http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971270
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Leopoldamys edwardsi (Rodentia: Muridae) Dan Zhu1, Jie Huang1, Chunlan Kang2, Xuhao Song1, Bisong Yue2, and Xiuyue Zhang1 1
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China and Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
2
Abstract
Keywords
The complete mitochondrial genome of L. edwardsi was first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand proteincoding genes of L. edwardsi and other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated that L. edwardsi was closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named as Leopoldamys edwardsi. This study suggested that R. edwardsi is inappropriate for the other name of L. edwardsi.
Complete mitochondrial genome, Leopoldamys edwardsi, phylogenetic analyses
In this study, we sequenced the complete mitochondrial genome of Leopoldamys edwardsi (Edward’s long-tailed rat). L. edwardsi is a widespread species recorded from close to sea level to around 1400 m asl, ranging from northeastern South Asia, into central and southern China, and parts of Southeast Asia (Aplin et al., 2008). Our sample was obtained from Laojun Mountain, Pingshan Country, Sichuan Province, China. Total genomic DNA was extracted from muscle tissue using a standard proteinase K/phenol extraction procedure (Sambrook & Russell, 2001). Eighteen primer sets were used to amplify overlapping segments of the mitochondrial genome. The amplification was carried out in 25 ml reaction volumes with 2.5 ml 10 EXTaq buffer (Mg2+ +), 1.5 ml dNTP (2.5 mM each), 1 ml of each primer (10 M), 0.2 ml 10 EXTaq polymerase(5 U/ml), and approximate 200 ng total genomic DNA as the template. PCR were an initial predenaturation for 5 min at 95 C, 34 cycles of 95 C for 30 s and 54–59 C for 50 s and 72 C for 90 s and a final extension step of 72 C for 10 min. The mtDNA of L. edwardsi was 16,284 bp circular molecule containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (GenBank accession no. KM434322). Most genes were encoded on H-strand, except for ND6 and 8 tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro). The gene arrangement is analogous to other mammals’ mitochondrial genomes (Bibb, 1981; Gadaleta et al., 1989; Schlick et al., 2006; Ursing & Arnason, 1998). Other 26 Muridae
History Received 12 September 2014 Accepted 26 September 2014 Published online 20 October 2014
complete mitochondrial genome sequences were used to construct phylogenetic trees based on the concatenated dataset of 12 H-strand protein-coding genes. The Sciurus vulgaris was used as outgroup taxa. Maximum likelihood (ML), Neighbor Joining (NJ) and Minimum Evolution (ME) frameworks were used to examine the phylogenetic position of L. edwardsi. The parameters and methods to build the three different phylogenetic trees were followed Li et al. (2012) and Lu et al. (2013). The three treebuilding methods yielded the same topology and strongly support for all nodes (Figure 1). L. edwardsi and Rattus edwardsi are usually regarded as the synonyms (Xiao et al. 2003). But the tree shows L. edwardsi is not clustered with genus Rattus but a sister taxon to two Niviventer specises, suggesting that L.edwardsi is closer to the genus Niviventer than Rattus. Based on the research of Latinne et al. (2012) and Martin et al. (2000), Edward’s longtailed rat is the sister species of Leopoldamys. neilli. It suggested that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named as L. edwardsi. We suggested that R. edwardsi is improper for the name of this species. Relationship between Rattus, Niviventer and Leopoldamys indicated in our study is consistent with some previous researches (Horner et al., 2007; Rowe et al., 2008). These species in Rattus, Niviventer, Mus and Apodemus formed a solid monophyletic group, respectively. Muridae is a large family, therefore, more complete mitochondrial genome sequences are required in order to be better understand the phylogenetic relationship within Muridae.
Correspondence: Xiuyue Zhang, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: +86 28 85412057. Fax: +86 28 85414886. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
2
D. Zhu et al.
Mitochondrial DNA, Early Online: 1–3
Figure 1. ML/NJ/ME phylogenetic of 27 species based on 12 heavy-strand protein-coding genes. ML/NJ/ME bootstrap values are shown below nodes.
Acknowledgements We would like to acknowledge Dr. Ting Huang and Dr. Chaochao Yan at Sichuan University for their help in this study.
