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
Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae) Lingming Kong, Yanlu Wang, Haiyan Cong, Wenquan Wang & Yuchun Li To cite this article: Lingming Kong, Yanlu Wang, Haiyan Cong, Wenquan Wang & Yuchun Li (2015) Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae), Mitochondrial DNA, 26:6, 871-872, DOI: 10.3109/19401736.2013.861436 To link to this article: http://dx.doi.org/10.3109/19401736.2013.861436
Published online: 10 Jan 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Otago]
Date: 28 September 2015, At: 20:20
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 871–872 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.861436
MITOGENOME ANNOUNCEMENT
Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae) Lingming Kong1, Yanlu Wang1, Haiyan Cong1, Wenquan Wang2, and Yuchun Li1 Marine College, Shandong University, Weihai 264209, China and 2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Downloaded by [University of Otago] at 20:20 28 September 2015
1
Abstract
Keywords
The complete mitochondrial genome of Petaurista hainana from Hainan Island of China is 16,502 bp in length. Similar to most other mammals, it contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 2 non-coding regions. The overall base composition of the H-strand is 31.77% A, 26.31% C, 13.31% G and 28.61% T. The base composition clearly showed the A-T skew. The mitochondrial genome of P. hainana presented in this report will be useful for species designation, conservation and phylogenetic study in Sciuridae.
Complete mitochondrial genome, Hainan giant flying squirrel, Petaurista hainana, Sciuridae
Hainan giant flying squirrel (Petaurista hainana) is endemic to Hainan Island of China. It had been regarded as a subspecies of the Indian giant flying squirrel (Petaurista philippensis) (Corbett & Hill, 1992; Ellerman & Morrison-Scott, 1951). Recently, Yu et al. (2006) regarded it as a distinct species based on molecular data and morphological traits. As a subspecies of P. philippensis, P. hainana was enlisted as a Least Concern species on the list of International Union for the Conservation of Nature (IUCN) (ver 3.1 2008) (Harris & Duckworth, 2008). Actually, as an endemic species of Hainan Island, P. hainana has declined severely during the past few years as a result of poaching and loss of habitat. By now, only a limited number of DNA sequences of P. hainana are available in GenBank. In this report, the complete mitochondrial genome (JX572159, 16,502 bp) of P. hainana was sequenced and characterized in detail. Our study provided a new independent genetic source of P. hainana for species designation, conservation and phylogenetic study in Sciuridae. The complete mitochondrial genome of P. hainana is 16,502 bp. All the 37 genes commonly found in vertebrate mitochondrial genomes are determined: 2 for rRNA, 22 for tRNA and 13 for protein-coding gene. These genes are arranged in the same order as the putative ancestral vertebrate mitochondrial genomes (Boore, 1999). Most of these genes are encoded on the H (heavy) strand, with exceptions of ND6 and eight tRNA genes (Table 1). The overall base composition of the H-strand is 31.77% A, 26.31% C, 13.31% G and 28.61% T. Most protein-coding genes begin with an ATG start codon, while ND3 and ND5 start with ATA, ND2 starts with ATC. Five genes end with an incomplete
Correspondence: Yuchun Li, Marine College, Shandong University, Weihai 264209, China. E-mail: [email protected]
History Received 17 October 2013 Accepted 24 October 2013 Published online 10 January 2014
Table 1. Characteristics of the mt genome of P. hainana. Position Gene/Region
From
To
tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr CO1 tRNA-Ser(UCN) tRNA-Asp CO2 tRNA-Lys ATP8 ATP6 CO3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro Control region
1 67 1035 1112 2677 2756 3713 3779 3852 3921 4963 5032 5108 5181 5211 5278 5353 6897 6970 7039 7726 7796 7957 8637 9420 9492 9839 9906 10,196 11,574 11,643 11,702 11,772 13,572 14,097 14,170 15,310 15,384 15,452
66 1034 1111 2676 2753 3712 3781 3849 3820 4963 5028 5100 5180 5214 5278 5345 6894 6966 7038 7722 7794 7999 8637 9421 9492 9838 9905 10,202 11,573 11,642 11,701 11,771 13,589 14,097 14,167 15,309 15,379 15,451 16,502
Codon Start
ATG
ATC
Stop
TAA
TA-
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA-
ATA
TA-
ATG ATG
TAA T- -
ATA ATG
TAA T- -
ATG
AGA
Size (bp) 66 968 77 1565 77 957 69 71 69 1043 66 49 73 34 68 68 1542 70 69 684 69 204 681 785 73 410 67 347 1378 69 59 70 1818 526 71 1140 70 71 1051
