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 Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li & Xin-Min Qin To cite this article: Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li & Xin-Min Qin (2014): The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.873923
Published online: 17 Jan 2014.
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Date: 28 September 2015, At: 18:48
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873923
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li, and Xin-Min Qin
Downloaded by [Karolinska Institutet, University Library] at 18:48 28 September 2015
Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, Guangxi, PR China
Abstract
Keywords
The complete mitochondrial genome sequence of Papilio bianor was determined in the present paper. The complete mtDNA from P. bianor was 15,358 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region. The P. bianor genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. To determine the phylogentic position of P. bianor with related species within Papilionidae, the Bayesian phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 13 protein-coding genes. The phylogenetic trees confirmed that P. bianor and four species of Papilionidae clustered into a clade, and shared a close relationship with Papilio maraho. Meanwhile, the molecular phylogenetic trees also confirmed that Papilionidae is a monophyletic group, and Pieridae is closely related with Lycaenidae and Nymphalidae.
Complete mitochondrial genome, Papilio bianor, phylogeny
The species Papilio bianor belongs to Papilionidae, which are mainly found in China, Japan, Vietnam, India and Burma (Chuo, 1994). Some pervious studies of this species have been focused on the physiology (Kuyo et al., 1996), behavior (Ono et al., 2000), evolution (Zhu et al., 2009), breed (Yang et al., 2004) and phylogeography (Zhu et al., 2011). Here, in order to determine the complete mitochondrial genome sequence of P. bianor, an individual was collected from Guangxi, China. Whole mitochondrial genome of P. bianor was amplified with 15 pairs of primers and was completely sequenced by experimental protocols that are routinely used in a laboratory (Qin et al., 2012). The complete mitochondrial genome of P. bianor consists of 15,358 bp (GenBank accession no. KF859738) and including 13 protein coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes, and a non-coding control region (D-loop). The gene arrangement pattern and transcribing directions were identical with that of other lepidopteran species (Kim et al., 2006; Qin et al., 2012; Wang et al., 2011). The base composition of the whole genome (39.67% A, 40.94% T, 11.76% C and 7.63% G) and genes or regions was similar to most other butterflies, showing high AT content (80.61%). The secondary structures of tRNAs were predicted by tRNAscan-SE on-line server (Schattner et al., 2005), all the tRNAs could form typical cloverleaf structure except for tRNA-Ser(AGY), whose D-arm was lacking. Except for COI start with CGA, the remaining 12 protein-coding genes start with
Correspondence: X.-M. Qin, College of Life Science, Guangxi Normal University, 15 Yucai Road, Guangxi, Guilin 541004, PR China. Tel: +86 773 5845952. Fax: +86 773 5845952. E-mail: xmqin@mailbox. gxnu.edu.cn
History Received 3 December 2013 Accepted 7 December 2013 Published online 17 January 2014
a typical ATN codon. Within stop codons of 13 protein-coding genes, three kinds of codon were found in P. bianor: TAA (COIII, ND4, ND4L, ND5, ND6, ATPase8 and Cytb), TAG (ND1 and ND3) and incomplete stop codon T (COI, COII, ND2 and ATPase6). To determine the phylogentic position of P. bianor with related species within Papilionidae, all 21 currently available complete mitochondrial sequences of Papilionoidea retrieved from GenBank were used in phylogenetic analysis, using Adoxophyes honmai as outgroup. The phylogenetic tree was reconstructed with Bayesian inference (BI) methods based on the concatenated nucleotide dataset of the 13 protein-coding genes. BI phylogenetic analysis was carried out using the program MrBayes ver3.1.2 (Dice Holdings, Inc. Company, New York, NY) (Ronquist & Huelsenbeck, 2003). The analysis was run for 100,000 generations, with a sampling frequency of 100 generations. The burn-in was set to 250 trees to ensure that stable likelihood values were achieved. BI phylogenetic trees showed that the P. bianor and four species of Papilionidae clustered into a clade, and shared a close relationship with Papilio maraho. Meanwhile, the phylogenetic trees indicated that the involved species clustered into two major clades. The first clade includes those of the Nymphalidae, Lycaenidae and Pieridae, the second clade includes five species of the Papilionidae. In the first major clade, 11 species of Nymphalidae clustered into the first small branch, three species of Lycaenidae clustered into the second small branch, Papilio rapae and Papilio melete of the Pieridae were in the third small branch. Furthermore, the BI phylogenetic trees also confirmed that Papilionidae is a monophyletic group, and Pieridae is closely related with Lycaenidae and Nymphalidae (Figure 1). The results are similar to its classification based on traditional morphological characters (Harvey, 1991).
Downloaded by [Karolinska Institutet, University Library] at 18:48 28 September 2015
2
L.-X. Hou et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. BI phylogenetic tree based on the nucleotide sequences of the concatenated 13 protein coding genes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The project was supported by Guangxi Key Laboratory of Rare and Endangered Animal Ecology (1401z006), Guangxi Normal University, PR China.
