http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2013 Informa UK Ltd. DOI: 10.3109/19401736.2013.848352
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a chipmunk species, Tamias sibiricus (Rodentia: Sciuridae) in Korea Kwang Bae Yoon1, Jae Youl Cho2, and Yung Chul Park1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/24/15 For personal use only.
Wildlife Conservation and Genomics, Forest Protection and Environment, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea and 2Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea Abstract
Keywords
We sequenced the complete mitochondrial genome (KF668525) of Tamias sibiricus in South Korea. The mitogenome of the Korean chipmunk T. sibiricus was 16,558 bp long with base composition of 33.8% A, 31.1% T, 22.9% C and 12.2% G. Total nucleotide similarity of T. sibiricus and Marmota himalayana (JX069958) genomes was 80.4% ranging from 66.9% (D-loop region) to 97.3% (tRNALeu(CUN)). The present study will contribute to understanding taxonomic status and genetic divergence of Northeast Asian T. sibiricus populations.
Chipmunk, complete mitochondrial genome, Tamias sibiricus
The Siberian chipmunks of Tamias sibiricus are distributed across northern Asia, ranging from central Russia to China, Korea and Hokkaido in northern Japan. This species is small ground-dwelling squirrel that lives in woodland habitats with bushy understory (Oshida et al., 1996). In South Korea, chipmunks of T. sibiricus are found in almost all forests. In this study, the complete mitochondrial genome (KF668525) of T. sibiricus in South Korea was sequenced and annotated in detail. Total genomic DNA was extracted from carcass muscle of a road-killed T. sibiricus individual in Pyeongchang-gun, South Korea, using the DNeasyÕ Blood & Tissue Kit (Qiagen, Valencia, CA) followed to the manufacturer’s instruction. Mitochondrial genome of the Marmota himalayana (JX069958) from GenBank was used to design primers for PCR amplification and as template for gene annotation of T. sibiricus mitogenome. The mitogenome of the Korean chipmunk T. sibiricus was 16,558 bp long with base composition of 33.8% A, 31.1% T, 22.9% C and 12.2% G. The base composition showed similar pattern to that of mitogenomes of other vertebrates (Kim et al., 2013; Yoon et al., 2012, 2013). All protein-coding genes (total 11,437 bp) were encoded in H-strand except for ND6 in L-strand and initiated with ATG except ND2 and ND5 (ATT) and ND3 (ATC). Four protein-coding genes ended (Cox2, ATP8, ND4L and ND5) with TAA, whereas COX1 and ND6 genes terminated with TAG and AGA, respectively. Incomplete stop codons were found in seven genes of ND2, ND3, COX3 and ND4 with T- - and ND1, ATP6 and Cytb with TA-, which may be completed by poly A of the 30 end of mRNA after transcription (Wei et al., 2007).
Correspondence: Yung Chul Park, Department of Forest Environment Protection, Kangwon National University, Chuncheon 200-701, Republic of Korea. Tel: 82 33 250 8366. Fax: 82 33 257 8361. E-mail: [email protected] Jae Youl Cho, Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea. Tel: 82 31 290 7868. Fax: 82 31 290 7870. E-mail: [email protected]
History Received 16 September 2013 Accepted 21 September 2013 Published online 11 November 2013
Table 1. Genome organization of Tamias sibiricus.
Gene tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(CUN) Nd1 tRNAIle tRNAGln tRNAMet Nd2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr Cox1 tRNASer(UCN) tRNAAsp Cox2 tRNALys ATP8 ATP6 Cox3 tRNAGly Nd3 tRNAArg Nd4L Nd4 tRNAHis tRNASer(AGY) tRNALeu(UUR) Nd5 Nd6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Start Stop Length Start Stop position position (bp) Anticodon codon codon Strand 1 71 1036 1105 2700 2778 3734 3801 3874 3943 4985 5054 5128 5201 5232 5299 5374 6918 6990 7060 7747 7816 7977 8657 9441 9510 9856 9925 10,215 11,593 11,663 11,721 11,791 13,592 14,117 14,190 15,329 15,401 15,469
70 1035 1104 2699 2774 3733 3803 3870 3942 4984 5050 5122 5200 5231 5298 5366 6915 6986 7059 7743 7814 8019 8656 9440 9509 9855 9922 10,221 11,592 11,661 11,720 11,790 13,608 14,116 14,185 15,328 15,396 15,468 16,558
70 965 69 1595 75 956 70 70 69 1042 66 69 73 31 67 68 1542 69 70 684 68 204 680 784 69 346 67 297 1378 69 58 70 1818 525 69 1139 68 68 1090
GAA TAC TAA ATG
TA-
ATT
T- -
ATG
TAG
GAT TTG CAT TCA TGC GTT GCA GTA TGA GTC ATG TAA TTT ATG TAA ATG TAATG T- TCC ATC
T- -
TCG ATG TAA ATG T- GTG GCT TAG ATT TAA ATG AGA TTC ATG TGT TGG
TA-
þ þ þ þ þ þ þ – þ þ þ – – þ – – þ – þ þ þ þ þ þ þ þ þ þ þ þ þ þ þ – – þ þ – þ
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/24/15 For personal use only.
