http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.898278
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Papilio syfanius (Lepidoptera: Papilionidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Ulster at Jordanstown on 03/26/15 For personal use only.
Yan Dong, Li-Xin Zhu, Meng-Juan Ding, Jia-Jia Wang, Lai-Gao Luo, Yang Liu, and Yong-Yue Ou College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the swallowtail butterfly Papilio syfanius has been completed. It is 15,359 bp, and contains the typical complement of 13 protein-coding (PCGs), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes. Two A + T-rich regions are included in this mitogenome. The nucleotide composition is very similar to other insects, showing a high bias towards A + T, especially the control region (92.8%). Gene order in P. syfanius mitogenome is basically identical to that of the inferred ancestral insect genome, with the exception of translocations of trnM, which is common in genus Papilio.
Mitogenome, Papilionidae, Papilio syfanius, swallowtail butterfly
Swallowtail butterflies belong to the Papilionidae family include over 570 species divided into 4 subfamilies and over 60 genera worldwide (Bridges, 1988). About 210 Papilio species have been documented worldwide, with some 27 species recorded in China (Wu, 2001). Swallowtail butterflies are used as model organisms for studies in evolutionary biology, ecology, genetics and conservation biology, because they are highly sensitive to habitat loss and fragmentation, pollution, pesticides or climate change (Dong et al., 2013a,b; Liu et al., 2011; Maes & Van Dyck, 2005; Settele et al., 2008; Zhu et al., 2011). Because of environmental change and human hunt, some of the swallowtail butterflies are regarded as the most severely threatened species group in China. Papilio syfanius is a rare species of swallowtail butterfly from the genus Papilio that is only found in China. The specimen of P. syfanius used in this study obtained in July 2004 from Lushan County, Sichuan province, China (30 30 N, 103 50 E). Total genomic DNA was extracted from the two legs using the DNeasy tissue kit (Qiagen China, Shanghai). The entire mitogenome was amplified in four short and six long overlapping fragments in the present study. Takara Taq and Takara LA Taq (Takara Biomedical, Japan) were used in PCR amplification. And the purified PCR products were sequenced directly with the amplified primers and internal walking primers in both directions. The organization of the P. syfanius mitochondrial genome is shown in Table 1. The complete mitogenome of the P. syfanius is 15,359 bp in length, and submitted to GenBank under accession number KJ396621. The complete mtDNA sequence of the P. syfanius is circular molecule, containing 13 PCGs, 2 rRNA genes, 22 tRNAs and two non-coding A + T-rich regions. Genes are contiguous, usually separated by 1–22 nt, or alternatively with
Correspondence: L.-X. Zhu, College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China. Tel: +86 05503512022. E-mail: [email protected]; [email protected]
History Received 8 February 2014 Revised 17 February 2014 Accepted 23 February 2014 Published online 12 March 2014
Table 1. Organization of the mitochondrial genome of Papilio syfanius.
Feature
From
To
Length (nt)
cox1 trnL2 cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1 trnE trnF* nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 nad1 trnL1 rrnL trnV rrnS CR1 trnM trnI
1 1531 1599 2281 2351 2418 2582 3275 4067 4133 4485 4548 4611 4678 4740 4804 4872 6613 6677 8040 8315 8379 8447 8988 10,142 10,223 11,160 11,232 12,558 12,625 13,399 13,913 13,981
1530 1598 2280 2351 2417 2588 3262 4063 4132 4484 4548 4611 4677 4739 4805 4871 6596 6676 8017 8312 8378 8443 8980 10,136 10,206 11,158 11,227 12,557 12,620 13,398 13,912 13,980 14,044
1530 68 682 71 67 171 681 789 66 354 64 64 67 62 66 68 1725 64 1341 273 64 65 534 1149 65 936 68 1326 63 774 514 68 64
Codons Start
Stop
CGA
CT
ATG
T
Spacer/ Overlap()
1 ATT ATG ATG
TAA TAA TAA
ATC
T
8 12 3 1 1 2
ATT
TAA
16
ATG ATG
TAA CAA
22 2
ATG ATG
TAA TAA
ATG
TAG
3 7 5 16 1 4 4
3 (continued )
2
Y. Dong et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Feature
From
To
trnQ CR2 nad2 trnW trnC trnY Total
14,042 14,110 14,155 15,167 15,225 15,291
14,109 14,154 15,166 15,232 15,290 15,355 15,359
Length (nt) 68 45 1012 66 66 65
Codons Start
Stop
ATT
T
Spacer/ Overlap()
References 8 4 98/24
*Underlines indicate the gene encoded on the opposite strand.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Ulster at Jordanstown on 03/26/15 For personal use only.