References Chou R. (1994). Monographia rhopalocerorum sinensium. Henan: Henan Science and Technology Press. Harvey DJ. (1991). Higher classification of the Nymphalidae [A], Appendix B. In: Nijhout HF, editor. Higher classification of the Nymphalidae. Washington, DC: Smithsonian Institution Press, p. 200–73. Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR. (2006). The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol 15:217–25. Kuyo Y, Katsuhiko E, Akira Y, Kanji K. (1996). Species-specificity in the action of big and small prothoracicotropic hormones (PTTHs) of the swallowtail butterflies, Papilio xuthus, P. machaon, P. bianor and P. helenus. Zool Sci 13:449–54. Ono H, Kuwahara Y, Nishida R. (2000). A dihydroxy-gamma-lactone as an oviposition stimulant for the swallotail butterfly, Papilio bianor,
from the Rutaceous plant, Orixa japonica. Biosci Biotechnol Biochem 64:1970–3. Qin XM, Guan QX, Zeng DL, Qin F, Li HM. (2012). Complete mitochondrial genome of Kallima inachus (Lepidoptera: Nymphalidae: Nymphalinae): Comparison of K. inachus and Argynnis hyperbius. Mitochondrial DNA 23:318–20. Ronquist F, Huelsenbeck JP. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–4. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–9. Wang XC, Sun XY, Sun QQ, Zhang DX, Hu J, Yang Q, Hao JS. (2011). Complete mitochondrial genome of the laced fritillary Argyreus hyperbius (Lepidoptera: Nymphalidae). Zool Res 32:465–75. Yang P, Deng HL, Qi B, Wu PH. (2004). Study on the breeding biology of Papilio bianor cramer. J Southwest Agric Univ 26:789–92. Zhu LX, Wu XB, Wu CS, Yang BH. (2009). Phylogenetic evaluation of Papilio bianor and P. polyctor (Lepidoptera: Papilionidae). Oriental Insects 43:25–32. Zhu LX, Wu XB, Wu CS. (2011). Phylogeographic history of the swallowtail Papilio bianor Cramer (Lepidoptera: Papilionidae) from China. Oriental Insects 45:93–102.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li & Xin-Min Qin To cite this article: Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li & Xin-Min Qin (2014): The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2013.873923
Published online: 17 Jan 2014.
Submit your article to this journal
Article views: 31
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: [Karolinska Institutet, University Library]
Date: 28 September 2015, At: 18:48
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873923
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Papilio bianor (Lepidoptera: Papilionidae), and its phylogenetic position within Papilionidae Li-Xia Hou, She Ying, Xiao-Wen Yang, Zhang Yu, Hui-Min Li, and Xin-Min Qin
Downloaded by [Karolinska Institutet, University Library] at 18:48 28 September 2015
Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, Guangxi, PR China
Abstract
Keywords
The complete mitochondrial genome sequence of Papilio bianor was determined in the present paper. The complete mtDNA from P. bianor was 15,358 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region. The P. bianor genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. To determine the phylogentic position of P. bianor with related species within Papilionidae, the Bayesian phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 13 protein-coding genes. The phylogenetic trees confirmed that P. bianor and four species of Papilionidae clustered into a clade, and shared a close relationship with Papilio maraho. Meanwhile, the molecular phylogenetic trees also confirmed that Papilionidae is a monophyletic group, and Pieridae is closely related with Lycaenidae and Nymphalidae.