Declaration of interest This research was funded by National Science and Technology Support Project of China (2012BAC01B06). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Aplin K, Lunde D, Molur S. (2008). Leopoldamysedwardsi. The IUCN Red List of Threatened Species. Version 2014.2. Bibb MJ. (1981). Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–80. Gadaleta G. (1989). The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol 28:497–516.
Horner DS, Lefkimmiatis K, Reyes A, Gissi C, Saccone C, Pesole G. (2007). Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evol Biol 7:16. Latinne A, Waengsothorn S, Rojanadilok P, Eiamampai K, Sribuarod K, Michaux JR. (2012). Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cavedwelling rodent of Thailand. PLoSONE 7:e47670. Li P, Yang CZ, Tu FY, Liu GX. (2012). The complete mitochondrial genome of the Elongate loach Leptobotia elongate (Cypriniformes: Cobitidae). Mitochondrial DNA 23:352–4. Lu L, Tu FY, Yan CC, Zhang XY, Yue BS, Zeng T. (2013). The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis. Mitochondrial DNA 24:179–82. Martin Y, Gerlach G, Schlotterer C, Meyer A. (2000). Molecular phylogeny of European muroid rodents based on complete Cytochrome b Sequences. Mol Phylogenet Evol 16:37–47. Rowe KC, Reno ML, Richmond DM, Adkins RM, Steppan SJ. (2008). Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): Multilocus systematics of the old endemic rodents (Muroidea: Murinae). Mol Phylogenet Evol 47:84–101.
DOI: 10.3109/19401736.2014.971270
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, Lazar J. (2006). Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains. AMJ Physiol-cell l291: C1183–92.
Mitogenome of L. edwardsi
3
Ursing BM, Arnason U. (1998). The complete mitochondrial DNA sequence of the pig (Susscrofa). J Mol Evol 47:302–6. Xiao ZS, Zhang ZB, Wang YS. (2003). Observations on tree seed selection and caching by Edward’s long-tailed rat (Leopoldamysedwardsi). Acta Theriol Sin 23:208–13 (in Chinese with English summary).
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Leopoldamys edwardsi (Rodentia: Muridae) Dan Zhu1, Jie Huang1, Chunlan Kang2, Xuhao Song1, Bisong Yue2, and Xiuyue Zhang1 1
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China and Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
2
Abstract
Keywords
The complete mitochondrial genome of L. edwardsi was first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand proteincoding genes of L. edwardsi and other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated that L. edwardsi was closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named as Leopoldamys edwardsi. This study suggested that R. edwardsi is inappropriate for the other name of L. edwardsi.
Complete mitochondrial genome, Leopoldamys edwardsi, phylogenetic analyses
In this study, we sequenced the complete mitochondrial genome of Leopoldamys edwardsi (Edward’s long-tailed rat). L. edwardsi is a widespread species recorded from close to sea level to around 1400 m asl, ranging from northeastern South Asia, into central and southern China, and parts of Southeast Asia (Aplin et al., 2008). Our sample was obtained from Laojun Mountain, Pingshan Country, Sichuan Province, China. Total genomic DNA was extracted from muscle tissue using a standard proteinase K/phenol extraction procedure (Sambrook & Russell, 2001). Eighteen primer sets were used to amplify overlapping segments of the mitochondrial genome. The amplification was carried out in 25 ml reaction volumes with 2.5 ml 10 EXTaq buffer (Mg2+ +), 1.5 ml dNTP (2.5 mM each), 1 ml of each primer (10 M), 0.2 ml 10 EXTaq polymerase(5 U/ml), and approximate 200 ng total genomic DNA as the template. PCR were an initial predenaturation for 5 min at 95 C, 34 cycles of 95 C for 30 s and 54–59 C for 50 s and 72 C for 90 s and a final extension step of 72 C for 10 min. The mtDNA of L. edwardsi was 16,284 bp circular molecule containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (GenBank accession no. KM434322). Most genes were encoded on H-strand, except for ND6 and 8 tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro). The gene arrangement is analogous to other mammals’ mitochondrial genomes (Bibb, 1981; Gadaleta et al., 1989; Schlick et al., 2006; Ursing & Arnason, 1998). Other 26 Muridae
