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 Colias erate (Lepidoptera: pieridae) Yunhe Wu, Jie Fang, Wenbo Li, Demin Han, Hui Wang & Baowei Zhang To cite this article: Yunhe Wu, Jie Fang, Wenbo Li, Demin Han, Hui Wang & Baowei Zhang (2015): The complete mitochondrial genome of Colias erate (Lepidoptera: pieridae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1022743
Published online: 26 May 2015.
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Date: 05 November 2015, At: 13:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1022743
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Colias erate (Lepidoptera: pieridae) Yunhe Wu*, Jie Fang*, Wenbo Li, Demin Han, Hui Wang, and Baowei Zhang
Downloaded by [University of California, San Diego] at 13:45 05 November 2015
School of Life Sciences, Anhui University, Hefei, Anhui, China
Abstract
Keywords
The complete mitochondrial genome of Colias erate was investigated and analyzed. The mitochondrial genome is a circular molecule of 15,184 bp, containing 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and an A + T-rich region. The nucleotide composition of the C. erate mitogenome is strongly biased toward A + T nucleotides (81.34%). Nine proteincoding genes and 14 tRNA genes are encoded on the H strand, and the other four proteincoding genes and eight tRNA genes are encoded on the L strand. The arrangement of genes is identical to all know the Pieridae species. Finally, the phylogenetic relationships of 12 Pieridae species were reconstructed based on the nucleotide sequences of 13 mitochondrial PCGs using the Bayesian inference method. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pieridae.
Colias erate, Lepidoptera, mitochondrial genome, phylogenetic analysis, Pieridae
The pale clouded yellow Colias erate is a small to middle size butterfly. They are widely distributed in Far East Russia, Sakhalin, the Korean Peninsula, China, and Japan (Narita et al., 2009). The specimen was collected in Yaoluoping nature reserve, Anhui Province, China in April 2014 with the voucher number YLP-1. The entire mitogenome was amplified using 10 primers in this study, four of them were used for long PCRs. Takara Taq and Takara LA Taq (Takara Biomedical, Otsu, Japan) were used for polymerase chain reaction (PCR) amplification. PCR products were sequenced directly with amplified primers and internal walking primers in both directions. Phylogenetic relationships of 12 Pieridae representative species were analyzed using the Bayesian inference (BI) method based on the concatenated nucleotide sequences of the 13 protein-coding genes (PCGs) of the mitochondrial genome, using the moth species Manduca sexta as the outgroup. The Bayesian analysis was performed using the MrBayes version 3.1.2 software (Software Foundation, Inc., Cambridge, MA) (Huelsenbeck & Ronquist, 2001). In this process, the best-fitting nucleotide substitution model (GTR + I + T) was selected via Modeltest version 3.06 (Software Foundation, Inc., Cambridge, MA) (Posa & Krandall, 1998); the Markov Chain Monte Carlo (MCMC) was run with four chains (one cold chain and three hot chains) for 5,000,000 generations until the average standard deviation of split frequencies reached a value less than 0.01, with Bayesian posterior probabilities calculated from the sample points after the MCMC algorithm had started to converge.
*These authors are the co-first authors of the article. Correspondence: Hui Wang, School of Life Sciences, Anhui University, Hefei 230601, Anhui, PR China. E-mail: [email protected]
History Received 30 January 2015 Revised 16 February 2015 Accepted 21 February 2015 Published online 26 May 2015
The mitogenome of C. erate is 15,184 bp in length and encode 37 genes totally containing 13 PCGs and 22 tRNA genes, 2 rRNA genes, and non-coding A + T-rich region. Among these, 15 genes were encoded on the L strand, including four PCGs (ND1, ND4, ND4L, and ND5), two rRNA genes, eight tRNA genes (tRNAGlu, tRNACys, tRNATyr, tRNAPhe, tRNAHis, tRNAPro, tRNAleu(CUN), and tRNAVal) and A + T-rich region. The remaining 23 genes are encoded on the H strand. The nucleotide composition of the C. erate mitogenome is biased toward A/T (81.34%), a common characteristic observed in insect mitochondrial genomes (Crozier & Crozier, 1993). For C. erate, genes are arranged in the same order and orientation as the complete sequenced mitochondrial genomes of the known Pieridae species. The nucleotide sequences of C. erate mitochondrial genome were deposited in GenBank (Accession number:KP715146). The phylogenetic tree was divided into two major clades (Figure 1). The first lineage, subfamily Pierinae, includes species of tribes Pierini (Pieris rapae, Pieris canidia, Pieris melete, Eurema hecabe, Aporia intercostat, Aporia crataegi and Delias hyparete), Anthocharini (Anthocharis bambusarum and Hebomoia glaucippe). The second lineage, subfamily Coliadinae, includes Gonepteryx rhamni, Colias erate, and Catopsilia Pomona. The conclusion that Pierini is a sister group to Anthocharini is consistent with those reported earlier (Braby et al., 2006, Ehrlich, 1958). These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pieridae. We wish the present study to provide a useful database for analyzing the phylogenetic relationship within C. erate. In addition, it is useful to construct molecular identification of this species.