Complete mitochondrial genome, Papilio bianor, phylogeny
The species Papilio bianor belongs to Papilionidae, which are mainly found in China, Japan, Vietnam, India and Burma (Chuo, 1994). Some pervious studies of this species have been focused on the physiology (Kuyo et al., 1996), behavior (Ono et al., 2000), evolution (Zhu et al., 2009), breed (Yang et al., 2004) and phylogeography (Zhu et al., 2011). Here, in order to determine the complete mitochondrial genome sequence of P. bianor, an individual was collected from Guangxi, China. Whole mitochondrial genome of P. bianor was amplified with 15 pairs of primers and was completely sequenced by experimental protocols that are routinely used in a laboratory (Qin et al., 2012). The complete mitochondrial genome of P. bianor consists of 15,358 bp (GenBank accession no. KF859738) and including 13 protein coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes, and a non-coding control region (D-loop). The gene arrangement pattern and transcribing directions were identical with that of other lepidopteran species (Kim et al., 2006; Qin et al., 2012; Wang et al., 2011). The base composition of the whole genome (39.67% A, 40.94% T, 11.76% C and 7.63% G) and genes or regions was similar to most other butterflies, showing high AT content (80.61%). The secondary structures of tRNAs were predicted by tRNAscan-SE on-line server (Schattner et al., 2005), all the tRNAs could form typical cloverleaf structure except for tRNA-Ser(AGY), whose D-arm was lacking. Except for COI start with CGA, the remaining 12 protein-coding genes start with
Correspondence: X.-M. Qin, College of Life Science, Guangxi Normal University, 15 Yucai Road, Guangxi, Guilin 541004, PR China. Tel: +86 773 5845952. Fax: +86 773 5845952. E-mail: xmqin@mailbox. gxnu.edu.cn
History Received 3 December 2013 Accepted 7 December 2013 Published online 17 January 2014
a typical ATN codon. Within stop codons of 13 protein-coding genes, three kinds of codon were found in P. bianor: TAA (COIII, ND4, ND4L, ND5, ND6, ATPase8 and Cytb), TAG (ND1 and ND3) and incomplete stop codon T (COI, COII, ND2 and ATPase6). To determine the phylogentic position of P. bianor with related species within Papilionidae, all 21 currently available complete mitochondrial sequences of Papilionoidea retrieved from GenBank were used in phylogenetic analysis, using Adoxophyes honmai as outgroup. The phylogenetic tree was reconstructed with Bayesian inference (BI) methods based on the concatenated nucleotide dataset of the 13 protein-coding genes. BI phylogenetic analysis was carried out using the program MrBayes ver3.1.2 (Dice Holdings, Inc. Company, New York, NY) (Ronquist & Huelsenbeck, 2003). The analysis was run for 100,000 generations, with a sampling frequency of 100 generations. The burn-in was set to 250 trees to ensure that stable likelihood values were achieved. BI phylogenetic trees showed that the P. bianor and four species of Papilionidae clustered into a clade, and shared a close relationship with Papilio maraho. Meanwhile, the phylogenetic trees indicated that the involved species clustered into two major clades. The first clade includes those of the Nymphalidae, Lycaenidae and Pieridae, the second clade includes five species of the Papilionidae. In the first major clade, 11 species of Nymphalidae clustered into the first small branch, three species of Lycaenidae clustered into the second small branch, Papilio rapae and Papilio melete of the Pieridae were in the third small branch. Furthermore, the BI phylogenetic trees also confirmed that Papilionidae is a monophyletic group, and Pieridae is closely related with Lycaenidae and Nymphalidae (Figure 1). The results are similar to its classification based on traditional morphological characters (Harvey, 1991).
Downloaded by [Karolinska Institutet, University Library] at 18:48 28 September 2015
2
L.-X. Hou et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. BI phylogenetic tree based on the nucleotide sequences of the concatenated 13 protein coding genes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The project was supported by Guangxi Key Laboratory of Rare and Endangered Animal Ecology (1401z006), Guangxi Normal University, PR China.
References Chou R. (1994). Monographia rhopalocerorum sinensium. Henan: Henan Science and Technology Press. Harvey DJ. (1991). Higher classification of the Nymphalidae [A], Appendix B. In: Nijhout HF, editor. Higher classification of the Nymphalidae. Washington, DC: Smithsonian Institution Press, p. 200–73. Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR. (2006). The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol 15:217–25. Kuyo Y, Katsuhiko E, Akira Y, Kanji K. (1996). Species-specificity in the action of big and small prothoracicotropic hormones (PTTHs) of the swallowtail butterflies, Papilio xuthus, P. machaon, P. bianor and P. helenus. Zool Sci 13:449–54. Ono H, Kuwahara Y, Nishida R. (2000). A dihydroxy-gamma-lactone as an oviposition stimulant for the swallotail butterfly, Papilio bianor,
from the Rutaceous plant, Orixa japonica. Biosci Biotechnol Biochem 64:1970–3. Qin XM, Guan QX, Zeng DL, Qin F, Li HM. (2012). Complete mitochondrial genome of Kallima inachus (Lepidoptera: Nymphalidae: Nymphalinae): Comparison of K. inachus and Argynnis hyperbius. Mitochondrial DNA 23:318–20. Ronquist F, Huelsenbeck JP. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–4. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–9. Wang XC, Sun XY, Sun QQ, Zhang DX, Hu J, Yang Q, Hao JS. (2011). Complete mitochondrial genome of the laced fritillary Argyreus hyperbius (Lepidoptera: Nymphalidae). Zool Res 32:465–75. Yang P, Deng HL, Qi B, Wu PH. (2004). Study on the breeding biology of Papilio bianor cramer. J Southwest Agric Univ 26:789–92. Zhu LX, Wu XB, Wu CS, Yang BH. (2009). Phylogenetic evaluation of Papilio bianor and P. polyctor (Lepidoptera: Papilionidae). Oriental Insects 43:25–32. Zhu LX, Wu XB, Wu CS. (2011). Phylogeographic history of the swallowtail Papilio bianor Cramer (Lepidoptera: Papilionidae) from China. Oriental Insects 45:93–102.
