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
Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae) Lingming Kong, Wenquan Wang, Haiyan Cong, Zexin Liu & Yuchun Li To cite this article: Lingming Kong, Wenquan Wang, Haiyan Cong, Zexin Liu & Yuchun Li (2015) Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae), Mitochondrial DNA, 26:5, 759-760, DOI: 10.3109/19401736.2013.855738 To link to this article: http://dx.doi.org/10.3109/19401736.2013.855738
Published online: 07 Jan 2014.
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Date: 28 September 2015, At: 20:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 759–760 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855738
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae) Lingming Kong1, Wenquan Wang2, Haiyan Cong1, Zexin Liu1 and Yuchun Li1 Marine College, Shandong University, Weihai, China and 2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Downloaded by [University of Otago] at 20:10 28 September 2015
1
Abstract
Keywords
The complete mitochondrial genome of black giant squirrel (Ratufa bicolor) from Hainan Island was sequenced and characterized in detail. The 16,563 bp genome was composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding regions. The mitochondrial genome of R. bicolor presented in this report will be useful for species identification, conversation and clarifying the controversial taxonomic status of genus Ratufa.
Black giant squirrel, complete mitochondrial genome, Ratufa bicolor, Sciuridae
Black giant squirrel (Ratufa bicolor) is a large tree squirrel which is an inhabitant of northern South Asia, southern China, much of mainland and western insular Southeast Asia. In China, this species was reported in southern Yunnan, southern Guangxi, eastern Tibet and Hainan Island (Smith et al., 2008). This species is especially vulnerable to hunting pressure and habitat disruption (Abramov & Kruskop, 2012). It was enlisted as a near threatened (NT) species on the list of International Union for the Conservation of Nature (IUCN; ver 3.1 2008; Harris & Duckworth, 2008). As the phylogenetic reconstruction of genus Ratufa using multiple independent loci yielded discordance in previous studies, the taxonomic status of genus Ratufa is still controversial (Mercer & Roth, 2003; Steppan et al., 2004). By now, none of other mitochondrial protein-coding genes of genus Ratufa has been published in GenBank. In this study, the complete mitochondrial genome (GenBank KF575124; 16,563 bp) of the black giant squirrel collected from Hainan Island was sequenced and characterized in detail (Table 1). Eleven primer pairs specific to R. bicolor were used for PCR. The characteristics of R. bicolor mitochondrial genome are identical to typical vertebrates. The genome is 16,563 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding control regions. With the exceptions of ND6 and 8 tRNA genes, all the other genes are on the H (heavy) strand. The overall composition of the H strand is 31.71% A, 28.61% T, 13.17% G and 26.51% C. Except for ND2, ND5 (ATT start codon) and ND3 (ATA start codon), all the protein-coding genes are initiated with ATG. Six protein-coding genes use TAA and three genes use TAG as stop codons. ND6 ends with AGA and
Correspondence: Yuchun Li, Marine College, Shandong University, Weihai 264209, China. Email: [email protected]
History Received 9 September 2013 Revised 15 September 2013 Accepted 21 September 2013 Published online 7 January 2014
Table 1. Characteristics of the mt genome of R. bicolor. 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 70 1041 1112 2694 2772 3727 3793 3867 3936 4978 5051 5123 5196 5227 5296 5370 6912 6985 7054 7741 7811 7972 8652 9436 9505 9852 9922 10,212 11,590 11,658 11,719 11,789 13,590 14,115 14,188 15,328 15,402 15,471
69 1040 1111 2693 2768 3728 3795 3864 3935 4979 5046 5119 5195 5226 5294 5361 6911 6981 7053 7737 7809 8014 8652 9434 9504 9851 9919 10,218 11,589 11,658 11,720 11,788 13,606 14,114 14,183 15,327 15,397 15,470 16,563
Codon Start
Stop
ATG
TAG
ATT
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA-
ATA
TA-
ATG ATG
TAA T- -
ATT ATG
TAA AGA
ATG
TAG
Size (bp) 69 971 71 1582 75 957 69 72 69 1044 69 69 73 31 68 66 1542 70 69 684 69 204 785 815 69 345 68 294 1378 69 63 70 1818 525 69 1140 70 69 1093
Intergenic nucleotides
3 2 3 2 2 4 3 1 8 3 3 1 43 1 1 2 7 1 2 17 4 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 20:10 28 September 2015