This research was supported by Natural Science Foundation of the Higher Education Institutions of Anhui Province (KJ2013Z245), Anhui Provincial Natural Science Foundation (1408085QC67), Foundation of ChuZhou University (2012qd13) and the key Natural Science Foundation of the Anhui Higher Education Institutions of China.
1–8 nt overlap. The major non-coding A + T-rich region of determined swallowtail mitogenome is 514 bp located between 12S rRNA and trnM (Table 1). The protein-coding genes account for 72.8% (11,177 bp) of the whole genome, the rRNA genes for 13.7% (2097 bp), the tRNA genes for 9.4% (1449 bp) and the non-coding DNA for 4.3% (657 bp). The A + T content of the complete mitochondrial DNA is 80.6%, which corresponds well to the percentage found in the mtDNA of other insect mitogenomes (Crozier & Crozier, 1993; Dotson & Beard, 2001). The higher A + T content was observed in control region 1 (92.8%). The starting codons inferred for the 13 protein-coding genes are the conventional starting types ATN, except that the cox1 start codon was identified as CGA (Table 1). This phenomenon has been reported in P. xuthus, P. bianor and P. maackii (Dong et al., 2013a, b; Feng et al., 2010). Nine PCGs terminate with the complete termination codon TAN (atp8, atp6, cox3, nad5, nad4, nad4L, nad6, cob and nad1), and the other four genes (cox1, cox2, nad2 and nad3) end with a single stop nucleotide T or absence. The secondary structure information of the tRNA genes might be responsible for the correct cleavage of the polycistronic transcript (Carapelli et al. 2008; Ojala et al., 1980).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Bridges CA. (1988). Catalogue of Papilionidae and Pieridae (Lepidoptera: Rhopalocera). Urbana, IL: C.A. Bridges. Carapelli A, Comandi S, Convey P, Nardi F, Frati F. (2008). The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola). BMC Genom 9:315. Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133:97–117. Dong Y, Zhu LX, Wu YF, Wu XB. (2013a). The complete mitochondrial genome of the Chinese peacock, Papilio bianor (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:636–8. Dong Y, Zhu LX, Wu YF, Wu XB. (2013b). The complete mitochondrial genome of the Alpine Black Swallowtail, Papilio Maackii (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:639–41. Dotson EM, Beard CB. (2001). Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Mol Biol 10:205–15. Feng X, Liu DF, Wang NX, Zhu CD, Jiang GF. (2010). The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol Biol Rep 37:3877–88. Liu XS, Zhang YL, Fang JH. (2011). A butterfly hotspot in western China, its environmental threats and conservation. J Insect Conserv 15: 617–32. Maes D, Van Dyck H. (2005). Habitat quality and biodiversity indicator performances of a threatened butterfly versus a multispecies group for wet heath lands in Belgium. Biol Conserv 123:177–87. Ojala D, Merkel C, Gelfand R, Attardi G. (1980). The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 2:393–403. Settele J, Kudrna O, Harpke A, Ku¨hn I, van Swaay C, Verovnik R, Warren M, et al. (2008). Climatic risk Atlas of European Butterflies. BioRisk 1:1–710. Wu CS. (2001). Fauna Sinica Insect Vol. 25 Lepidoptera Papilionidae (in Chinese). Beijing: Science Press. Zhu LX, Wu XB, Wu CS. (2011). Phylogeographic history of the swallowtail Papilio bianor Cramer (Lepidoptera: Papilionidae) from China. Oriental Insects 45:98–102.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Papilio syfanius (Lepidoptera: Papilionidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Ulster at Jordanstown on 03/26/15 For personal use only.
