http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908364
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the striped-tailed rat-snake, Orthriophis taeniurus (Reptilia, Serpentes, Colubridae) En Li, Fuxiao Sun, Ruidong Zhang, Jing Chen, and Xiaobing Wu
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 12/11/14 For personal use only.
Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the striped-tailed rat-snake Orthriophis taeniurus was determined in the present study. The genome is 17,183 bp in size, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 control regions (CRI and CRII). The gene order and orientation in O. taeniurus mitogenome are basically identical to that of other alethinophidian snakes. Nucleotide composition is very similar with other vertebrates, showing an AT bias.
Mitogenome, Orthriophis taeniurus, striped-tailed rat-snake
Orthriophis taeniurus (synonym: Elaphe taeniura), belonging to genus Orthriophis of family Colubridae (Utiger et al., 2002), is a large and slender ratsnake, which is widely distributed in Asia. In this study, we determined the complete mitogenome of O. taeniurus (GenBank accession number: KC990021 will be shown after the manuscript is accepted). Organization of the complete mitogenome of O. taeniurus is shown in Figure 1. The total length of the O. taeniurus mtDNA is 17,183 bp. It consists of 13 PCGs, 2 rRNA genes, 22 tRNA genes, and 2 CRs (CRI and CRII), which is similar to that of other reported alethinophidian snakes (He et al., 2010; Jang & Hwang, 2011; Kumazawa et al., 1998). As found in other vertebrates, most of these genes are coded on the heavy strand (H-strand) except for ND6 and eight tRNA genes. The overall base composition of the light strand (L-strand) is 35.05% A, 25.25% T, 12.45% G, and 27.25% C, with an obvious AT bias (60.30%), as generally shown in other vertebrates mitogenomes (Jang & Hwang, 2011;
Correspondence: Dr. Xiao-Bing Wu, Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, P.R. China. Tel/Fax: + 86 553 3836873. E-mail: [email protected]
History Received 4 March 2014 Accepted 22 March 2014 Published online 14 April 2014
Lee et al., 2008; Mulcahy & Macey, 2009). The 22 tRNA genes with the size ranging from 57 to 73 bp are interspersed along the whole genome. Most of tRNAs have less than 5 bp in the T C arm, which is similar to other snakes (Kumazawa et al., 1998; Wang et al., 2009). All 21 tRNA genes can fold into a typical cloverleaf secondary structure except for tRNASer(AGY), which has no dihydrouridine arm (D-arm). A 35 bp pseudo-tRNAPro gene, found in most of the Caenophidia (He et al., 2010), also appears in the mitochondrial genome of O. taeniurus in 50 -upstream region of CRII. The mitogenome of O. taeniurus contains two identical CRs (1017 bp in length, high AT content of 60.57%) surrounded by tRNAPro and tRNAPhe, and by tRNAIle and tRNALeu(UUR), respectively. CRI and CRII have putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) (Clayton, 1991; Saccone et al., 2002; Shadel & Clayton, 1997). In addition, a 20 bp C-rich segment (50 -CCCCCCCCCTACCCCC CCCC-30 ) was found in the 50 regions of CRI and CRII, which has been observed in the order Squamata in general (He et al., 2010; Jang & Hwang, 2011). The sequence length of the 12S and 16S rRNA is 934 and 1489 bp, respectively. They are located between the tRNAPhe and ND1 genes and are separated by the tRNAVal gene, as observed in other snakes. Except for ND2 (ATT start codon), COXI (GTG), and ND6 (ATA), the remaining ten PCGs start with ATG. As for stop codon, seven PCGs end with the complete stop codon TAA (ATP8, ATP6, ND4L, ND4 and ND5), AGA (COXI and ND6), whereas six PCGs (ND1, ND2, COXII, COXIII, ND3 and Cytb) end with incomplete stop codon with T, which may be completed by polyadenylation after transcript processing (Boore, 2001; Ojala et al., 1981). The putative origin of L-strand replication (OL) with length of 35 bp in the WANCY cluster of five tRNA genes has the potential to fold into a stem-loop secondary structure, similar to most vertebrates (Boore, 1999; Su et al., 2007). The present study will facilitate the further research of the population genetics of this species and systematic analyses of colubroids.
