| Mitochondrial genome contains a large amount of molecular genetic information, whichmakes it become an important molecular marker in the analysis of population genetic structureand phylogenetic researches. In addition, more and more researches on mitochondrial genome ofendangered wildlife can provide appropriate methods for wildlife conservation and introductionstrategy through molecular genetic basis.The whole mitochondrial genome of gemsbok (Oryx gazella) and scimitar-horned oryx (Oryxdammah) were sequenced in this study and compared with other bovid species. Phylogeneticanalysis and estimation of divergence time were executed among these ten bovid species. Theresults are as follows.1. The length of mitochondrial genome of gemsbok and scimitar-horned oryx were16661bp and16756bp respectively.22tRNA genes, one12S rRNA gene, one16S rRNA gene,13protein-coding genes and one control region were included. The A-T bias was also evident inthe base usage of the mitochondrial genome. Except for ND2gene, ND3gene and ND5genetake ATA as their initiation codon, the rest of the protein-coding genes take ATG as initiationcodon. Most protein-coding genes take TAA as their terminator codon, whereas ND2gene andCytb gene take TAG and AGA as their terminator codon respectively. Besides, COXIII gene,ND3gene and ND4gene take incomplete TA or T as their terminator codon. All the tRNA genesare able to be folded into typical cloverleaf-shaped secondary structure except tRNA-Ser(AGY)which has a dihydrouridine stem and loop deletion. The control region can be separated intothree parts: ETAS region, CD region and CSB region. There were6repeats of a short coresequence of alternating purines and pyrimidines and constituting a GYRCAT (Y=C/T, R=A/G)motif in the RS2region of ETAS region. The central domain was the most conserved part of theCR, and several conserved blocks(F, E, D, C, and B boxes) previously reported within bovidaespecies could be clearly identified. Within the CSB domain of oryx, a putative initiation site forH strand replication (O_H)was identified, along with putative LSP, HSP, CSB1region,CSB1-like region and the fused CSB2+3region. No repetitive sequences were found in theregion between CSB1and CSB2.2. Based on the concatenated gene set of12S rRNA gene,16S rRNA gene and12H-standencoded protein-coding genes, we constructed the phylogenetic relationship of these ten bovidspecies by NJ method, MP method, ML method and Bayesian method respectively. The resultindicated that gemsbok and scimitar-horned oryx had the closet genetic relationship while theyhad a less close genetic relationship with Capainae and a farthest genetic relationship withBovinae. Four different methods differed when it came to the analysis of the genetic relationship among three Caprinae species; accordingly we did a comparison to find the reason. Our resultfrom analysis of phylogenetic relationship among Bovinae species was in accordance withexisting relevant research results.3. The nucleotide substitution rates of tRNA gene and rRNA gene of ten bovid species werecalculated and compared with the synonymous substitution rates and nonsynonymoussubstitution rates of protein coding genes. Taking the average substitution rates of different geneswhich were already reported as the molecular clock, we estimated the divergence time among tenbovid species. Estimates for the divergence time were3.35-6.03MYBP between gemsbok andscimitar-horned oryx,9.49-12.12MYBP between gemsbok and bontebok,8.96-12.65MYBPbetween gemsbok and goat,8.50-13.93MYBP between gemsbok and sheep,10.65-17.77MYBPbetween gemsbok and cattle and11.95-15.12MYBP between gemsbok and water buffalo, whichwere in accordance with the genetic relationship inferred through the phylogenetic tree. Inaddition, the estimates for the divergence among four bovid species and between Bovinae andCarprinae coincided with the existing results obtained through the fossils or other moleculargenetic data. |
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