http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971255
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Pallas’s squirrel Callosciurus erythraeus (Rodentia: Sciuridae) Lanlin Hu, Rui Peng, and Fangdong Zou
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/09/15 For personal use only.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China Abstract
Keywords
The complete mitochondrial genome of Pallas’s squirrel (Callosciurus erythraeus) from Sichuan Province was sequenced and characterized in detail. It was 16,550 bp in length and composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The mitochondrial genome of C. erythraeus presented in this report will be useful for species identification, genetic variability and clarifying the controversial taxonomic status of genus Callosciurus.
Callosciurus erythraeus, complete mitochondrial genome, Pallas’s squirrel, sciuridae History Received 10 September 2014 Accepted 19 September 2014 Published online 16 October 2014
Pallas’s squirrel (Callosciurus erythraeus) is a medium-sized, arboreal squirrel. It mainly inhabits in southeastern Asia, and has been introduced into Europe and South Africa. This species was reported to cause damage to the artificial growth of many secondary forests in China, beginning in the 1950s (Kuo, 1957) and became more serious since 1980s (Liu et al., 2001). However, by now, most studies on the genetic variability of C. erythraeus were based on limited genetic markers, and more markers will be needed regarding its wide distribution (Bertolino et al., 2013; Gabrielli et al., 2014). In this study, the complete mito-genome (GenBank accession no. KM502568; 16,550 bp) of the Pallas’s squirrel collected from Mount Emei, Sichuan Province, China, was sequenced and characterized in detail (Table 1). It is the first report for the complete mitochondrial genome of C. erythraeus, which will be useful for further genetic study on C. erythraeus as well as genus Callosciurus. Thirteen primer pairs were used to amplify the whole mitogenome of C. erythraeus. The characteristics of C. erythraeus mitochondrial genome were identical to typical vertebrates. The mito-genome of C. erythraeus was 16,550 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and
1 control region. With the exceptions of ND6 and 8 tRNA genes, all the other genes were encoded on the H (heavy) strand. The overall composition of the H strand was 31.36% A, 29.35% T, 13.04% G, and 26.25% C. Except for ND2 (ATT start codon), and ND5 (ATA start codon), all the other protein-coding genes were initiated with ATG. Six protein-coding genes used TAA and four genes used TAG as stop codons. Cytb, COX3, and ND4 ended with AGA, TA– and T– –, respectively. And TA– and T– – suggest that these might be modified by the polyadenylation after transcript processing (Ojala et al., 1981). The length of 22 tRNA ranges from 67 to 75 bp; with the exception of tRNASer (AGG), all the tRNA genes could be folded into typical cloverleaf secondary structures. The mito-genome of C. erythraeus had two non-coding regions: an L (light) strand replication origin (OL) and a control region (CR). The OL was located between tRNA-Asn and tRNA-Cys in a cluster of five tRNA genes (WANCY region). It was represented by a 31 bp non-coding sequence, which could fold into a secondary structure consisting of a perfect 16 bp stem and a 12 bp loop. The control region (CR) was 1081 bp in length and flanked by tRNA-Pro and tRNA-Phe genes.
Correspondence: Fang-Dong Zou, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: +89 28 8541 2805. Fax: +86 28 8541 2805. E-mail: [email protected]
2
L. Hue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of C. erythraeus. Position Gene/Region
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/09/15 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S RNA tRNALeu(UUA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer (UCA) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGG) tRNALeu(CUA) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control Region
Codon
From
To
Size (bp)
1 69 1038 1106 2684 2763 3720 3786 3860 3930 4972 5042 5116 5189 5220 5289 5363 6908 6980 7050 7737 7806 7967 8647 9431 9503 9851 9919 10,209 11,587 11,660 11,719 11,789 13,591 14,115 14,188 15,329 15,401 15,470
68 1037 1105 2683 2758 3719 3788 3857 3929 4973 5038 5110 5188 5219 5287 5354 6904 6976 7048 7733 7804 8009 8647 9431 9502 9850 9917 10,215 11,586 11,658 11,717 11,788 13,606 14,114 14,183 15,327 15,396 15,469 16,550
68 969 68 1578 75 957 71 72 70 1045 67 69 73 31 68 66 1542 69 69 684 68 204 681 785 72 348 67 297 1378 72 58 70 1818 524 69 1140 68 69 1081
Acknowledgements The authors thank all the stuffs in Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, and Key Laboratory of Bio-resources and Eco-environment.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bertolino S, Lurz PW. (2013). Callosciurus squirrels: Worldwide introductions, ecological impacts and recommendations
Start
Stop
Intergenic nucleotides
4 ATG
TAG -3 2
ATT
TAG
ATG
TAA
ATG
TAG
ATG ATG ATG
TAA TAA TA–
ATG
TAA
ATG ATG
TAA T– –
-2 3 5 1 8 3 3 1 3 1 -43 -1 -1 1 -7 1 1
ATA ATG
TAA TAG
ATG
AGA
-16 4 1 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
to prevent the establishment of new invasive populations. Mammal Rev 43:22–33. Gabrielli M, Cardoso P, Benitez V, Gozzi AC, Guicho´n ML, Lizarralde MS. (2014). Genetic characterization of Callosciurus (Rodentia: Sciuridae) Asiatic squirrels introduced in Argentina. Italian J Zool 1–16. Kuo PC. (1957). A preliminary survey of squirrel damage to forest trees in taiwan. tech. Bull Exp Forest Natl Taiwan Univ Taipei 12: 3–15. Liu S, Ran J, Lin Q, Zhao D. (2001). The reason analysis of rodent damage in plantation. Forest Res 15:614–19. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of rna processing in human mitochondria. Nature 290:470–4.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Pallas’s squirrel Callosciurus erythraeus (Rodentia: Sciuridae) Lanlin Hu, Rui Peng, and Fangdong Zou
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/09/15 For personal use only.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China Abstract
Keywords
The complete mitochondrial genome of Pallas’s squirrel (Callosciurus erythraeus) from Sichuan Province was sequenced and characterized in detail. It was 16,550 bp in length and composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The mitochondrial genome of C. erythraeus presented in this report will be useful for species identification, genetic variability and clarifying the controversial taxonomic status of genus Callosciurus.