Yan Dong, Li-Xin Zhu, Meng-Juan Ding, Jia-Jia Wang, Lai-Gao Luo, Yang Liu, and Yong-Yue Ou College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the swallowtail butterfly Papilio syfanius has been completed. It is 15,359 bp, and contains the typical complement of 13 protein-coding (PCGs), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes. Two A + T-rich regions are included in this mitogenome. The nucleotide composition is very similar to other insects, showing a high bias towards A + T, especially the control region (92.8%). Gene order in P. syfanius mitogenome is basically identical to that of the inferred ancestral insect genome, with the exception of translocations of trnM, which is common in genus Papilio.
Mitogenome, Papilionidae, Papilio syfanius, swallowtail butterfly
Swallowtail butterflies belong to the Papilionidae family include over 570 species divided into 4 subfamilies and over 60 genera worldwide (Bridges, 1988). About 210 Papilio species have been documented worldwide, with some 27 species recorded in China (Wu, 2001). Swallowtail butterflies are used as model organisms for studies in evolutionary biology, ecology, genetics and conservation biology, because they are highly sensitive to habitat loss and fragmentation, pollution, pesticides or climate change (Dong et al., 2013a,b; Liu et al., 2011; Maes & Van Dyck, 2005; Settele et al., 2008; Zhu et al., 2011). Because of environmental change and human hunt, some of the swallowtail butterflies are regarded as the most severely threatened species group in China. Papilio syfanius is a rare species of swallowtail butterfly from the genus Papilio that is only found in China. The specimen of P. syfanius used in this study obtained in July 2004 from Lushan County, Sichuan province, China (30 30 N, 103 50 E). Total genomic DNA was extracted from the two legs using the DNeasy tissue kit (Qiagen China, Shanghai). The entire mitogenome was amplified in four short and six long overlapping fragments in the present study. Takara Taq and Takara LA Taq (Takara Biomedical, Japan) were used in PCR amplification. And the purified PCR products were sequenced directly with the amplified primers and internal walking primers in both directions. The organization of the P. syfanius mitochondrial genome is shown in Table 1. The complete mitogenome of the P. syfanius is 15,359 bp in length, and submitted to GenBank under accession number KJ396621. The complete mtDNA sequence of the P. syfanius is circular molecule, containing 13 PCGs, 2 rRNA genes, 22 tRNAs and two non-coding A + T-rich regions. Genes are contiguous, usually separated by 1–22 nt, or alternatively with
Correspondence: L.-X. Zhu, College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China. Tel: +86 05503512022. E-mail: [email protected]; [email protected]
History Received 8 February 2014 Revised 17 February 2014 Accepted 23 February 2014 Published online 12 March 2014
Table 1. Organization of the mitochondrial genome of Papilio syfanius.
Feature
From
To
Length (nt)
cox1 trnL2 cox2 trnK trnD atp8 atp6 cox3 trnG nad3 trnA trnR trnN trnS1 trnE trnF* nad5 trnH nad4 nad4L trnT trnP nad6 cob trnS2 nad1 trnL1 rrnL trnV rrnS CR1 trnM trnI
1 1531 1599 2281 2351 2418 2582 3275 4067 4133 4485 4548 4611 4678 4740 4804 4872 6613 6677 8040 8315 8379 8447 8988 10,142 10,223 11,160 11,232 12,558 12,625 13,399 13,913 13,981
1530 1598 2280 2351 2417 2588 3262 4063 4132 4484 4548 4611 4677 4739 4805 4871 6596 6676 8017 8312 8378 8443 8980 10,136 10,206 11,158 11,227 12,557 12,620 13,398 13,912 13,980 14,044
1530 68 682 71 67 171 681 789 66 354 64 64 67 62 66 68 1725 64 1341 273 64 65 534 1149 65 936 68 1326 63 774 514 68 64
Codons Start
Stop
CGA
CT
ATG
T
Spacer/ Overlap()
1 ATT ATG ATG
TAA TAA TAA
ATC
T
8 12 3 1 1 2
ATT
TAA
16
ATG ATG
TAA CAA
22 2
ATG ATG
TAA TAA
ATG
TAG
3 7 5 16 1 4 4
3 (continued )
2
Y. Dong et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Feature
From
To
trnQ CR2 nad2 trnW trnC trnY Total
14,042 14,110 14,155 15,167 15,225 15,291
14,109 14,154 15,166 15,232 15,290 15,355 15,359
Length (nt) 68 45 1012 66 66 65
Codons Start
Stop
ATT
T
Spacer/ Overlap()
References 8 4 98/24
*Underlines indicate the gene encoded on the opposite strand.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Ulster at Jordanstown on 03/26/15 For personal use only.