2
K. B. Yoon et al.
The total length of 22 tRNA genes was 1511 bp varying from 58 bp (tRNASer(AGY)) to 75 bp (tRNALeu(CUN)). Except the tRNASer(AGY) with D-loop structure, the other 21 tRNA genes could be fold into typical cloverleaf secondary structure. The OL region (H-strand replication origin) is located between tRNAAsn and tRNACys within the WANCY region containing the five tRNA genes (tRNATrp, tRNAAla, tRNAAsn, tRNACys and tRNATyr) as found in most vertebrates (Seutin et al., 1994). The D-loop region is 1090 bp long and located between tRNAPro and tRNAPhe genes. In comparison between the genomes of T. sibiricus and M. himalayana, the total nucleotide similarity of the two genomes was 80.4% ranging from 66.9% (D-loop region) to 97.3% (tRNALeu(CUN)) along the gene regions (Table 1). There are 25 chipmunk species currently recognized in the world, of which only T. sibiricus inhabits in Asia. Genetic variations including T. sibiricus populations from Korea and neighboring countries have been previously conducted based on cytochrome b gene sequences (Koh et al., 2009; Lee et al., 2008). The present study will contribute to understanding taxonomic status and genetic divergence of T. sibiricus populations.
Acknowledgements The authors thank anonymous reviewers for providing valuable comments on this article.
Declaration of interest This study was carried out with the support of ‘‘Forest Science & Technology Projects (Project No. S211013L020100)’’ provided by Korea
Mitochondrial DNA, Early Online: 1–2
Forest Service. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Kim HR, Park JK, Cho JY, Park YC. (2013). Complete mitochondrial genome of an Asian Lesser White-toothed Shrew, Crocidura shantungensis (Soricidae). Mitochondrial DNA 24:202–4. Koh HS, Wang J, Lee BK, Yang BG, Heo SW, Jang KH, Chun TY. (2009). A phylogroup of the Siberian Chipmunk from Korea (Tamias sibiricus barberi) revealed from the mitochondrial DNA cytochrome b Gene. Biochem Genet 47:1–7. Lee MY, Lissovsky AA, Park SK, Obolenskaya EV, Dokuchaev NE, Zhang YP, Yu L, et al. (2008). Mitochondrial cytochrome b sequence variations and population structure of Siberian chipmunk (Tamias sibiricus) in Northeastern Asia and population substructure in South Korea. Mol Cells 26:566–75. Oshida T, Masuda R, Yoshida MC. (1996). Phylogenetic relationships among japanese species ofthe family Sciuridae (Mammalia, Rodentia), inferred from nucleotide sequences of mitochondrial 12s ribosomal RNA genes. Zool Sci 13:615–20. Seutin G, Lang BF, Mindell DP, Morais R. (1994). Evolution of the WANCY region in amniote mitochondrial DNA. Mol Biol Evol 11: 329–41. Wei L, Wu X, Jiang Z. (2007). The complete mitochondrial genome structure of snow leopard Panthera uncial. Mol Biol Rep 36:871–8. Yoon KB, Kim JY, Kim HR, Cho JY, Park YC. (2012). The complete mitochondrial DNA genome of a greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis (Chiroptera: Rhinolophidae). Mitochondrial DNA 24:22–4. Yoon KB, Kim HR, Kim JY, Jeon SH, Park YC. (2013). The complete mitochondrial genome of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae) in Korea. Mitochondrial DNA 24:397–9.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a chipmunk species, Tamias sibiricus (Rodentia: Sciuridae) in Korea Kwang Bae Yoon1, Jae Youl Cho2, and Yung Chul Park1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/24/15 For personal use only.
