http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945567
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of lesser long-tailed Hamster Cricetulus longicaudatus (Milne-Edwards, 1867) and phylogenetic implications Ziqi Zhang1, Tong Sun1, Chunlan Kang2, Yang Liu3, Shaoying Liu3, Bisong Yue2, and Tao Zeng2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/01/14 For personal use only.
1
West China School of Medicine, Sichuan University, Chengdu, P.R. China, 2Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China, and 3Sichuan Academy of Forestry, Chengdu, P.R. China Abstract
Keywords
The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents’ mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.
Complete mitochondrial genome, Cricetulus longicaudatus, phylogenetic inference
The lesser long-tailed Hamster Cricetulus longicaudatus belongs to the family Cricetidae and distributes in North China, northwest China, Inner Mongolia and Northwest Leah. The Cricetidae has more than 600 species (Luo et al., 2000) and the phylogenetic relationships of many species or genera were highly disputed (Corbet, 1978; Liu et al., 2012; Neumann et al., 2006). The complete mt-genome could provide abundant phylogenetic information and thus has been widely used in phylogenetic relationship research (Shen et al., 2010). However, the resource of the complete mt-genome is highly limited and only 14 complete mt-genomes were reported in Cricetidae. Here, we sequenced the complete mt-genome of C. longicaudatus and hoped that the knowledge of the mitochondrial genome of C. longicaudatus could contribute to the research of phylogenetic relationship within Cricetidae. The sample was collected in Qinhai, China. Total DNA was extracted using standard phenol/chloroform methods (Sambrook & Russell, 2001). These primer sets from Hao et al. (2011) and Fan et al. (2011) were used to amplify overlapping segments of the complete mitochondrial genome. A few primer sets not-amplified were redesigned based on the sequences obtained in present study. The details of the PCR and sequencing protocols were following previous study (Hao et al., 2011). The mitochondrial genome of C. longicaudatus was 16,302 bases in length. Its organization and order were similar to that of other rodents’
Correspondence: Tao Zeng, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: + 86 28 85412057. E-mail: [email protected]
History Received 3 July 2014 Accepted 11 July 2014 Published online 4 August 2014
mitochondrial genomes, which consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (GenBank accession no. KM067270). All genes were encoded on the H strand, except for ND6 and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Pro, tRNA-Glu). The ATP8 and ATP6, ATP6 and COX3, and ND4L and ND4 shared 43 bp, 1 bp and 11 bp overlap, respectively. ATG is the common initiation codon for most protein-coding genes, while GTG was for ND1, ATT for ND2 and ND5, and ATA for ND3. Three types of termination codon were observed as following: TAA for COX1, ATP8, ATP6, ND4L, ND5, ND6, and Cytb, TAG for ND3 and CO2, and incomplete stop codon T– – for ND1, COX3, ND2 and ND4. The concatenated 12 heavy-strand protein-coding genes of C. longicaudatus and other 25 rodent mit-genomes were used for the phylogenetic analysis by Bayesian inference (BI). Mogera wogura and Urotrichus talpoides were chosen as outgroups. The details of BI analysis methods were following previous studies (Yue et al., 2012; Zeng et al., 2013). The BI tree showed these species in Muridae, Cricetidae and spalacidae formed a solid monophyletic group, respectively. The monophyly of the Cricetinae and Arvicolines were also supported with high posterior probability. Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively (Figure 1). Their unusual phylogenetic positions remain further study in the future. Cricetulus clustered together with Tscherskia, indicating their close phylogenetic relationship. However, the Cricetinae includes 7 genera and 18 species, but only three species have complete mitochondrial genome sequences, and thus more complete mitogenome sequences are needed to understand the phylogenetic relationships within Cricetinae.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/01/14 For personal use only.
2
Z. Zhang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Molecular phylogenetic tree of 26 rodent species derived from the DNA sequence of 12 mitochondrial protein-coding genes of each species using Bayesian inference. The numbers beside the nodes are Bayesian posterior probabilities (BPP). Mogera wogura and Urotrichus talpoides were set as outgroup species.
Acknowledgements The authors would like to thank Xuhao Song and Chaochao Yan in Sichuan University for their assistance in this study.
