Mitochondrial DNA Part B Resources ISSN: (Print) 2380-2359 (Online) Journal homepage: http://www.tandfonline.com/loi/tmdn20 Complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae) Leping Zhang, Yuanyuan Huang, Kenneth B Storey, Danna Yu & Jia-Yong Zhang To cite this article: Leping Zhang, Yuanyuan Huang, Kenneth B Storey, Danna Yu & Jia- Yong Zhang (2016) Complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae), Mitochondrial DNA Part B, 1:1, 359-360, DOI: 10.1080/23802359.2016.1168716 To link to this article: http://dx.doi.org/10.1080/23802359.2016.1168716 © 2016 The Author(s). Published by Informa Published online: 20 Jun 2016. UK Limited, trading as Taylor & Francis Group. Submit your article to this journal Article views: 92 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=tmdn20 Download by: [134.117.97.124] Date: 30 October 2017, At: 09:30 MITOCHONDRIAL DNA PART B: RESOURCES, 2016 VOL. 1, NO. 1, 359–360 http://dx.doi.org/10.1080/23802359.2016.1168716 MITOGENOME ANNOUNCEMENT Complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae) Leping Zhanga, Yuanyuan Huanga, Kenneth B Storeyb, Danna Yua,c and Jia-Yong Zhanga,c aCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China; bDepartment of Biology, Carleton University, Ottawa, Ontario, Canada; cKey Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China ABSTRACT ARTICLE HISTORY The complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Received 2 March 2016 Sciuridae) were sequenced to analyze the gene arrangement and discuss the phylogenetic relationship Revised 15 March 2016 of species within the Xerinae. The genomes are circular molecules of 16,457 bp and 16,460 bp in length, Accepted 17 March 2016 respectively, including the 37 genes typically found in other squirrels. The AT content of the overall base composition is 63.2% for both species. The length of control region for C. lateralis is 1009 bp with 62.8% KEYWORDS Golden-mantled ground AT content; the corresponding values for U. richardsonii are 1012 bp and 62.0% AT content. In BI and ML squirrel; mitochondrial phylogenetic trees, the monophyly of the family Sciuridae and subfamilies Callosciurinae and Sciurinae genome; Richardson’s are well supported, but the monophyly of Xerinae is not supported. Within the Xerinae, the relationship ground squirrel; Sciuridae of (Tamias sibiricus þ (Callospermophilus lateralis þ (Marmota himalayana þ (Urocitellus richardsonii þ (Ictidomys tridecemlineatus þ (Cynomys leucurus þ Cynomys ludovicianus)))))) is well sup- ported. However, Tamiops swinhoei (Xerinae) within the subfamily Callosciurinae is a clade sister to Dremomys rufigenis (Callosciurinae). Spermophilus dauricus (Xerinae) within subfamily Sciurinae is a sister clade to Sciurus vulgaris (Sciurinae). The monophyly of Xerinae is failed to support in this study. Ground squirrels (Spermophilus), prairie dogs (Cynomys) and Li et al. (2015) and Zhang et al. (2015). DNA was amplified by their relatives are among the most intensively studied groups PCR and both strands were sequenced. of mammals with respect to their ecology and behavior Callospermophilus lateralis and U. richardsonii showed the (Harrison et al. 2003). The phylogenetic relationship of the typical rodent-type arrangement of their mitocondrial family Sciuridae has been revised and discussed based on genomes, being circular molecules of 16,457 bp and 16,460 bp molecular markers (Harrison et al. 2003; Herron et al. 2004; in length, respectively. Each encoded the 37 genes typically Helgen et al. 2009). We determined the sequences of the found in other squirrel species. The AT content of the overall complete mitochondrial genomes of Callospermophilus lateralis base composition is 63.2% for both species. The length of (¼Spermophilus lateralis) and Urocitellus richardsonii control region of C. lateralis is 1009 bp with 62.8% AT content (¼Spermophilus richardsonii) (Rodentia: Sciuridae) to analyze whereas the length of control region of U. richardsonii is the gene arrangement and to further explore the phylogen- 1012 bp with 62.0% AT content. Bayesian inference (BI) and Downloaded by [134.117.97.124] at 09:30 30 October 2017 etic relationship of species within the Xerinae. Both species maximum-likelihood (ML) trees were constructed using the 13 are well-studied models of mammalian hibernation. protein-coding genes (PCGs) from 20 species including