760
L. Kong et al.
three genes end with an incomplete stop codon TA- (CO3 and ND3) and T- - (ND4), suggesting that these might be modified by the polyadenylation after transcript processing (Ojala et al., 1981). The length of 22 tRNA genes ranges from 68 to 75 bp, with an exception of tRNA-Ser (AGY), all the tRNA genes can be folded into typical cloverleaf secondary structures. The genome of R. bicolor has two non-coding regions, an L (light) strand replication origin (OL) and a control region (CR). The OL is located between tRNA-Asn and tRNA-Cys in a cluster of five tRNA genes (WANCY region). It is represented by a 31 bp noncoding sequence, which can fold into a secondary structure consisting of a perfect 16 bp stem and a 12 bp loop. The control region (CR) is flanked by tRNA-Pro and tRNA-Phe genes. Although the concatenated mitochondrial gene sequence may be more potent in phylogenetic inferences of deeper branches (Miya et al., 2003), there are only three complete mitochondrial genomes of the family Sciuridae available in GenBank. Our results provide the first available complete mitochondrial genome in the database for R. bicolor, and the information will be useful for species identification, phylogenetic research in Sciuridae and solving conservation problems of this endangered species.
Acknowledgements The authors thank the anonymous reviewers for providing valuable comments on the manuscript.
Mitochondrial DNA, 2015; 26(5): 759–760
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This research was funded by the Major International (Regional) Joint Research Project of NSFC (Grant No. 31110103910).
References Abramov AV, Kruskop SV. (2012). The mammal fauna of Cat Ba Island, northern Vietnam. Russian J Theriol 11:57–72. Harris RB, Duckworth JW. (2008). Ratufa bicolor. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. [Online] Available online at: www.iucnredlist.org. Gland: IUCN. Mercer JM, Roth VL. (2003). The effects of Cenozoic global change on squirrel phylogeny. Science 299:1568–72. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, et al. (2003). Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–38. Ojala DM, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Smith AT, Xie Y, Hoffmann RS, Lunde D, MacKinnon J, Wilson DE, Wozencraft WC. (2008). A guide to the mammals of China. Princeton, NJ: Princeton University Press. p 173. Steppan SJ, Storz BL, Hoffmann RS. (2004). Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Mol Phylogenet Evol 30:703–19.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae) Lingming Kong, Wenquan Wang, Haiyan Cong, Zexin Liu & Yuchun Li To cite this article: Lingming Kong, Wenquan Wang, Haiyan Cong, Zexin Liu & Yuchun Li (2015) Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae), Mitochondrial DNA, 26:5, 759-760, DOI: 10.3109/19401736.2013.855738 To link to this article: http://dx.doi.org/10.3109/19401736.2013.855738
Published online: 07 Jan 2014.
Submit your article to this journal
Article views: 25
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: 20:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 759–760 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855738
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae) Lingming Kong1, Wenquan Wang2, Haiyan Cong1, Zexin Liu1 and Yuchun Li1 Marine College, Shandong University, Weihai, China and 2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Downloaded by [University of Otago] at 20:10 28 September 2015
1
Abstract
Keywords
The complete mitochondrial genome of black giant squirrel (Ratufa bicolor) from Hainan Island was sequenced and characterized in detail. The 16,563 bp genome was composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding regions. The mitochondrial genome of R. bicolor presented in this report will be useful for species identification, conversation and clarifying the controversial taxonomic status of genus Ratufa.