This research was supported by Natural Science Foundation of the Higher Education Institutions of Anhui Province (KJ2013Z245), Anhui Provincial Natural Science Foundation (1408085QC67), Foundation of ChuZhou University (2012qd13) and the key Natural Science Foundation of the Anhui Higher Education Institutions of China.
1–8 nt overlap. The major non-coding A + T-rich region of determined swallowtail mitogenome is 514 bp located between 12S rRNA and trnM (Table 1). The protein-coding genes account for 72.8% (11,177 bp) of the whole genome, the rRNA genes for 13.7% (2097 bp), the tRNA genes for 9.4% (1449 bp) and the non-coding DNA for 4.3% (657 bp). The A + T content of the complete mitochondrial DNA is 80.6%, which corresponds well to the percentage found in the mtDNA of other insect mitogenomes (Crozier & Crozier, 1993; Dotson & Beard, 2001). The higher A + T content was observed in control region 1 (92.8%). The starting codons inferred for the 13 protein-coding genes are the conventional starting types ATN, except that the cox1 start codon was identified as CGA (Table 1). This phenomenon has been reported in P. xuthus, P. bianor and P. maackii (Dong et al., 2013a, b; Feng et al., 2010). Nine PCGs terminate with the complete termination codon TAN (atp8, atp6, cox3, nad5, nad4, nad4L, nad6, cob and nad1), and the other four genes (cox1, cox2, nad2 and nad3) end with a single stop nucleotide T or absence. The secondary structure information of the tRNA genes might be responsible for the correct cleavage of the polycistronic transcript (Carapelli et al. 2008; Ojala et al., 1980).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Bridges CA. (1988). Catalogue of Papilionidae and Pieridae (Lepidoptera: Rhopalocera). Urbana, IL: C.A. Bridges. Carapelli A, Comandi S, Convey P, Nardi F, Frati F. (2008). The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola). BMC Genom 9:315. Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133:97–117. Dong Y, Zhu LX, Wu YF, Wu XB. (2013a). The complete mitochondrial genome of the Chinese peacock, Papilio bianor (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:636–8. Dong Y, Zhu LX, Wu YF, Wu XB. (2013b). The complete mitochondrial genome of the Alpine Black Swallowtail, Papilio Maackii (Insecta: Lepidoptera: Papilionidae). Mitochondrial DNA 24:639–41. Dotson EM, Beard CB. (2001). Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Mol Biol 10:205–15. Feng X, Liu DF, Wang NX, Zhu CD, Jiang GF. (2010). The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol Biol Rep 37:3877–88. Liu XS, Zhang YL, Fang JH. (2011). A butterfly hotspot in western China, its environmental threats and conservation. J Insect Conserv 15: 617–32. Maes D, Van Dyck H. (2005). Habitat quality and biodiversity indicator performances of a threatened butterfly versus a multispecies group for wet heath lands in Belgium. Biol Conserv 123:177–87. Ojala D, Merkel C, Gelfand R, Attardi G. (1980). The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 2:393–403. Settele J, Kudrna O, Harpke A, Ku¨hn I, van Swaay C, Verovnik R, Warren M, et al. (2008). Climatic risk Atlas of European Butterflies. BioRisk 1:1–710. Wu CS. (2001). Fauna Sinica Insect Vol. 25 Lepidoptera Papilionidae (in Chinese). Beijing: Science Press. Zhu LX, Wu XB, Wu CS. (2011). Phylogeographic history of the swallowtail Papilio bianor Cramer (Lepidoptera: Papilionidae) from China. Oriental Insects 45:98–102.