Declaration of interest This research was funded by National Science and Technology Support Project of China, 2012BAC01B06. This study had no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Corbet GB. (1978). The mammals of the Palaearctic region. A taxonomic review. Ithaca, London: Cornell University Press. Fan LQ, Fan ZX, Yue H, Zhang XY, Liu Y, Sun ZY, Liu SY, Yue BS. (2011). Complete mitochondrial genome sequence of the Chinese scrub vole (Neodon irene). Mitochondrial DNA 22:50–2. Hao HB, Liu SY, Zhang XY, Chen WC, Song ZB, Peng HY, Liu Y, et al. (2011). Complete mitochondrial genome of a new vole Proedromys liangshanensis (Rodentia: Cricetidae) and phylogenetic analysis with related species: Are there implications for the validity of the genus Proedromys. Mitochondrial DNA 22:28–34.
Liu SY, Liu Y, Guo P, Sun ZY, Murphy RW, Fan ZX, Fu JR, Zhang YP. (2012). Phylogeny of oriental voles (Rodentia: Muridae: Arvicolinae): Molecular and morphological evidence. Zool Sci 29:610–22. Luo ZX, Chen W, Cao W, Wang YX, Li CY, Li H, Huang WJ, et al. (2000). Fauna sinica, Mammalia, Vol. 6 Rodentia, Part III: Cricetidae. Beijing, China: Science Press. Neumann K, Michaux J, Lebedev V, Yigit N, Colak E, Ivanova N, Poltoraus A, et al. (2006). Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochromeband 12S rRNA genes and the nuclear vWF gene. Mol Phylogenet Evol 39:135–48. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP. (2010). A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 10:132. Yue H, Fan ZX, Liu SY, Liu Y, Song ZB, Zhang XY. (2012). A mitogenome of the Chevrier’s field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b Gene. DNA Cell Biol 31:460–9. Zeng T, Tu FY, Ma LL, Yan CC, Yang N, Zhang XY, Yue BS, Ran JH. (2013). Complete mitochondrial genome of blood pheasant (Ithaginis cruentus). Mitochondrial DNA 24:484–6.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of lesser long-tailed Hamster Cricetulus longicaudatus (Milne-Edwards, 1867) and phylogenetic implications Ziqi Zhang1, Tong Sun1, Chunlan Kang2, Yang Liu3, Shaoying Liu3, Bisong Yue2, and Tao Zeng2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/01/14 For personal use only.
1
West China School of Medicine, Sichuan University, Chengdu, P.R. China, 2Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China, and 3Sichuan Academy of Forestry, Chengdu, P.R. China Abstract
Keywords
The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents’ mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.
Complete mitochondrial genome, Cricetulus longicaudatus, phylogenetic inference
The lesser long-tailed Hamster Cricetulus longicaudatus belongs to the family Cricetidae and distributes in North China, northwest China, Inner Mongolia and Northwest Leah. The Cricetidae has more than 600 species (Luo et al., 2000) and the phylogenetic relationships of many species or genera were highly disputed (Corbet, 1978; Liu et al., 2012; Neumann et al., 2006). The complete mt-genome could provide abundant phylogenetic information and thus has been widely used in phylogenetic relationship research (Shen et al., 2010). However, the resource of the complete mt-genome is highly limited and only 14 complete mt-genomes were reported in Cricetidae. Here, we sequenced the complete mt-genome of C. longicaudatus and hoped that the knowledge of the mitochondrial genome of C. longicaudatus could contribute to the research of phylogenetic relationship within Cricetidae. The sample was collected in Qinhai, China. Total DNA was extracted using standard phenol/chloroform methods (Sambrook & Russell, 2001). These primer sets from Hao et al. (2011) and Fan et al. (2011) were used to amplify overlapping segments of the complete mitochondrial genome. A few primer sets not-amplified were redesigned based on the sequences obtained in present study. The details of the PCR and sequencing protocols were following previous study (Hao et al., 2011). The mitochondrial genome of C. longicaudatus was 16,302 bases in length. Its organization and order were similar to that of other rodents’
Correspondence: Tao Zeng, Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: + 86 28 85412057. E-mail: [email protected]