Downloaded by [University of California, San Diego] at 13:45 05 November 2015
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Y. Wu et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Inferred phylogenetic relationships among Lepidoptera based on the nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference (BI). Numbers at each node indicate percentages of Bayesian posterior probabilities (BPPs). GenBank accession numbers for the published sequences are NC_015895.1 (Pieris rapae), KP162184.1 (Pieris canidia), NC_010568.1 (Pieris melete), NC_022685.1 (Eurema hecabe), NC_025273.1 (Aporia intercostata), NC_018346.1 (Aporia crataegi), NC_020428.1 (Delias hyparete), NC_025274.1 (Anthocharis bambusarum), NC_021123.1 (Hebomoia glaucippe), NC_026046.1 (Gonepteryx rhamni), KP715146 (Colias erate), NC_022687.1 (Catopsilia Pomona), and NC_010266.1 (Manduca sexta).
Acknowledgements We sincerely thank Tao Pan, Ling Ding, Tao Song, Wenliang Zhou, Zhonglou Sun, Mei Ding, Lifu Qian, Yanan Zhang, Xiaonan Sun, and Xing Hang for their help in this study.
Declaration of interest This project was supported by the Foundation for Young and Key Teachers Project (No. 02303301). The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Braby MF, Vila R, Pierce NE. (2006). Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): Higher classification and biogeography. Zool J Linn Soc 147:238–75.
Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 1:13–18. Ehrlich PR. (1958). The comparative morphology, phylogeny and higher classification of the butterflies (Lepidoptera: Papilionoidea). Univ Kansas Sci Bull 39:305–70. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic tree. Bioinformatics 17:754–5. Narita S, Shimajiri Y, Nomura M. (2009). Strong cytoplasmic incompatibility and high vertical transmission rate can explain the high frequencies of Wolbachia infection in Japanese populations of Colias erate poliographus (Lepidoptera: Pieridae). Bull Entomol Res 99: 385–91. Posa D, Krandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Colias erate (Lepidoptera: pieridae) Yunhe Wu, Jie Fang, Wenbo Li, Demin Han, Hui Wang & Baowei Zhang To cite this article: Yunhe Wu, Jie Fang, Wenbo Li, Demin Han, Hui Wang & Baowei Zhang (2015): The complete mitochondrial genome of Colias erate (Lepidoptera: pieridae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1022743
Published online: 26 May 2015.
Submit your article to this journal
Article views: 20
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 California, San Diego]
Date: 05 November 2015, At: 13:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1022743
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Colias erate (Lepidoptera: pieridae) Yunhe Wu*, Jie Fang*, Wenbo Li, Demin Han, Hui Wang, and Baowei Zhang
Downloaded by [University of California, San Diego] at 13:45 05 November 2015
School of Life Sciences, Anhui University, Hefei, Anhui, China
Abstract
Keywords
The complete mitochondrial genome of Colias erate was investigated and analyzed. The mitochondrial genome is a circular molecule of 15,184 bp, containing 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and an A + T-rich region. The nucleotide composition of the C. erate mitogenome is strongly biased toward A + T nucleotides (81.34%). Nine proteincoding genes and 14 tRNA genes are encoded on the H strand, and the other four proteincoding genes and eight tRNA genes are encoded on the L strand. The arrangement of genes is identical to all know the Pieridae species. Finally, the phylogenetic relationships of 12 Pieridae species were reconstructed based on the nucleotide sequences of 13 mitochondrial PCGs using the Bayesian inference method. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pieridae.
Colias erate, Lepidoptera, mitochondrial genome, phylogenetic analysis, Pieridae
The pale clouded yellow Colias erate is a small to middle size butterfly. They are widely distributed in Far East Russia, Sakhalin, the Korean Peninsula, China, and Japan (Narita et al., 2009). The specimen was collected in Yaoluoping nature reserve, Anhui Province, China in April 2014 with the voucher number YLP-1. The entire mitogenome was amplified using 10 primers in this study, four of them were used for long PCRs. Takara Taq and Takara LA Taq (Takara Biomedical, Otsu, Japan) were used for polymerase chain reaction (PCR) amplification. PCR products were sequenced directly with amplified primers and internal walking primers in both directions. Phylogenetic relationships of 12 Pieridae representative species were analyzed using the Bayesian inference (BI) method based on the concatenated nucleotide sequences of the 13 protein-coding genes (PCGs) of the mitochondrial genome, using the moth species Manduca sexta as the outgroup. The Bayesian analysis was performed using the MrBayes version 3.1.2 software (Software Foundation, Inc., Cambridge, MA) (Huelsenbeck & Ronquist, 2001). In this process, the best-fitting nucleotide substitution model (GTR + I + T) was selected via Modeltest version 3.06 (Software Foundation, Inc., Cambridge, MA) (Posa & Krandall, 1998); the Markov Chain Monte Carlo (MCMC) was run with four chains (one cold chain and three hot chains) for 5,000,000 generations until the average standard deviation of split frequencies reached a value less than 0.01, with Bayesian posterior probabilities calculated from the sample points after the MCMC algorithm had started to converge.
