Abstract
The Sichuan deer (Cervus elaphus macneilli) is a rare animal native to western Sichuan and southeastern Tibet, China. In this study, the entire Sichuan deer mitochondrial genome was sequenced; it was 16350 bp long (GenBank accession No: KX449334) and contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region (D-loop). Ten PCGs started with ATG, but ND2, ND3, and ND5 used ATA as the start codon. PCG homology between C.e.macneilli and four other red deer subspecies ranged from 93.9 to 96%, which indicates a clear difference among subspecies. Phylogenetic analysis revealed that the Sichuan deer clustered into a clade with other red deer subspecies with high bootstrap support. This work provides additional molecular information for studying red deer conservation genetics and evolutionary relationships.
References
Burland TG (1999) DNASTAR’S Lasergene Sequence Analysis Software. Bioinformatics Methods and Protocols, 2nd edn. Humana Press, New Jersey, pp 71–91
Conant GC, Wolfe KH (2008) Genomevx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24(6):861–862
Jin YC, Zhang MH (2012) Review of molecular ecology research and prospects of red deer (cervus elaphus) in china based on feces molecular biology technology. Chin J Wildl 33(3):152–157 (in Chinese with English abstract)
Laslett D, Canback B (2008) ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24(2):172–175
Li Y, Ba H, Yang F (2016) Complete mitochondrial genome of Cervus elaphus songaricus (Cetartiodactyla: Cervinae) and a phylogenetic analysis with related species. Mitochondr DNA Part A 27(1):620–621
Liu YH, Zhang MH, Ma JZ (2013) Phylogeography of red deer (cervus elaphus) in china based on mtdna cytochrome b gene. Res J Biotechnol 8(10):34–41
Ma YQ, Zhao YF, Yu YM (1998) Biological characteristics of red deer and subspecies classification. Territory Nat Resour Study (1):63–66 (in Chinese)
Ronquist F, Teslenko M, Mark PVD et al (2012) Mrbayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. 3rd edn, Cold Spring Harbor Laboratory Press, New York, pp 12–72
Sun PF (2015) China’s five deer mitochondrial d-loop sequence analysis and system evolution. Gansu Anim Vet Sci 45(7):32–34 (in Chinese)
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739
Zhang L, Gun SB, Lei TY, Liu LX, Qin DW, Zhao SF (2010) Analysis of genetic diversity and phylogeny of five Chinese subspecies of Wapiti using mitochondrial Cytb complete sequence. Acta Agric Boreali Sinica 25(4):12–16 (in Chinese with English abstract)
Zhou CL, Turdy R, Halik M (2015) Genetic differentiation between red deer from different sample sites on the Tianshan Mountains (Cervus elaphus), China. Mitochondr DNA 26(1):101–111
Acknowledgements
This work was supported by grants from the National Natural Science Foundation of China (31370407). We thank the Forest Public Security Bureau of Tianquan County in Sichuan Province for supports in field sampling, and Qian Su, Pu Zhao, Junsong Zhao, Dingju Wei and Xue Liu for their assistance in experiments and data analysis.
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Zhao, Q., Xu, H., Li, D. et al. Complete mitochondrial genome and phylogenetic analysis of Sichuan deer (Cervus elaphus macneilli). Conservation Genet Resour 10, 431–435 (2018). https://doi.org/10.1007/s12686-017-0842-x
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DOI: https://doi.org/10.1007/s12686-017-0842-x