First Complete Mitochondrial Genome of the Alashan Ground Squirrel () (Rodentia: Sciuridae) from Ningxia, China

Overview

Journal Mitochondrial DNA B Resour

Date 2024 Jan 26

PMID 38274853

Authors

Yao Zhao

Jun Liang

Jingyao Li

Zhirong Zhang

Yue Sun

Fubin Liu

Xu Zhang

Yongliang Liang

Liwei Teng

Zhensheng Liu

Affiliations

Soon will be listed here.

Abstract

The Alashan ground squirrel () is primarily distributed in the regions of Inner Mongolia and Ningxia, China. In this study, we present the first complete mitochondrial genome of . The genome spans 16,464 base pairs and comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region with a marked AT bias. The overall GC content is 35.4%. Phylogenetic analyses indicate that clusters are closely associated with . This comprehensive characterization of the mitochondrial genome serves as a foundational resource for future studies on mitochondrial evolution, species identification, population genomics, and phylogenetics.

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Ibis O, Selcuk A, Teber S, Baran M, Koepfli K, Kefelioglu H Ecol Evol. 2025; 15(2):e70956.

PMID: 39949887 PMC: 11821457. DOI: 10.1002/ece3.70956.

References

Zheng S, Poczai P, Hyvonen J, Tang J, Amiryousefi A . Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet. 2020; 11:576124. PMC: 7545089. DOI: 10.3389/fgene.2020.576124. View

Emser S, Schaschl H, Millesi E, Steinborn R . Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet. 2022; 12:685806. PMC: 8749263. DOI: 10.3389/fgene.2021.685806. View

Kapustina S, Brandler O, Adiya Y . [Phylogeny of genus Spermophilus and position of Alashan ground squirrel (Spermophilus alashanicus, Buchner, 1888) on phylogenetic tree of Paleartic short-tailed ground squirrels]. Mol Biol (Mosk). 2015; 49(3):442-8. DOI: 10.7868/S0026898415030088. View

Brown J, Pirrung M, McCue L . FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics. 2017; 33(19):3137-3139. PMC: 5870778. DOI: 10.1093/bioinformatics/btx373. View

Krystufek B, Bryja J, Buzan E . Mitochondrial phylogeography of the European ground squirrel, Spermophilus citellus, yields evidence on refugia for steppic taxa in the southern Balkans. Heredity (Edinb). 2009; 103(2):129-35. DOI: 10.1038/hdy.2009.41. View

Sangster G, Luksenburg J . Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies. Genome Biol Evol. 2021; 13(9). PMC: 8462277. DOI: 10.1093/gbe/evab210. View

Li B, Yu D, Cheng H, Storey K, Zhang J . The complete mitochondrial genomes of Cynomys leucurus and C. ludovicianus (Rodentia: Sciuridae). Mitochondrial DNA A DNA Mapp Seq Anal. 2015; 27(5):3295-6. DOI: 10.3109/19401736.2015.1015010. View

Chao Q, Li Y, Geng X, Zhang L, Dai X, Zhang X . Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia. Genet Mol Res. 2014; 13(2):2739-51. DOI: 10.4238/2014.April.14.3. View

Zhang L, Storey K, Yu D, Hu Y, Zhang J . The complete mitochondrial genome of Ictidomys tridecemlineatus (Rodentia: Sciuridae). Mitochondrial DNA A DNA Mapp Seq Anal. 2015; 27(4):2608-9. DOI: 10.3109/19401736.2015.1041117. View

10.

Tsvirka M, Chelomina G, Korablev B . [Genetic evidence of hybridization between paletailed Spermophilus pallidicauda Satunin, 1903 and alashanic S. alaschanicus Buchner, 1888 ground squirrels in Mongolia]. Genetika. 2006; 42(4):530-7. View

11.

Tamura K, Stecher G, Kumar S . MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021; 38(7):3022-3027. PMC: 8233496. DOI: 10.1093/molbev/msab120. View

12.

Hao Z, Cao Y . The Complete mitochondrial genome of (Vancouver Island Marmot). Mitochondrial DNA B Resour. 2020; 4(2):3151-3152. PMC: 7707224. DOI: 10.1080/23802359.2019.1668308. View

13.

Walker L, Soto M, Spotorno A . Similarities and differences among the chromosomes of the wild guinea pig Cavia tschudii and the domestic guinea pig Cavia porcellus (Rodentia, Caviidae). Comp Cytogenet. 2014; 8(2):153-67. PMC: 4137285. DOI: 10.3897/CompCytogen.v8i2.7509. View

14.

Wahedi A, Gunther A, Weyrich A, Sondheimer N . The mitochondrial genome of . Mitochondrial DNA B Resour. 2021; 5(3):2147-2148. PMC: 7782685. DOI: 10.1080/23802359.2020.1768918. View

15.

Jo H, Koh G . Faster single-end alignment generation utilizing multi-thread for BWA. Biomed Mater Eng. 2015; 26 Suppl 1:S1791-6. DOI: 10.3233/BME-151480. View

16.

Voloch C, Vilela J, Loss-Oliveira L, Schrago C . Phylogeny and chronology of the major lineages of New World hystricognath rodents: insights on the biogeography of the Eocene/Oligocene arrival of mammals in South America. BMC Res Notes. 2013; 6:160. PMC: 3644239. DOI: 10.1186/1756-0500-6-160. View

17.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

18.

Kapustina S, Brandler O . Species affiliation of the complete mitochondrial genome of Daurian ground squirrel Brandt, 1843 (Rodentia, Sciuridae). Mitochondrial DNA B Resour. 2021; 2(1):296-297. PMC: 7799678. DOI: 10.1080/23802359.2017.1331324. View

19.

Zhang L, Huang Y, Storey K, Yu D, Zhang J . Complete mitochondrial genomes of and (Rodentia: Sciuridae). Mitochondrial DNA B Resour. 2021; 1(1):359-360. PMC: 7800758. DOI: 10.1080/23802359.2016.1168716. View