2
E. Li et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 12/11/14 For personal use only.
Figure 1. Gene organization of the O. taeniurus mitochondrial genome. tRNA genes are designated by single-letter amino acid codes.
Acknowledgements We thank Dr Hailong Wu for his comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the National Natural Science Foundation of China (No. 31272337) and the Doctoral Fund of Ministry of Education of China (No. 20113424110005).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Boore JL. (2001). Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Mol Biol Evol 18:1413–16. Clayton DA. (1991). Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem Sci 16:107–11. He M, Feng JC, Zhao EM. (2010). The complete mitochondrial genome of the Sichuan hot-spring kell-back (Thermophis zhaoermii; Serpentes: Colubridae) and amitogenomic phylogeny of the snakes. Mitochondrial DNA 21:8–18. Jang KH, Hwang UW. (2011). Complete mitochondrial genome of the black-headed snake Sibynophis collaris (Squamata, Serpentes, Colubridae). Mitochondrial DNA 22:77–9.
Kumazawa Y, Ota H, Nishida M, Ozawa T. (1998). The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313–29. Lee YS, Oh J, Kim YU, Kim N, Yang SJ, Hwang UW. (2008). Mitome: Dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. Nucl Acids Res 36: D938–42. Mulcahy DG, Macey JR. (2009). Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California. Mol Phylogenet Evol 53:537–46. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Saccone C, Gissi C, Reyes A, Larizza A, Sbisa E, Pesole G. (2002). Mitochondrial DNA in metazoa: Degree of freedom in a frozen event. Gene 286:3–12. Shadel GS, Clayton DA. (1997). Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409–35. Su X, Wu XB, Yan P, Cao SY, Hu YL. (2007). Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene 394:25–34. Utiger U, Helfenberger N, Scha¨tti B, Schmidt C, Ruf M, Ziswiler V. (2002). Molecular systematics and phylogeny of Old and New World ratsnakes, Elaphe Auct., and related genera (Reptilia, Squamata, Colubridae). Russ J Herpetol 9:105–24. Wang GL, He SP, Huang S, He M, Zhao EM. (2009). The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata). Chinese Sci Bull 54: 1713–24.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the striped-tailed rat-snake, Orthriophis taeniurus (Reptilia, Serpentes, Colubridae) En Li, Fuxiao Sun, Ruidong Zhang, Jing Chen, and Xiaobing Wu
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 12/11/14 For personal use only.
Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, P.R. China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the striped-tailed rat-snake Orthriophis taeniurus was determined in the present study. The genome is 17,183 bp in size, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 control regions (CRI and CRII). The gene order and orientation in O. taeniurus mitogenome are basically identical to that of other alethinophidian snakes. Nucleotide composition is very similar with other vertebrates, showing an AT bias.
Mitogenome, Orthriophis taeniurus, striped-tailed rat-snake
Orthriophis taeniurus (synonym: Elaphe taeniura), belonging to genus Orthriophis of family Colubridae (Utiger et al., 2002), is a large and slender ratsnake, which is widely distributed in Asia. In this study, we determined the complete mitogenome of O. taeniurus (GenBank accession number: KC990021 will be shown after the manuscript is accepted). Organization of the complete mitogenome of O. taeniurus is shown in Figure 1. The total length of the O. taeniurus mtDNA is 17,183 bp. It consists of 13 PCGs, 2 rRNA genes, 22 tRNA genes, and 2 CRs (CRI and CRII), which is similar to that of other reported alethinophidian snakes (He et al., 2010; Jang & Hwang, 2011; Kumazawa et al., 1998). As found in other vertebrates, most of these genes are coded on the heavy strand (H-strand) except for ND6 and eight tRNA genes. The overall base composition of the light strand (L-strand) is 35.05% A, 25.25% T, 12.45% G, and 27.25% C, with an obvious AT bias (60.30%), as generally shown in other vertebrates mitogenomes (Jang & Hwang, 2011;
Correspondence: Dr. Xiao-Bing Wu, Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, P.R. China. Tel/Fax: + 86 553 3836873. E-mail: [email protected]
History Received 4 March 2014 Accepted 22 March 2014 Published online 14 April 2014