Intergenic nucleotides
2 3 2 1 3 7 4 1 7 2 3 3 1 43 1 2 1 7
18 1 2 4
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
Downloaded by [University of Otago] at 20:20 28 September 2015
872
L. Kong et al.
stop codon TA- (ND2, CO3 and ND3) or T- (ND4 and ND6), Cytb ends on AGA, whereas the other seven genes end on the usual TAA stop codon. Presumably, these incomplete stop codons are completed by post-transcriptional polyadenylation (Ojala et al., 1981). The mitochondrial genome contains two rRNA genes, 12S and 16S, which are separated by the gene tRNA-Val. A total of 22 tRNA genes, which encode small RNA molecules of 59–77 nucleotides, are found in the mitochondrial genome of P. hainana. All the tRNAs encoded by this genome show a canonical cloverleaf structure, as in the case of most other mammals, with the exception of tRNA-Ser(AGY), which dose not contain the ‘‘DHU’’ arm and could not form a stable stem-loop structure. In general, the lack of DHU arm in tRNA-Ser(AGY) is common in metazoan mitochondrial genome (Hoffman et al., 1992). The mitochondrial genome contains a control region that is flanked by the genes for tRNA-Pro and tRNA-Phe. The L (light) strand origin of replication (OL) is located between tRNA-Asn and tRNA-Cys gene in a cluster of five tRNA genes (WANCY region). It is represented by a 34 bp non-coding sequence, which can fold into a secondary structure that consists of a perfect 22 bp stem and a 12 bp loop.
Acknowledgements We thank the anonymous reviewers for providing valuable comments on the manuscript.
Mitochondrial DNA, 2015; 26(6): 871–872
Declaration of interest The authors report no confilicts of interest. The authors alone are responsible for the content and writing of the paper. This research was funded by Major International (Regional) Joint Research Project of NSFC (Grant No. 31110103910).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Corbett GB, Hill JE. (1992). The mammals of the Indomalayan region: a systematic review. Oxford: Natural History Museum Publications, Oxford University Press. Ellerman JR, Morrison-Scott TCS. (1951). Checklist of Palaearctic and Indian mammals, 1758–1940. London: British Museum (Natural History). Harris RB, Duckworth JW. (2008). Petaurista philippensis. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. Gland: IUCN. Available at: www.iucnredlist.org Hoffman RJ, Boore JL, Brown WM. (1992). A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131: 397–412. Ojala DM, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Yu FR, Yu FH, Pang JF, Kilpatrick CW, McGuire PM, Wang YX, Lu SQ, Woods CA. (2006). Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia: Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis. Mol Phylogenet Evol 38:755–66.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae) Lingming Kong, Yanlu Wang, Haiyan Cong, Wenquan Wang & Yuchun Li To cite this article: Lingming Kong, Yanlu Wang, Haiyan Cong, Wenquan Wang & Yuchun Li (2015) Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae), Mitochondrial DNA, 26:6, 871-872, DOI: 10.3109/19401736.2013.861436 To link to this article: http://dx.doi.org/10.3109/19401736.2013.861436
Published online: 10 Jan 2014.
Submit your article to this journal
Article views: 20
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Otago]
Date: 28 September 2015, At: 20:20
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 871–872 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.861436
MITOGENOME ANNOUNCEMENT
Characterization of the complete mitochondrial genome of the Hainan giant flying squirrel Petaurista hainana (Rodentia: Sciuridae) Lingming Kong1, Yanlu Wang1, Haiyan Cong1, Wenquan Wang2, and Yuchun Li1 Marine College, Shandong University, Weihai 264209, China and 2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Downloaded by [University of Otago] at 20:20 28 September 2015
1
Abstract
Keywords
The complete mitochondrial genome of Petaurista hainana from Hainan Island of China is 16,502 bp in length. Similar to most other mammals, it contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 2 non-coding regions. The overall base composition of the H-strand is 31.77% A, 26.31% C, 13.31% G and 28.61% T. The base composition clearly showed the A-T skew. The mitochondrial genome of P. hainana presented in this report will be useful for species designation, conservation and phylogenetic study in Sciuridae.