*These authors are the co-first authors of the article. Correspondence: Hui Wang, School of Life Sciences, Anhui University, Hefei 230601, Anhui, PR China. E-mail: [email protected]
History Received 30 January 2015 Revised 16 February 2015 Accepted 21 February 2015 Published online 26 May 2015
The mitogenome of C. erate is 15,184 bp in length and encode 37 genes totally containing 13 PCGs and 22 tRNA genes, 2 rRNA genes, and non-coding A + T-rich region. Among these, 15 genes were encoded on the L strand, including four PCGs (ND1, ND4, ND4L, and ND5), two rRNA genes, eight tRNA genes (tRNAGlu, tRNACys, tRNATyr, tRNAPhe, tRNAHis, tRNAPro, tRNAleu(CUN), and tRNAVal) and A + T-rich region. The remaining 23 genes are encoded on the H strand. The nucleotide composition of the C. erate mitogenome is biased toward A/T (81.34%), a common characteristic observed in insect mitochondrial genomes (Crozier & Crozier, 1993). For C. erate, genes are arranged in the same order and orientation as the complete sequenced mitochondrial genomes of the known Pieridae species. The nucleotide sequences of C. erate mitochondrial genome were deposited in GenBank (Accession number:KP715146). The phylogenetic tree was divided into two major clades (Figure 1). The first lineage, subfamily Pierinae, includes species of tribes Pierini (Pieris rapae, Pieris canidia, Pieris melete, Eurema hecabe, Aporia intercostat, Aporia crataegi and Delias hyparete), Anthocharini (Anthocharis bambusarum and Hebomoia glaucippe). The second lineage, subfamily Coliadinae, includes Gonepteryx rhamni, Colias erate, and Catopsilia Pomona. The conclusion that Pierini is a sister group to Anthocharini is consistent with those reported earlier (Braby et al., 2006, Ehrlich, 1958). These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pieridae. We wish the present study to provide a useful database for analyzing the phylogenetic relationship within C. erate. In addition, it is useful to construct molecular identification of this species.
Downloaded by [University of California, San Diego] at 13:45 05 November 2015
2
Y. Wu et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Inferred phylogenetic relationships among Lepidoptera based on the nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference (BI). Numbers at each node indicate percentages of Bayesian posterior probabilities (BPPs). GenBank accession numbers for the published sequences are NC_015895.1 (Pieris rapae), KP162184.1 (Pieris canidia), NC_010568.1 (Pieris melete), NC_022685.1 (Eurema hecabe), NC_025273.1 (Aporia intercostata), NC_018346.1 (Aporia crataegi), NC_020428.1 (Delias hyparete), NC_025274.1 (Anthocharis bambusarum), NC_021123.1 (Hebomoia glaucippe), NC_026046.1 (Gonepteryx rhamni), KP715146 (Colias erate), NC_022687.1 (Catopsilia Pomona), and NC_010266.1 (Manduca sexta).
Acknowledgements We sincerely thank Tao Pan, Ling Ding, Tao Song, Wenliang Zhou, Zhonglou Sun, Mei Ding, Lifu Qian, Yanan Zhang, Xiaonan Sun, and Xing Hang for their help in this study.
Declaration of interest This project was supported by the Foundation for Young and Key Teachers Project (No. 02303301). The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Braby MF, Vila R, Pierce NE. (2006). Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): Higher classification and biogeography. Zool J Linn Soc 147:238–75.
Crozier RH, Crozier YC. (1993). The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics 1:13–18. Ehrlich PR. (1958). The comparative morphology, phylogeny and higher classification of the butterflies (Lepidoptera: Papilionoidea). Univ Kansas Sci Bull 39:305–70. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic tree. Bioinformatics 17:754–5. Narita S, Shimajiri Y, Nomura M. (2009). Strong cytoplasmic incompatibility and high vertical transmission rate can explain the high frequencies of Wolbachia infection in Japanese populations of Colias erate poliographus (Lepidoptera: Pieridae). Bull Entomol Res 99: 385–91. Posa D, Krandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18.
