisis banksi Krivokhatsky, 1998 (Neuroptera: Myrmeleontidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.855910. Dong Y, Zhu LX, Wu YF, Wu XB. (2013). The complete mitochondrial genome of the Alpine Black Swallowtail, Papilio maackii (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:639–41. Dong Y, Zhu LX, Ding MJ, Wang JJ, Luo LG, Liu Y, Ou YY. (2014). Complete mitochondrial genome of Papilio syfanius (Lepidoptera: Papilionidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.898278. 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. Hou LX, Ying S, Yang XW, Yu Z, Li HM, Qin XM. (2014). The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.873923. Park JS, Cho Y, Kim MJ, Nam SH, Kim I. (2012). Description of complete mitochondrial genome of the black-veined white, Aporia
DOI: 10.3109/19401736.2014.1003838
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/23/15 For personal use only.
crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species. J Asia Pac Entomol 15:331–41. Qin F, Jiang GF, Zhou SY. (2012). Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mitochondrial DNA 23:123–5. Wang L, Du XJ, Li XF. (2014). The complete mitogenome of the Common Mormon Papilio polytes (Insecta: Lepidoptera:
Mitogenome of G. chironides
3
Papilionoidea). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.945550. Wu LW, Lees DC, Yen SH, Hsu YF. (2010). The Complete mitochondrial genome of the near–threatened swallowtail, Agehana maraho (Lepidoptera: Papilionidae): Evaluating sequence variability and suitable markers for conservation genetic studies. Entomol News 121:267–80.