Wildlife Conservation and Genomics, Forest Protection and Environment, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea and 2Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea Abstract
Keywords
We sequenced the complete mitochondrial genome (KF668525) of Tamias sibiricus in South Korea. The mitogenome of the Korean chipmunk T. sibiricus was 16,558 bp long with base composition of 33.8% A, 31.1% T, 22.9% C and 12.2% G. Total nucleotide similarity of T. sibiricus and Marmota himalayana (JX069958) genomes was 80.4% ranging from 66.9% (D-loop region) to 97.3% (tRNALeu(CUN)). The present study will contribute to understanding taxonomic status and genetic divergence of Northeast Asian T. sibiricus populations.
Chipmunk, complete mitochondrial genome, Tamias sibiricus
The Siberian chipmunks of Tamias sibiricus are distributed across northern Asia, ranging from central Russia to China, Korea and Hokkaido in northern Japan. This species is small ground-dwelling squirrel that lives in woodland habitats with bushy understory (Oshida et al., 1996). In South Korea, chipmunks of T. sibiricus are found in almost all forests. In this study, the complete mitochondrial genome (KF668525) of T. sibiricus in South Korea was sequenced and annotated in detail. Total genomic DNA was extracted from carcass muscle of a road-killed T. sibiricus individual in Pyeongchang-gun, South Korea, using the DNeasyÕ Blood & Tissue Kit (Qiagen, Valencia, CA) followed to the manufacturer’s instruction. Mitochondrial genome of the Marmota himalayana (JX069958) from GenBank was used to design primers for PCR amplification and as template for gene annotation of T. sibiricus mitogenome. The mitogenome of the Korean chipmunk T. sibiricus was 16,558 bp long with base composition of 33.8% A, 31.1% T, 22.9% C and 12.2% G. The base composition showed similar pattern to that of mitogenomes of other vertebrates (Kim et al., 2013; Yoon et al., 2012, 2013). All protein-coding genes (total 11,437 bp) were encoded in H-strand except for ND6 in L-strand and initiated with ATG except ND2 and ND5 (ATT) and ND3 (ATC). Four protein-coding genes ended (Cox2, ATP8, ND4L and ND5) with TAA, whereas COX1 and ND6 genes terminated with TAG and AGA, respectively. Incomplete stop codons were found in seven genes of ND2, ND3, COX3 and ND4 with T- - and ND1, ATP6 and Cytb with TA-, which may be completed by poly A of the 30 end of mRNA after transcription (Wei et al., 2007).
Correspondence: Yung Chul Park, Department of Forest Environment Protection, Kangwon National University, Chuncheon 200-701, Republic of Korea. Tel: 82 33 250 8366. Fax: 82 33 257 8361. E-mail: [email protected] Jae Youl Cho, Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea. Tel: 82 31 290 7868. Fax: 82 31 290 7870. E-mail: [email protected]
History Received 16 September 2013 Accepted 21 September 2013 Published online 11 November 2013
Table 1. Genome organization of Tamias sibiricus.
Gene tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(CUN) Nd1 tRNAIle tRNAGln tRNAMet Nd2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr Cox1 tRNASer(UCN) tRNAAsp Cox2 tRNALys ATP8 ATP6 Cox3 tRNAGly Nd3 tRNAArg Nd4L Nd4 tRNAHis tRNASer(AGY) tRNALeu(UUR) Nd5 Nd6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Start Stop Length Start Stop position position (bp) Anticodon codon codon Strand 1 71 1036 1105 2700 2778 3734 3801 3874 3943 4985 5054 5128 5201 5232 5299 5374 6918 6990 7060 7747 7816 7977 8657 9441 9510 9856 9925 10,215 11,593 11,663 11,721 11,791 13,592 14,117 14,190 15,329 15,401 15,469
70 1035 1104 2699 2774 3733 3803 3870 3942 4984 5050 5122 5200 5231 5298 5366 6915 6986 7059 7743 7814 8019 8656 9440 9509 9855 9922 10,221 11,592 11,661 11,720 11,790 13,608 14,116 14,185 15,328 15,396 15,468 16,558
70 965 69 1595 75 956 70 70 69 1042 66 69 73 31 67 68 1542 69 70 684 68 204 680 784 69 346 67 297 1378 69 58 70 1818 525 69 1139 68 68 1090
GAA TAC TAA ATG
TA-
ATT
T- -
ATG
TAG
GAT TTG CAT TCA TGC GTT GCA GTA TGA GTC ATG TAA TTT ATG TAA ATG TAATG T- TCC ATC
T- -
TCG ATG TAA ATG T- GTG GCT TAG ATT TAA ATG AGA TTC ATG TGT TGG
TA-
þ þ þ þ þ þ þ – þ þ þ – – þ – – þ – þ þ þ þ þ þ þ þ þ þ þ þ þ þ þ – – þ þ – þ
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/24/15 For personal use only.
