Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers

TIAN Mei; SHEN Xin; MENG Xue-ping; CHENG Han-liang

Article Contents

Article Navigation > Haiyang Xuebao > 2011 > 33(5): 104-114

TIAN Mei, SHEN Xin, MENG Xue-ping, CHENG Han-liang. Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers[J]. Haiyang Xuebao, 2011, 33(5): 104-114.

Citation:

TIAN Mei, SHEN Xin, MENG Xue-ping, CHENG Han-liang. Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers[J]. Haiyang Xuebao, 2011, 33(5): 104-114.

TIAN Mei, SHEN Xin, MENG Xue-ping, CHENG Han-liang. Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers[J]. Haiyang Xuebao, 2011, 33(5): 104-114.

Citation:

TIAN Mei, SHEN Xin, MENG Xue-ping, CHENG Han-liang. Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers[J]. Haiyang Xuebao, 2011, 33(5): 104-114.

PDF( 936 KB)

Analysis of the characteristics of whales mitochondrial genomes and exploration of molecular markers

College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005,China

Received Date: 2010-05-18

Abstract

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.
- Cetacea,
- mitochondrial genome,
- genetic different loci,
- molecular marker

FullText(HTML)

References(20)

References

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.

Relative Articles

Supplements(0)

Cited By

Proportional views