鲸类线粒体基因组特征分析及分子标记探讨
Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers
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摘要: 综合分析鲸类32个物种的线粒体基因组全序列,全面揭示了鲸类线粒体基因组的基本特征、蛋白质编码基因、选择压力和差异位点等。鲸类线粒体基因组均编码后生动物标准的37个基因。绝大多数鲸类线粒体基因组的基因排列顺序完全相同,而且与脊椎动物线粒体基因组的典型排列一致。4个类群(真露脊鲸属、须鲸属、原海豚属和宽吻海豚属)线粒体基因组的13个蛋白质编码基因的Ka/Ks比值介于0和0.587 7之间,均低于1,显示为纯化(负)选择。其中,cox3基因的Ka/Ks均值最低,其次为 cox1,cox2 和cob基因,说明这些基因承受较强的选择压力和功能束缚;而nad6基因的Ka/Ks均值最高,其次为atp8, nad2和atp6 基因,说明这些基因的选择压力较弱。从32种鲸类物种间和属内(真露脊鲸属、须鲸属、原海豚属和宽吻海豚属)线粒体基因组主编码基因(13个蛋白质编码基因和2个核糖体RNA基因)和D-loop区的变异位点分析显示,在鲸类群体遗传的研究中, nad5,nad4和nad2 基因是理想的分子标记,可以作为 cox1 基因辅助的分子标记,用于分析鲸类不同群体之间的遗传多样性,为其生物多样性的保护及其生物资源的合理利用提供参考。Abstract: The basic characteristics (including protein coding genes, selection pressure and different loci etc.) of whales mitochondrial genomes were fully revealed by comprehensive analysis of 32 whales mitochondrial genomes. Whales mitochondrial genomes contain 37 standard metazoan genes and their gene order is identical.. The Ka/Ks ratio of the whales (Eubalaena, Balaenoptera, Stenella and Tursiops) 13 mitochondrial protein coding genes is lower than 1 (range between 0 and 0.587 7), indicating for the purifying selection (negative selection). The average Ka/Ks of cox3 gene is the lowest, followed by cox1 , cox2 and cob genes, indicating that these genes bear a strong selection pressure and functional constraints. Meanwhile, the average Ka/Ks of nad6 gene is the highest, followed by atp8 , nad2 and atp6 gene, indicating these genes bear weaker selection pressure. The genetic variation analysis of main genes (13 protein coding genes and 2 ribosomal RNA genes) and D-loop region within 32 species and intra-genus (Eubalaena, Balaenoptera, Stenella and Tursiops) showed that nad5 , nad4 and nad2 gene are ideal molecular markers and can be used as supplementary molecular markers to cox1 gene, which providing a reference for the conservation of whales biological diversity and use of the biological resources rationally.
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Key words:
- Cetacea /
- mitochondrial genome /
- genetic different loci /
- molecular marker
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DELLAPORTA S L, XU A, SAGASSER S, et al. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum [J]. Proceedings of the National Academy of Sciences of the United States of America,2006; 103(23):8751-8756. HELFENBEIN K G, FOURCADE H M, VANJANI R G, et al. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes[J]. Proceedings of the National Academy of Sciences of the United States of America,2004, 101(29):10639-10643. BOORE J L. Animal mitochondrial genomes[J]. Nucleic Acids Res, 1999, 27(8):1767-1780. BOORE J L, BROWN W M. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool[J]. Current Opinion in Genetics & Development, 1998, 8(6):668-674. 杨光, 季国庆, 魏辅文. 鲸类分子系统学研究进展[J]. 动物分类学报, 2003, 28(3):367-373. 刘珊, 杨光. 鲸类保护遗传学研究进展[J]. 动物学杂志, 2002, 37(5):83-86. ARNASON U, GULLBERG A. Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature[J]. Journal of Molecular Evolution, 1993, 37(4):312-322. ARNASON U, GULLBERG A, GRETARSDOTTIR S, et al. The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates[J]. Journal of Molecular Evolution, 2000, 50(6):569-578. ARNASON U, GULLBERG A, JANKE. Mitogenomic analyses provide new insights into cetacean origin and evolution[J]. Gene, 2004, 333:27-34. ARNASON U, GULLBERG A, WIDEGREN B. The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus[J]. Journal of Molecular Evolution, 1991, 33(6):556-568. ARNASON U, GULLBERG A, WIDEGREN B. Cetacean mitochondrial DNA control region: sequences of all extant baleen whales and two sperm whale species[J]. Molecular Biology and Evolution, 1993, 10(5):960-970. SASAKI T, NIKAIDO M, HAMILTON H, et al. Mitochondrial phylogenetics and evolution of mysticete whales[J]. Systematic Biology, 2005, 54(1):77-90. SASAKI T, NIKAIDO M, WADA S, et al. Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage[J]. Molecular Phylogenetics and Evolution, 2006, 41(1):40-52. VALVERDE J R, MARCO R, GARESSE R. A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria[J]. Proc Natl Acad Sci U S A, 1994, 91(12):5368-5371. XIONG Y, BRANDLEY MC, XU S, et al. Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales[J]. BMC Evolutionary Biology, 2009, 9:20. YAN J, ZHOU K, YANG G. Molecular phylogenetics of 'river dolphins' and the baiji mitochondrial genome[J]. Molecular Phylogenetics and Evolution 2005; 37(3):743-750. THOMPSON J D, GIBSON T J, PLEWNIAK F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res, 1997, 25(24):4876-4882. YANG Z. PAML 4: phylogenetic analysis by maximum likelihood[J]. Mol Biol Evol, 2007, 24(8):1586-1591. ROZAS J, SANCHEZ-DELBARRIO J C, MESSEGUER X, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics (Oxford, England), 2003, 19(18):2496-2497. SCHINDEL D E, MILLER S E. DNA barcoding a useful tool for taxonomists[J]. Nature, 2005, 435(7038):17.
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