Callosciurus erythraeus, complete mitochondrial genome, Pallas’s squirrel, sciuridae History Received 10 September 2014 Accepted 19 September 2014 Published online 16 October 2014
Pallas’s squirrel (Callosciurus erythraeus) is a medium-sized, arboreal squirrel. It mainly inhabits in southeastern Asia, and has been introduced into Europe and South Africa. This species was reported to cause damage to the artificial growth of many secondary forests in China, beginning in the 1950s (Kuo, 1957) and became more serious since 1980s (Liu et al., 2001). However, by now, most studies on the genetic variability of C. erythraeus were based on limited genetic markers, and more markers will be needed regarding its wide distribution (Bertolino et al., 2013; Gabrielli et al., 2014). In this study, the complete mito-genome (GenBank accession no. KM502568; 16,550 bp) of the Pallas’s squirrel collected from Mount Emei, Sichuan Province, China, was sequenced and characterized in detail (Table 1). It is the first report for the complete mitochondrial genome of C. erythraeus, which will be useful for further genetic study on C. erythraeus as well as genus Callosciurus. Thirteen primer pairs were used to amplify the whole mitogenome of C. erythraeus. The characteristics of C. erythraeus mitochondrial genome were identical to typical vertebrates. The mito-genome of C. erythraeus was 16,550 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and
1 control region. With the exceptions of ND6 and 8 tRNA genes, all the other genes were encoded on the H (heavy) strand. The overall composition of the H strand was 31.36% A, 29.35% T, 13.04% G, and 26.25% C. Except for ND2 (ATT start codon), and ND5 (ATA start codon), all the other protein-coding genes were initiated with ATG. Six protein-coding genes used TAA and four genes used TAG as stop codons. Cytb, COX3, and ND4 ended with AGA, TA– and T– –, respectively. And TA– and T– – suggest that these might be modified by the polyadenylation after transcript processing (Ojala et al., 1981). The length of 22 tRNA ranges from 67 to 75 bp; with the exception of tRNASer (AGG), all the tRNA genes could be folded into typical cloverleaf secondary structures. The mito-genome of C. erythraeus had two non-coding regions: an L (light) strand replication origin (OL) and a control region (CR). The OL was located between tRNA-Asn and tRNA-Cys in a cluster of five tRNA genes (WANCY region). It was represented by a 31 bp non-coding sequence, which could fold into a secondary structure consisting of a perfect 16 bp stem and a 12 bp loop. The control region (CR) was 1081 bp in length and flanked by tRNA-Pro and tRNA-Phe genes.
Correspondence: Fang-Dong Zou, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: +89 28 8541 2805. Fax: +86 28 8541 2805. E-mail: [email protected]
2
L. Hue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of C. erythraeus. Position Gene/Region
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/09/15 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S RNA tRNALeu(UUA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer (UCA) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGG) tRNALeu(CUA) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control Region
Codon
From
To
Size (bp)
1 69 1038 1106 2684 2763 3720 3786 3860 3930 4972 5042 5116 5189 5220 5289 5363 6908 6980 7050 7737 7806 7967 8647 9431 9503 9851 9919 10,209 11,587 11,660 11,719 11,789 13,591 14,115 14,188 15,329 15,401 15,470
68 1037 1105 2683 2758 3719 3788 3857 3929 4973 5038 5110 5188 5219 5287 5354 6904 6976 7048 7733 7804 8009 8647 9431 9502 9850 9917 10,215 11,586 11,658 11,717 11,788 13,606 14,114 14,183 15,327 15,396 15,469 16,550
68 969 68 1578 75 957 71 72 70 1045 67 69 73 31 68 66 1542 69 69 684 68 204 681 785 72 348 67 297 1378 72 58 70 1818 524 69 1140 68 69 1081
Acknowledgements The authors thank all the stuffs in Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, and Key Laboratory of Bio-resources and Eco-environment.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bertolino S, Lurz PW. (2013). Callosciurus squirrels: Worldwide introductions, ecological impacts and recommendations
Start
Stop
Intergenic nucleotides
4 ATG
TAG -3 2
ATT
TAG
ATG
TAA
ATG
TAG
ATG ATG ATG
TAA TAA TA–
ATG
TAA
ATG ATG
TAA T– –
-2 3 5 1 8 3 3 1 3 1 -43 -1 -1 1 -7 1 1
ATA ATG
TAA TAG
ATG
AGA
-16 4 1 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
to prevent the establishment of new invasive populations. Mammal Rev 43:22–33. Gabrielli M, Cardoso P, Benitez V, Gozzi AC, Guicho´n ML, Lizarralde MS. (2014). Genetic characterization of Callosciurus (Rodentia: Sciuridae) Asiatic squirrels introduced in Argentina. Italian J Zool 1–16. Kuo PC. (1957). A preliminary survey of squirrel damage to forest trees in taiwan. tech. Bull Exp Forest Natl Taiwan Univ Taipei 12: 3–15. Liu S, Ran J, Lin Q, Zhao D. (2001). The reason analysis of rodent damage in plantation. Forest Res 15:614–19. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of rna processing in human mitochondria. Nature 290:470–4.