Complete mitochondrial genome, Hainan giant flying squirrel, Petaurista hainana, Sciuridae
Hainan giant flying squirrel (Petaurista hainana) is endemic to Hainan Island of China. It had been regarded as a subspecies of the Indian giant flying squirrel (Petaurista philippensis) (Corbett & Hill, 1992; Ellerman & Morrison-Scott, 1951). Recently, Yu et al. (2006) regarded it as a distinct species based on molecular data and morphological traits. As a subspecies of P. philippensis, P. hainana was enlisted as a Least Concern species on the list of International Union for the Conservation of Nature (IUCN) (ver 3.1 2008) (Harris & Duckworth, 2008). Actually, as an endemic species of Hainan Island, P. hainana has declined severely during the past few years as a result of poaching and loss of habitat. By now, only a limited number of DNA sequences of P. hainana are available in GenBank. In this report, the complete mitochondrial genome (JX572159, 16,502 bp) of P. hainana was sequenced and characterized in detail. Our study provided a new independent genetic source of P. hainana for species designation, conservation and phylogenetic study in Sciuridae. The complete mitochondrial genome of P. hainana is 16,502 bp. All the 37 genes commonly found in vertebrate mitochondrial genomes are determined: 2 for rRNA, 22 for tRNA and 13 for protein-coding gene. These genes are arranged in the same order as the putative ancestral vertebrate mitochondrial genomes (Boore, 1999). Most of these genes are encoded on the H (heavy) strand, with exceptions of ND6 and eight tRNA genes (Table 1). The overall base composition of the H-strand is 31.77% A, 26.31% C, 13.31% G and 28.61% T. Most protein-coding genes begin with an ATG start codon, while ND3 and ND5 start with ATA, ND2 starts with ATC. Five genes end with an incomplete
Correspondence: Yuchun Li, Marine College, Shandong University, Weihai 264209, China. E-mail: [email protected]
History Received 17 October 2013 Accepted 24 October 2013 Published online 10 January 2014
Table 1. Characteristics of the mt genome of P. hainana. Position Gene/Region
From
To
tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr CO1 tRNA-Ser(UCN) tRNA-Asp CO2 tRNA-Lys ATP8 ATP6 CO3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro Control region
1 67 1035 1112 2677 2756 3713 3779 3852 3921 4963 5032 5108 5181 5211 5278 5353 6897 6970 7039 7726 7796 7957 8637 9420 9492 9839 9906 10,196 11,574 11,643 11,702 11,772 13,572 14,097 14,170 15,310 15,384 15,452
66 1034 1111 2676 2753 3712 3781 3849 3820 4963 5028 5100 5180 5214 5278 5345 6894 6966 7038 7722 7794 7999 8637 9421 9492 9838 9905 10,202 11,573 11,642 11,701 11,771 13,589 14,097 14,167 15,309 15,379 15,451 16,502
Codon Start
ATG
ATC
Stop
TAA
TA-
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA-
ATA
TA-
ATG ATG
TAA T- -
ATA ATG
TAA T- -
ATG
AGA
Size (bp) 66 968 77 1565 77 957 69 71 69 1043 66 49 73 34 68 68 1542 70 69 684 69 204 681 785 73 410 67 347 1378 69 59 70 1818 526 71 1140 70 71 1051
Intergenic nucleotides
2 3 2 1 3 7 4 1 7 2 3 3 1 43 1 2 1 7
18 1 2 4
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
Downloaded by [University of Otago] at 20:20 28 September 2015
872
L. Kong et al.
stop codon TA- (ND2, CO3 and ND3) or T- (ND4 and ND6), Cytb ends on AGA, whereas the other seven genes end on the usual TAA stop codon. Presumably, these incomplete stop codons are completed by post-transcriptional polyadenylation (Ojala et al., 1981). The mitochondrial genome contains two rRNA genes, 12S and 16S, which are separated by the gene tRNA-Val. A total of 22 tRNA genes, which encode small RNA molecules of 59–77 nucleotides, are found in the mitochondrial genome of P. hainana. All the tRNAs encoded by this genome show a canonical cloverleaf structure, as in the case of most other mammals, with the exception of tRNA-Ser(AGY), which dose not contain the ‘‘DHU’’ arm and could not form a stable stem-loop structure. In general, the lack of DHU arm in tRNA-Ser(AGY) is common in metazoan mitochondrial genome (Hoffman et al., 1992). The mitochondrial genome contains a control region that is flanked by the genes for tRNA-Pro and tRNA-Phe. The L (light) strand origin of replication (OL) is located between tRNA-Asn and tRNA-Cys gene in a cluster of five tRNA genes (WANCY region). It is represented by a 34 bp non-coding sequence, which can fold into a secondary structure that consists of a perfect 22 bp stem and a 12 bp loop.
Acknowledgements We thank the anonymous reviewers for providing valuable comments on the manuscript.
Mitochondrial DNA, 2015; 26(6): 871–872
Declaration of interest The authors report no confilicts of interest. The authors alone are responsible for the content and writing of the paper. This research was funded by Major International (Regional) Joint Research Project of NSFC (Grant No. 31110103910).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Corbett GB, Hill JE. (1992). The mammals of the Indomalayan region: a systematic review. Oxford: Natural History Museum Publications, Oxford University Press. Ellerman JR, Morrison-Scott TCS. (1951). Checklist of Palaearctic and Indian mammals, 1758–1940. London: British Museum (Natural History). Harris RB, Duckworth JW. (2008). Petaurista philippensis. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. Gland: IUCN. Available at: www.iucnredlist.org Hoffman RJ, Boore JL, Brown WM. (1992). A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131: 397–412. Ojala DM, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Yu FR, Yu FH, Pang JF, Kilpatrick CW, McGuire PM, Wang YX, Lu SQ, Woods CA. (2006). Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia: Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis. Mol Phylogenet Evol 38:755–66.
