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日本鼓虾与鲜明鼓虾线粒体基因组全序列的分析比较

, PP. 147-153

Keywords: 鼓虾,线粒体基因组,选择压力,基因排列,分子标记

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Abstract:

首先通过基因组DNA的提取、通用引物PCR扩增和长PCR扩增,从而获得日本鼓虾(Alpheusjaponicus)的线粒体DNA;应用鸟枪法和引物步移法测序,获得了日本鼓虾的线粒体基因组全序列。结合GenBank线粒体基因组数据库中鲜明鼓虾(A.distinguendus)的线粒体基因组,比较分析了鼓虾线粒体基因组的基本特征、基因排列、蛋白质编码基因、选择压力和差异位点等。研究结果表明,在日本鼓虾线粒体基因组中共存在9对基因的重叠。日本鼓虾线粒体基因组全长16487bp,较鲜明鼓虾线粒体基因组(15700bp)长,主要是由于最大非编码区的长度存在差异。日本鼓虾与鲜明鼓虾线粒体基因组均编码37个基因,且37个基因的基因排列完全一致;与泛甲壳动物线粒体基因组的原始排列相比,仅出现1个转运RNA基因(trnE)的易位和倒位。2个鼓虾线粒体基因组蛋白质编码基因的起始密码子和终止密码子存在差异。除了cob基因外,其余12个蛋白质编码基因所编码氨基酸的数目均完全相同。鼓虾线粒体基因组13个线粒体蛋白质编码基因的Ka/Ks比值都远远低于1,显示出较强的负选择。在15个主编码基因中,nad5基因的变异位点数最多,其次是nad4基因和lrRNA基因。因此,nad5,nad4和lrRNA基因可以作为备选的分子标记,用于分析鼓虾不同物种和群体之间的生物多样性。

References

[1]  HURT C, ANKER A, KNOWLTON N. A multilocus test of simultaneous divergence across the Isthmus of Panama using snapping shrimp in the genus Alpheus[J]. Evolution, 2009, 63(2):514-530.
[2]  QIAN G H,ZHAO Q,WANG A,et al.Two new decapod(Crustacea,Malacostraca)complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda[J].Zool J Linn Soc,2011,162(3):471-481.
[3]  LOWE T M., EDDY S R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Res, 1997, 25(5):955-964.
[4]  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.
[5]  YANG Z. PAML 4: phylogenetic analysis by maximum likelihood[J]. Mol Biol Evol, 2007, 24(8):1586-1591.
[6]  ROZAS J, SANCHEZ-DELBARRIO J C, MESSEGUER X, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics, 2003, 19(18):2496-2497.
[7]  SHEN X, REN J F, CUI Z X, et al. The complete mitochondrial genomes of two common shrimps(Litopenaeus vannamei and Fenneropenaeus chinensis)and their phylogenomic considerations[J]. Gene, 2007, 403(1/2):98-109.
[8]  WILLIAMS S T, KNOWLTON N, WEIGT L A, et al. Evidence for three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data[J]. Mol Phylogenet Evol, 2001, 20(3):375-389.
[9]  MATHEWS L M, ANKER A. Molecular phylogeny reveals extensive ancient and ongoing radiations in a snapping shrimp species complex (Crustacea, Alpheidae, Alpheus armillatus)[J]. Mol Phylogenet Evol, 2009, 50(2):268-281.
[10]  EWING B, HILLIER L, WENDL M C, et al. Base-calling of automated sequencer traces using phred:Ⅰ. Accuracy assessment[J]. Genome Res, 1998, 8(3):175-185.
[11]  GORDON D, ABAJIAN C, GREEN P. Consed: a graphical tool for sequence finishing[J]. Genome Res, 1998, 8(3):195-202.
[12]  WYMAN S K, JANSEN R K, BOORE J L. Automatic annotation of organellar genomes with DOGMA[J]. Bioinformatics, 2004, 20(17):3252-3255.
[13]  MILLER A D, MURPHY N P, BURRIDGE C P, et al. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas(Menippidae) and Macrobrachium rosenbergii(Palaemonidae)[J]. Mar Biotechnol, 2005, 7(4):339-349.
[14]  SUN H Y, ZHOU K Y, SONG D X. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis(Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements[J]. Gene, 2005, 349:207-217.
[15]  SHEN X, SUN M A, WU Z G, et al. The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes[J]. Gene, 2009, 437(1/2):1-8.
[16]  SHEN X, WANG H Q, REN J F, et al. The mitochondrial genome of Euphausia superba(Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers[J]. Mol Biol Rep, 2010, 37(2):771-784.

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