Complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae)

Abstract

The complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae) were sequenced to analyze the gene arrangement and discuss the phylogenetic relationship of species within the Xerinae. The genomes are circular molecules of 16,457 bp and 16,460 bp in length, 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% AT content; the corresponding values for U. richardsonii are 1012 bp and 62.0% AT content. In BI and ML phylogenetic trees, the monophyly of the family Sciuridae and subfamilies Callosciurinae and Sciurinae are well supported, but the monophyly of Xerinae is not supported. Within the Xerinae, the relationship of (Tamias sibiricus + (Callospermophilus lateralis + (Marmota himalayana + (Urocitellus richardsonii + (Ictidomys tridecemlineatus + (Cynomys leucurus + Cynomys ludovicianus)))))) is well supported. 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.

Keywords:

• Golden-mantled ground squirrel
• mitochondrial genome
• Richardson’s ground squirrel
• Sciuridae

Ground squirrels (Spermophilus), prairie dogs (Cynomys) and their relatives are among the most intensively studied groups of mammals with respect to their ecology and behavior (Harrison et al. 2003). The phylogenetic relationship of the family Sciuridae has been revised and discussed based on molecular markers (Harrison et al. 2003; Herron et al. 2004; Helgen et al. 2009). We determined the sequences of the complete mitochondrial genomes of Callospermophilus lateralis (=Spermophilus lateralis) and Urocitellus richardsonii (=Spermophilus richardsonii) (Rodentia: Sciuridae) to analyze the gene arrangement and to further explore the phylogenetic relationship of species within the Xerinae. Both species are well-studied models of mammalian hibernation.

Golden-mantled ground squirrels (C. lateralis) were collected in the Crooked Creek area of the White Mountains of California, CA, whereas Richardson’s ground squirrels (U. richardsonii) were collected near Calgary, Alberta, Canada. The tissues samples (JBHS2015 and DSS2015) are stored and archived at the Biology Department, Carleton University, Canada. Liver samples from both species were sampled, flash frozen in liquid nitrogen and held at −80 °C until use. Whole genomic DNA was extracted from a liver sample of each species. The DNA samples of C. lateralis (JBHS2015) and U. richardsonii (DSS2015) were stored at College of Chemistry and Life Science, Zhejiang Normal University, China. DNA fragments were amplified using 10 pairs of highly conserved primers which were designed according to the method of Li et al. (2015) and Zhang et al. (2015). DNA was amplified by PCR and both strands were sequenced.

Callospermophilus lateralis and U. richardsonii showed the typical rodent-type arrangement of their mitocondrial genomes, being circular molecules of 16,457 bp and 16,460 bp in length, respectively. Each encoded the 37 genes typically found in other squirrel species. The AT content of the overall base composition is 63.2% for both species. The length of control region of C. lateralis is 1009 bp with 62.8% AT content whereas the length of control region of U. richardsonii is 1012 bp with 62.0% AT content. Bayesian inference (BI) and maximum-likelihood (ML) trees were constructed using the 13 protein-coding genes (PCGs) from 20 species including Castor fiber, C. canadensis (Castoridae) and Myoxus glis (Gliridae) as outgroups to confirm the phylogenetic relationship among the Sciuridae (Figure 1). To select conserved regions of the nucleotide, each alignment was performed by Gblock 0.91b (Castresana 2000) using default settings. BI analysis and ML analysis was performed by MrBayes3.1.2 (Huelsenbeck & Ronquist 2001) and PAUP*4.0b10 (Swofford 2002), respectively. In BI and ML phylogenetic trees, the monophyly of the family Sciuridae and the subfamilies Callosciurinae and Sciurinae are well supported (1.00 in BI, 100% in ML), but the monophyly of Xerinae failed. Within the Xerinae, the relationship of (Tamias sibiricus + (Callospermophilus lateralis + (Marmota himalayana + (Urocitellus richardsonii + (Ictidomys tridecemli-neatus + (Cynomys leucurus + Cynomys ludovicianus))))))) is also well supported (1.00 in BI and 100% in ML). However, Tamiops swinhoei (Xerinae) within the subfamily Callosciurinae is a clade sister to Dremomys rufigenis (Callosciurinae) and Spermophilus dauricus (Xerinae) within the subfamily Sciurinae is a sister clade to Sciurus vulgaris (Sciurinae). The monophyly of Xerinae is failed to support in this study. Overall, the sequences of more mitochondrial genomes from Sciruidae species are needed in order to fully assess the monophyly of 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.

Nucleotide sequence accession numbers

The complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae) have been assigned GenBank accession numbers KP698975 and KP698976, respectively.

Funding information

This research was supported by a grant from the Natural Sciences and Engineering Research Council of Canada (No. 6793) and the Science Technology Commission of Zhejiang Province of China (No. 2014C32068).

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.