日本鼓虾与鲜明鼓虾线粒体基因组全序列的分析比较

申欣; 李晓; 徐启华

日本鼓虾与鲜明鼓虾线粒体基因组全序列的分析比较

1.
淮海工学院海洋学院, 江苏连云港 222005;中国科学院海洋研究所, 山东青岛 266071
2.
山东省花生研究所, 山东青岛 266100
3.
淮海工学院电子工程学院, 江苏连云港 222005

基金项目: 国家自然科学基金(40906067);江苏省"青蓝工程"人才基金(苏教师[2010]27号);江苏省海洋生物技术重点实验室基金(2009HS13);淮海工学院自然科学基金(Z2009048)。

计量
- 文章访问数: 1529
- HTML全文浏览量: 5
- PDF下载量: 1855
- 被引次数: 0
出版历程
- 收稿日期: 2011-07-06
- 修回日期: 2011-09-11

Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences

1.
College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China;Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
2.
Shandong Peanut Research Institute, Qingdao 266100, China
3.
College of Electronic Engineering, Huaihai Institute of Technology, Lianyungang 222005, China

摘要

摘要: 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(Alpheus japonicus)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16 487 bp,较鲜明鼓虾线粒体基因组(15 700 bp)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。
- 鼓虾 /
- 线粒体基因组 /
- 选择压力 /
- 基因排列 /
- 分子标记
Abstract: The mitochondrial genomic DNA of Alpheus japonicus was obtained by genomic DNA extraction combined with universal primers PCR and long PCR amplification. The complete mitochondrial genome sequence was sequenced using shotgun and primer-walking strategies. Comparative analyses were done combined with A. distinguendus mitochondrial genome, including the basic characteristics, gene order, protein-coding genes, selection pressure, and different sites and so on. The results show that overlapping is found in nine pairs genes of A. japonicus mitochondrial genome. The A. japonicus mitochondrial genome is 16 487 bp in length and is longer than A. distinguendus mitochondrial genome (15 700 bp), mainly due to the length difference of the largest non-coding region. The mitochondrial genomes of A. japonicus and A. distinguendus both contain 37 genes. Gene order of the A. japonicus and A. distinguendus mitochondrial genomes is identical. The translocation of one transfer RNA gene (trnE) involving inversion is found in 2 Alpheus mitochondrial genomes when compared with the pancrustacean ground pattern. There are differences in the usage of start codon and stop codon in protein-coding genes of 2 Alpheus mitochondrial genomes. Except for the cob gene, the numbers of amino acids encoded by the remaining 12 protein-coding genes are identical. The Ka/Ks ratio of all 13 mitochondrial protein coding genes is much lower than 1, indicating a strong negative selection. In 15 major coding genes, nad5 has the largest number of different loci, followed by nad4 and lrRNA genes, can be used as alternative molecular markers to analyze biodiversity among Alpheus species and populations.
- Alpheus /
- mitochondrial genome /
- selection pressure /
- gene order /
- molecular marker

HTML全文

参考文献(16)

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.

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.

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.

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.

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.

GORDON D, ABAJIAN C, GREEN P. Consed: a graphical tool for sequence finishing[J]. Genome Res, 1998, 8(3):195-202.

WYMAN S K, JANSEN R K, BOORE J L. Automatic annotation of organellar genomes with DOGMA[J]. Bioinformatics, 2004, 20(17):3252-3255.

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.

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, 2003, 19(18):2496-2497.

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.

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.

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.

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.

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.

施引文献

资源附件(0)

访问统计