The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer ( Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae

• Published in: Small ruminant research Vol. 69; no. 1; pp. 46 - 54
• Main Authors: Wada, Kenta, Nishibori, Masahide, Yokohama, Michinari
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.05.2007
• Subjects: amino acid sequences; Bovidae; Cervidae; Cervus nippon; cytochrome b; deer; divergent evolution; Equidae; genes; genetic distance; genome; mitochondrial DNA; Mitochondrial genome; molecular genetics; Molecular phylogeny; molecular sequence data; nucleotide sequences; peptides; phylogeny; polymerase chain reaction; races; Sika deer; species differences; tandem repeat sequences; Japan; Sika deer; Mitochondrial genome; Molecular phylogeny
• ISSN: 0921-4488; 1879-0941
• DOI: 10.1016/j.smallrumres.2005.12.002

We determined the complete nucleotide sequence of the mitochondrial genome in the Japanese Sika deer ( Cervus nippon); Yeso ( C. n. yesoensis), Honshu ( C. n. centralis) and Yakushima Sika deer ( C. n. yakushimae), and its genome sizes were 16,543, 16,663 and 16,440 bp, respectively. The D-loop was observed to have a various number of tandem repeats in the Japanese Sika deer (4–10 repeats). In the present study, the Honshu Sika deer collected from Okutama-city in Tokyo had 10 repeats, which was a novel number in the Japanese Sika deer. The similarity of entire nucleotide sequence of mitochondrial DNA ranged from 94.1 to 96.7%, and amino-acid sequence similarity was 98.5–99.4%. The phylogenetic tree that was inferred from nucleotide sequence of 13 peptide coding genes and amino-acid sequence of 12 peptide coding genes were presented topology that is, ((Cervidae) (Bovidae [cattle], Bovidae [sheep]), Equidae) with high bootstrap values. On the other hand, the cytochrome b ( Cytb) gene that was often used in some mammalian phylogenetic analyses showed topology that is, ((Cervidae, Bovidae [sheep]) (Bovidae [cattle]), Equidae). In Cervidae, phylogenetic analyses were mainly conducted using a Cytb gene. Therefore, in order to provide conclusive phylogenetic relationships are required more comprehensive molecular phylogenetic analyses among Cervidae. We suggest that the molecular phylogeny of Cervidae should be reviewed carefully using 13 or 12 mitochondrial peptide coding genes. Our complete mitochondrial DNA data of the Japanese Sika deer will be useful information in phylogenetics, and will be available as basic data for the breeding and genetics in Cervidae.