Castor Golden-mantled ground squirrels (C. lateralis) were col- fiber, C. canadensis (Castoridae) and Myoxus glis (Gliridae) as lected in the Crooked Creek area of the White Mountains of outgroups to confirm the phylogenetic relationship among California, CA, whereas Richardson’s ground squirrels (U. the Sciuridae (Figure 1). To select conserved regions of the richardsonii) were collected near Calgary, Alberta, Canada. The nucleotide, each alignment was performed by Gblock 0.91b tissues samples (JBHS2015 and DSS2015) are stored and (Castresana 2000) using default settings. BI analysis and ML archived at the Biology Department, Carleton University, analysis was performed by MrBayes3.1.2 (Huelsenbeck & Canada. Liver samples from both species were sampled, flash Ronquist 2001) and PAUP*4.0b10 (Swofford 2002), respect- frozen in liquid nitrogen and held at À80 C until use. Whole ively. In BI and ML phylogenetic trees, the monophyly of the genomic DNA was extracted from a liver sample of each spe- family Sciuridae and the subfamilies Callosciurinae and cies. The DNA samples of C. lateralis (JBHS2015) and U. Sciurinae are well supported (1.00 in BI, 100% in ML), but the richardsonii (DSS2015) were stored at College of Chemistry monophyly of Xerinae failed. Within the Xerinae, the relation- and Life Science, Zhejiang Normal University, China. DNA frag- ship of (Tamias sibiricus þ (Callospermophilus lateralis þ (Marmota ments were amplified using 10 pairs of highly conserved pri- himalayana þ (Urocitellus richardsonii þ (Ictidomys tridecemli- mers which were designed according to the method of neatus þ (Cynomys leucurus þ Cynomys ludovicianus))))))) is also CONTACT Jia-Yong Zhang [email protected] Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China ß 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, dis- tribution, and reproduction in any medium, provided the original work is properly cited. 360 L. ZHANG ET AL. Castor fiber NC015072 Castoridae Castor canadensis NC015108 Myoxus glis AJ001562 Gliridae Ratufa bicolor KF575124 Ratufinae 1.00 1.00 Callosciurus erythraeus KM502568 100 100 Callosciurinae Dremomys rufigenis KC447304 0.99 1.00 100 100 Tamiops swinhoei KP027416 Xerinae 1.00 100 Tamias sibiricus KF668525 1.00 100 Callospermophilus lateralis KP698975 1.00 100 Marmota himalayana JX069958 0.93 Urocitellus richardsonii KP698976 Xerinae Sciuridae 79 1.00 100 Ictidomys tridecemlineatus KP698974 1.00 1.00 82 100 Cynomys leucurus KP326309 1.00 100 Cynomys ludovicianus KP326310 0.99 79 Hylopetes phayrei KC447305 1.00 100 Pteromys volans JQ230001 1.00 Sciurinae 100 Petaurista alborufus JQ743657 1.00 Petaurista hainana JX572159 100 BI 1.00 ML 100 Sciurus vulgaris AJ238588 0.1 Spermophilus dauricus KR534854 Xerinae Figure 1. Phylogenetic tree of the relationships among 20 species of Rodentia based on the nucleotide dataset of the 13 mitochondrial protein-coding genes of 11,349 nucleotides. Branch lengths and topology are from the BI analysis. Numbers above branches specify posterior probabilities from Bayesian inference (BI) and bootstrap percentages from maximum likelihood (ML, 1000 replications) analyses. The GenBank numbers for the mitochondrial genomes of all species are also shown. well supported (1.00 in BI and 100% in ML). However, Tamiops Technology Commission of Zhejiang Province of China (No. swinhoei (Xerinae) within the subfamily Callosciurinae is a clade 2014C32068). sister to Dremomys rufigenis (Callosciurinae) and Spermophilus dauricus (Xerinae) within the subfamily Sciurinae is a sister clade References to Sciurus vulgaris (Sciurinae). The monophyly of Xerinae is failed to support in this study. Overall, the sequences of more mito- Castresana J. 2000. Selection of conserved blocks from multiple align- chondrial genomes from Sciruidae species are needed in order ments for their use in phylogenetic analysis. Mol Biol Evol. 17:540–552. to fully assess the monophyly of Xerinae. Harrison RG, Bogdanowicz SM, Hoffmann RS, Yensen E, Sherman PW. 2003. Phylogeny and evolutionary history of the ground squirrels (Rodentia: Marmotinae). J Mamm Evol. 10:249–276. Nucleotide sequence accession numbers Helgen KM, Cole FR, Helgen LE, Wilson DE. 2009. Generic revision in the Holarctic ground squirrel genus Spermophilus. J Mammal. 90:270–305. The complete mitochondrial genomes of Callospermophilus Downloaded by [134.117.97.124] at 09:30