History Received 12 September 2014 Accepted 26 September 2014 Published online 20 October 2014
complete mitochondrial genome sequences were used to construct phylogenetic trees based on the concatenated dataset of 12 H-strand protein-coding genes. The Sciurus vulgaris was used as outgroup taxa. Maximum likelihood (ML), Neighbor Joining (NJ) and Minimum Evolution (ME) frameworks were used to examine the phylogenetic position of L. edwardsi. The parameters and methods to build the three different phylogenetic trees were followed Li et al. (2012) and Lu et al. (2013). The three treebuilding methods yielded the same topology and strongly support for all nodes (Figure 1). L. edwardsi and Rattus edwardsi are usually regarded as the synonyms (Xiao et al. 2003). But the tree shows L. edwardsi is not clustered with genus Rattus but a sister taxon to two Niviventer specises, suggesting that L.edwardsi is closer to the genus Niviventer than Rattus. Based on the research of Latinne et al. (2012) and Martin et al. (2000), Edward’s longtailed rat is the sister species of Leopoldamys. neilli. It suggested that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named as L. edwardsi. We suggested that R. edwardsi is improper for the name of this species. Relationship between Rattus, Niviventer and Leopoldamys indicated in our study is consistent with some previous researches (Horner et al., 2007; Rowe et al., 2008). These species in Rattus, Niviventer, Mus and Apodemus formed a solid monophyletic group, respectively. Muridae is a large family, therefore, more complete mitochondrial genome sequences are required in order to be better understand the phylogenetic relationship within Muridae.
Correspondence: Xiuyue Zhang, Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China. Tel: +86 28 85412057. Fax: +86 28 85414886. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
2
D. Zhu et al.
Mitochondrial DNA, Early Online: 1–3
Figure 1. ML/NJ/ME phylogenetic of 27 species based on 12 heavy-strand protein-coding genes. ML/NJ/ME bootstrap values are shown below nodes.
Acknowledgements We would like to acknowledge Dr. Ting Huang and Dr. Chaochao Yan at Sichuan University for their help in this study.
Declaration of interest This research was funded by National Science and Technology Support Project of China (2012BAC01B06). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Aplin K, Lunde D, Molur S. (2008). Leopoldamysedwardsi. The IUCN Red List of Threatened Species. Version 2014.2. Bibb MJ. (1981). Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–80. Gadaleta G. (1989). The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol 28:497–516.
Horner DS, Lefkimmiatis K, Reyes A, Gissi C, Saccone C, Pesole G. (2007). Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evol Biol 7:16. Latinne A, Waengsothorn S, Rojanadilok P, Eiamampai K, Sribuarod K, Michaux JR. (2012). Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cavedwelling rodent of Thailand. PLoSONE 7:e47670. Li P, Yang CZ, Tu FY, Liu GX. (2012). The complete mitochondrial genome of the Elongate loach Leptobotia elongate (Cypriniformes: Cobitidae). Mitochondrial DNA 23:352–4. Lu L, Tu FY, Yan CC, Zhang XY, Yue BS, Zeng T. (2013). The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis. Mitochondrial DNA 24:179–82. Martin Y, Gerlach G, Schlotterer C, Meyer A. (2000). Molecular phylogeny of European muroid rodents based on complete Cytochrome b Sequences. Mol Phylogenet Evol 16:37–47. Rowe KC, Reno ML, Richmond DM, Adkins RM, Steppan SJ. (2008). Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): Multilocus systematics of the old endemic rodents (Muroidea: Murinae). Mol Phylogenet Evol 47:84–101.
DOI: 10.3109/19401736.2014.971270
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 12/31/14 For personal use only.
Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, Lazar J. (2006). Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains. AMJ Physiol-cell l291: C1183–92.
Mitogenome of L. edwardsi
3
Ursing BM, Arnason U. (1998). The complete mitochondrial DNA sequence of the pig (Susscrofa). J Mol Evol 47:302–6. Xiao ZS, Zhang ZB, Wang YS. (2003). Observations on tree seed selection and caching by Edward’s long-tailed rat (Leopoldamysedwardsi). Acta Theriol Sin 23:208–13 (in Chinese with English summary).