History Received 3 July 2014 Accepted 11 July 2014 Published online 4 August 2014
mitochondrial genomes, which consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (GenBank accession no. KM067270). All genes were encoded on the H strand, except for ND6 and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Pro, tRNA-Glu). The ATP8 and ATP6, ATP6 and COX3, and ND4L and ND4 shared 43 bp, 1 bp and 11 bp overlap, respectively. ATG is the common initiation codon for most protein-coding genes, while GTG was for ND1, ATT for ND2 and ND5, and ATA for ND3. Three types of termination codon were observed as following: TAA for COX1, ATP8, ATP6, ND4L, ND5, ND6, and Cytb, TAG for ND3 and CO2, and incomplete stop codon T– – for ND1, COX3, ND2 and ND4. The concatenated 12 heavy-strand protein-coding genes of C. longicaudatus and other 25 rodent mit-genomes were used for the phylogenetic analysis by Bayesian inference (BI). Mogera wogura and Urotrichus talpoides were chosen as outgroups. The details of BI analysis methods were following previous studies (Yue et al., 2012; Zeng et al., 2013). The BI tree showed these species in Muridae, Cricetidae and spalacidae formed a solid monophyletic group, respectively. The monophyly of the Cricetinae and Arvicolines were also supported with high posterior probability. Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively (Figure 1). Their unusual phylogenetic positions remain further study in the future. Cricetulus clustered together with Tscherskia, indicating their close phylogenetic relationship. However, the Cricetinae includes 7 genera and 18 species, but only three species have complete mitochondrial genome sequences, and thus more complete mitogenome sequences are needed to understand the phylogenetic relationships within Cricetinae.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Sydney on 09/01/14 For personal use only.
2
Z. Zhang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Molecular phylogenetic tree of 26 rodent species derived from the DNA sequence of 12 mitochondrial protein-coding genes of each species using Bayesian inference. The numbers beside the nodes are Bayesian posterior probabilities (BPP). Mogera wogura and Urotrichus talpoides were set as outgroup species.
Acknowledgements The authors would like to thank Xuhao Song and Chaochao Yan in Sichuan University for their assistance in this study.
Declaration of interest This research was funded by National Science and Technology Support Project of China, 2012BAC01B06. This study had no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Corbet GB. (1978). The mammals of the Palaearctic region. A taxonomic review. Ithaca, London: Cornell University Press. Fan LQ, Fan ZX, Yue H, Zhang XY, Liu Y, Sun ZY, Liu SY, Yue BS. (2011). Complete mitochondrial genome sequence of the Chinese scrub vole (Neodon irene). Mitochondrial DNA 22:50–2. Hao HB, Liu SY, Zhang XY, Chen WC, Song ZB, Peng HY, Liu Y, et al. (2011). Complete mitochondrial genome of a new vole Proedromys liangshanensis (Rodentia: Cricetidae) and phylogenetic analysis with related species: Are there implications for the validity of the genus Proedromys. Mitochondrial DNA 22:28–34.
Liu SY, Liu Y, Guo P, Sun ZY, Murphy RW, Fan ZX, Fu JR, Zhang YP. (2012). Phylogeny of oriental voles (Rodentia: Muridae: Arvicolinae): Molecular and morphological evidence. Zool Sci 29:610–22. Luo ZX, Chen W, Cao W, Wang YX, Li CY, Li H, Huang WJ, et al. (2000). Fauna sinica, Mammalia, Vol. 6 Rodentia, Part III: Cricetidae. Beijing, China: Science Press. Neumann K, Michaux J, Lebedev V, Yigit N, Colak E, Ivanova N, Poltoraus A, et al. (2006). Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochromeband 12S rRNA genes and the nuclear vWF gene. Mol Phylogenet Evol 39:135–48. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP. (2010). A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 10:132. Yue H, Fan ZX, Liu SY, Liu Y, Song ZB, Zhang XY. (2012). A mitogenome of the Chevrier’s field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b Gene. DNA Cell Biol 31:460–9. Zeng T, Tu FY, Ma LL, Yan CC, Yang N, Zhang XY, Yue BS, Ran JH. (2013). Complete mitochondrial genome of blood pheasant (Ithaginis cruentus). Mitochondrial DNA 24:484–6.