2
K. B. Yoon et al.
The total length of 22 tRNA genes was 1511 bp varying from 58 bp (tRNASer(AGY)) to 75 bp (tRNALeu(CUN)). Except the tRNASer(AGY) with D-loop structure, the other 21 tRNA genes could be fold into typical cloverleaf secondary structure. The OL region (H-strand replication origin) is located between tRNAAsn and tRNACys within the WANCY region containing the five tRNA genes (tRNATrp, tRNAAla, tRNAAsn, tRNACys and tRNATyr) as found in most vertebrates (Seutin et al., 1994). The D-loop region is 1090 bp long and located between tRNAPro and tRNAPhe genes. In comparison between the genomes of T. sibiricus and M. himalayana, the total nucleotide similarity of the two genomes was 80.4% ranging from 66.9% (D-loop region) to 97.3% (tRNALeu(CUN)) along the gene regions (Table 1). There are 25 chipmunk species currently recognized in the world, of which only T. sibiricus inhabits in Asia. Genetic variations including T. sibiricus populations from Korea and neighboring countries have been previously conducted based on cytochrome b gene sequences (Koh et al., 2009; Lee et al., 2008). The present study will contribute to understanding taxonomic status and genetic divergence of T. sibiricus populations.
Acknowledgements The authors thank anonymous reviewers for providing valuable comments on this article.
Declaration of interest This study was carried out with the support of ‘‘Forest Science & Technology Projects (Project No. S211013L020100)’’ provided by Korea
Mitochondrial DNA, Early Online: 1–2
Forest Service. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Kim HR, Park JK, Cho JY, Park YC. (2013). Complete mitochondrial genome of an Asian Lesser White-toothed Shrew, Crocidura shantungensis (Soricidae). Mitochondrial DNA 24:202–4. Koh HS, Wang J, Lee BK, Yang BG, Heo SW, Jang KH, Chun TY. (2009). A phylogroup of the Siberian Chipmunk from Korea (Tamias sibiricus barberi) revealed from the mitochondrial DNA cytochrome b Gene. Biochem Genet 47:1–7. Lee MY, Lissovsky AA, Park SK, Obolenskaya EV, Dokuchaev NE, Zhang YP, Yu L, et al. (2008). Mitochondrial cytochrome b sequence variations and population structure of Siberian chipmunk (Tamias sibiricus) in Northeastern Asia and population substructure in South Korea. Mol Cells 26:566–75. Oshida T, Masuda R, Yoshida MC. (1996). Phylogenetic relationships among japanese species ofthe family Sciuridae (Mammalia, Rodentia), inferred from nucleotide sequences of mitochondrial 12s ribosomal RNA genes. Zool Sci 13:615–20. Seutin G, Lang BF, Mindell DP, Morais R. (1994). Evolution of the WANCY region in amniote mitochondrial DNA. Mol Biol Evol 11: 329–41. Wei L, Wu X, Jiang Z. (2007). The complete mitochondrial genome structure of snow leopard Panthera uncial. Mol Biol Rep 36:871–8. Yoon KB, Kim JY, Kim HR, Cho JY, Park YC. (2012). The complete mitochondrial DNA genome of a greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis (Chiroptera: Rhinolophidae). Mitochondrial DNA 24:22–4. Yoon KB, Kim HR, Kim JY, Jeon SH, Park YC. (2013). The complete mitochondrial genome of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae) in Korea. Mitochondrial DNA 24:397–9.