Black giant squirrel, complete mitochondrial genome, Ratufa bicolor, Sciuridae
Black giant squirrel (Ratufa bicolor) is a large tree squirrel which is an inhabitant of northern South Asia, southern China, much of mainland and western insular Southeast Asia. In China, this species was reported in southern Yunnan, southern Guangxi, eastern Tibet and Hainan Island (Smith et al., 2008). This species is especially vulnerable to hunting pressure and habitat disruption (Abramov & Kruskop, 2012). It was enlisted as a near threatened (NT) species on the list of International Union for the Conservation of Nature (IUCN; ver 3.1 2008; Harris & Duckworth, 2008). As the phylogenetic reconstruction of genus Ratufa using multiple independent loci yielded discordance in previous studies, the taxonomic status of genus Ratufa is still controversial (Mercer & Roth, 2003; Steppan et al., 2004). By now, none of other mitochondrial protein-coding genes of genus Ratufa has been published in GenBank. In this study, the complete mitochondrial genome (GenBank KF575124; 16,563 bp) of the black giant squirrel collected from Hainan Island was sequenced and characterized in detail (Table 1). Eleven primer pairs specific to R. bicolor were used for PCR. The characteristics of R. bicolor mitochondrial genome are identical to typical vertebrates. The genome is 16,563 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding control regions. With the exceptions of ND6 and 8 tRNA genes, all the other genes are on the H (heavy) strand. The overall composition of the H strand is 31.71% A, 28.61% T, 13.17% G and 26.51% C. Except for ND2, ND5 (ATT start codon) and ND3 (ATA start codon), all the protein-coding genes are initiated with ATG. Six protein-coding genes use TAA and three genes use TAG as stop codons. ND6 ends with AGA and
Correspondence: Yuchun Li, Marine College, Shandong University, Weihai 264209, China. Email: [email protected]
History Received 9 September 2013 Revised 15 September 2013 Accepted 21 September 2013 Published online 7 January 2014
Table 1. Characteristics of the mt genome of R. bicolor. 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 70 1041 1112 2694 2772 3727 3793 3867 3936 4978 5051 5123 5196 5227 5296 5370 6912 6985 7054 7741 7811 7972 8652 9436 9505 9852 9922 10,212 11,590 11,658 11,719 11,789 13,590 14,115 14,188 15,328 15,402 15,471
69 1040 1111 2693 2768 3728 3795 3864 3935 4979 5046 5119 5195 5226 5294 5361 6911 6981 7053 7737 7809 8014 8652 9434 9504 9851 9919 10,218 11,589 11,658 11,720 11,788 13,606 14,114 14,183 15,327 15,397 15,470 16,563
Codon Start
Stop
ATG
TAG
ATT
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA-
ATA
TA-
ATG ATG
TAA T- -
ATT ATG
TAA AGA
ATG
TAG
Size (bp) 69 971 71 1582 75 957 69 72 69 1044 69 69 73 31 68 66 1542 70 69 684 69 204 785 815 69 345 68 294 1378 69 63 70 1818 525 69 1140 70 69 1093
Intergenic nucleotides
3 2 3 2 2 4 3 1 8 3 3 1 43 1 1 2 7 1 2 17 4 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 20:10 28 September 2015
760
L. Kong et al.
three genes end with an incomplete stop codon TA- (CO3 and ND3) and T- - (ND4), suggesting that these might be modified by the polyadenylation after transcript processing (Ojala et al., 1981). The length of 22 tRNA genes ranges from 68 to 75 bp, with an exception of tRNA-Ser (AGY), all the tRNA genes can be folded into typical cloverleaf secondary structures. The genome of R. bicolor has two non-coding regions, an L (light) strand replication origin (OL) and a control region (CR). The OL is located between tRNA-Asn and tRNA-Cys in a cluster of five tRNA genes (WANCY region). It is represented by a 31 bp noncoding sequence, which can fold into a secondary structure consisting of a perfect 16 bp stem and a 12 bp loop. The control region (CR) is flanked by tRNA-Pro and tRNA-Phe genes. Although the concatenated mitochondrial gene sequence may be more potent in phylogenetic inferences of deeper branches (Miya et al., 2003), there are only three complete mitochondrial genomes of the family Sciuridae available in GenBank. Our results provide the first available complete mitochondrial genome in the database for R. bicolor, and the information will be useful for species identification, phylogenetic research in Sciuridae and solving conservation problems of this endangered species.
Acknowledgements The authors thank the anonymous reviewers for providing valuable comments on the manuscript.
Mitochondrial DNA, 2015; 26(5): 759–760
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article. This research was funded by the Major International (Regional) Joint Research Project of NSFC (Grant No. 31110103910).
References Abramov AV, Kruskop SV. (2012). The mammal fauna of Cat Ba Island, northern Vietnam. Russian J Theriol 11:57–72. Harris RB, Duckworth JW. (2008). Ratufa bicolor. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. [Online] Available online at: www.iucnredlist.org. Gland: IUCN. Mercer JM, Roth VL. (2003). The effects of Cenozoic global change on squirrel phylogeny. Science 299:1568–72. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, et al. (2003). Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–38. Ojala DM, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Smith AT, Xie Y, Hoffmann RS, Lunde D, MacKinnon J, Wilson DE, Wozencraft WC. (2008). A guide to the mammals of China. Princeton, NJ: Princeton University Press. p 173. Steppan SJ, Storz BL, Hoffmann RS. (2004). Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Mol Phylogenet Evol 30:703–19.