Lee et al., 2008; Mulcahy & Macey, 2009). The 22 tRNA genes with the size ranging from 57 to 73 bp are interspersed along the whole genome. Most of tRNAs have less than 5 bp in the T C arm, which is similar to other snakes (Kumazawa et al., 1998; Wang et al., 2009). All 21 tRNA genes can fold into a typical cloverleaf secondary structure except for tRNASer(AGY), which has no dihydrouridine arm (D-arm). A 35 bp pseudo-tRNAPro gene, found in most of the Caenophidia (He et al., 2010), also appears in the mitochondrial genome of O. taeniurus in 50 -upstream region of CRII. The mitogenome of O. taeniurus contains two identical CRs (1017 bp in length, high AT content of 60.57%) surrounded by tRNAPro and tRNAPhe, and by tRNAIle and tRNALeu(UUR), respectively. CRI and CRII have putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) (Clayton, 1991; Saccone et al., 2002; Shadel & Clayton, 1997). In addition, a 20 bp C-rich segment (50 -CCCCCCCCCTACCCCC CCCC-30 ) was found in the 50 regions of CRI and CRII, which has been observed in the order Squamata in general (He et al., 2010; Jang & Hwang, 2011). The sequence length of the 12S and 16S rRNA is 934 and 1489 bp, respectively. They are located between the tRNAPhe and ND1 genes and are separated by the tRNAVal gene, as observed in other snakes. Except for ND2 (ATT start codon), COXI (GTG), and ND6 (ATA), the remaining ten PCGs start with ATG. As for stop codon, seven PCGs end with the complete stop codon TAA (ATP8, ATP6, ND4L, ND4 and ND5), AGA (COXI and ND6), whereas six PCGs (ND1, ND2, COXII, COXIII, ND3 and Cytb) end with incomplete stop codon with T, which may be completed by polyadenylation after transcript processing (Boore, 2001; Ojala et al., 1981). The putative origin of L-strand replication (OL) with length of 35 bp in the WANCY cluster of five tRNA genes has the potential to fold into a stem-loop secondary structure, similar to most vertebrates (Boore, 1999; Su et al., 2007). The present study will facilitate the further research of the population genetics of this species and systematic analyses of colubroids.
2
E. Li et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 12/11/14 For personal use only.
Figure 1. Gene organization of the O. taeniurus mitochondrial genome. tRNA genes are designated by single-letter amino acid codes.
Acknowledgements We thank Dr Hailong Wu for his comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the National Natural Science Foundation of China (No. 31272337) and the Doctoral Fund of Ministry of Education of China (No. 20113424110005).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Boore JL. (2001). Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Mol Biol Evol 18:1413–16. Clayton DA. (1991). Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem Sci 16:107–11. He M, Feng JC, Zhao EM. (2010). The complete mitochondrial genome of the Sichuan hot-spring kell-back (Thermophis zhaoermii; Serpentes: Colubridae) and amitogenomic phylogeny of the snakes. Mitochondrial DNA 21:8–18. Jang KH, Hwang UW. (2011). Complete mitochondrial genome of the black-headed snake Sibynophis collaris (Squamata, Serpentes, Colubridae). Mitochondrial DNA 22:77–9.
Kumazawa Y, Ota H, Nishida M, Ozawa T. (1998). The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313–29. Lee YS, Oh J, Kim YU, Kim N, Yang SJ, Hwang UW. (2008). Mitome: Dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. Nucl Acids Res 36: D938–42. Mulcahy DG, Macey JR. (2009). Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California. Mol Phylogenet Evol 53:537–46. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Saccone C, Gissi C, Reyes A, Larizza A, Sbisa E, Pesole G. (2002). Mitochondrial DNA in metazoa: Degree of freedom in a frozen event. Gene 286:3–12. Shadel GS, Clayton DA. (1997). Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409–35. Su X, Wu XB, Yan P, Cao SY, Hu YL. (2007). Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene 394:25–34. Utiger U, Helfenberger N, Scha¨tti B, Schmidt C, Ruf M, Ziswiler V. (2002). Molecular systematics and phylogeny of Old and New World ratsnakes, Elaphe Auct., and related genera (Reptilia, Squamata, Colubridae). Russ J Herpetol 9:105–24. Wang GL, He SP, Huang S, He M, Zhao EM. (2009). The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata). Chinese Sci Bull 54: 1713–24.
