棘皮动物线粒体基因组的基因重排、分子标记及系统发生分析

申欣; 田美; 孟学平; 程汉良; 阎斌伦

doi:10.3969/j.issn.0253-4193.2013.05.015

棘皮动物线粒体基因组的基因重排、分子标记及系统发生分析

doi: 10.3969/j.issn.0253-4193.2013.05.015

1.
淮海工学院海洋学院, 江苏省海洋生物技术重点实验室, 江苏连云港 222005;中国科学院北京生命科学研究院, 北京 100101
2.
淮海工学院海洋学院, 江苏省海洋生物技术重点实验室, 江苏连云港 222005

基金项目: 国家自然科学基金(40906067);香江学者计划(XJ2012056);中国博士后科学基金(2012M510054,2012T50218);中央财政支持地方高校发展专项资金(CXTD04,CXTD01);江苏省海洋生物技术重点实验室资助项目(2009HS13、2011HS009);江苏省"青蓝工程"人才基金资助项目(苏教师[2010]27号);江苏高校优势学科建设工程资助项目。

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出版历程
- 收稿日期: 2012-12-05

Gene rearrangement,molecular markers and phylogenetic analyses of echinoderms mitochondrial genomes

1.
College of Marine Science Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang 222005, China;Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
2.
College of Marine Science Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang 222005, China

摘要

摘要: 棘皮动物(echinoderms)是海洋生境中所特有的无脊椎动物重要类群,本文全面比较分析了棘皮动物29个物种的线粒体全基因组。线粒体基因组主编码基因的分析结果显示,海胆纲Echinoidea和海参纲Holothuroidea物种的基因排列完全相同;海星纲Asteroidea物种之间的基因排列也完全相同,然而与海胆纲、海参纲相比,存在一个长片段的倒位。海百合纲Crinoidea的栉羽星Phanogenia gracilis和花形羽枝Florometra serratissima主编码基因的基因排列完全相同,地中海海羊齿和海百合Neogymnocrinus richeri与此相比,均存在一个蛋白质编码基因(nad4L)的易位。蛇尾纲Ophiuroidea真蛇尾目Ophiurida的3个科(阳遂足科Amphiuridae、辐蛇尾科Ophiactidae和栉蛇尾科Ophiocomidae)主编码基因的基因排列完全相同,而同属于真蛇尾目,另外一个科(真蛇尾科Ophiuridae)的白色真蛇尾Ophiura albida和灰色真蛇尾Ophiura lutkeni,与同目的前3个科相比,存在3个蛋白质编码基因(nad1、nad2和cob)的倒位。蛇尾纲蔓蛇尾目Euryalida的海盘Astrospartus mediterraneus,与真蛇尾目5个线粒体基因组相比,存在主编码基因的重排。棘皮动物线粒体单基因的变异位点特征显示,nad5、nad4和nad2基因是理想的分子标记基因。基于29个线粒体基因组的氨基酸序列,通过两种方法(邻接法和最大似然法)所构建系统发生树的拓扑结构完全一致。支持其下分的5个纲(蛇尾纲、海参纲、海胆纲、海星纲和海百合纲)均为单系群。线粒体基因组的数据支持棘皮动物动物在纲层次的亲缘关系为:(((海胆纲+海星纲)+海参纲)+蛇尾纲)+海百合纲,海百合纲作为棘皮动物中最为古老的类群,位于系统发生树的根部。基于线粒体基因组构建的系统发生树,支持所有的科均为单系群;综合系统发生树及主编码基因的基因重排分析,均支持真蛇尾目并非单系发生,真蛇尾目的有效性还值得今后深入研究。
- 线粒体基因组 /
- 蛋白质编码基因 /
- 基因重排 /
- 分子标记 /
- 系统发生 /
- 棘皮动物
Abstract: Echinoderms are important group of invertebrates,which only found in marine habitats. Twenty-nine echinoderms mitochondrial genomes were fully analyzed in this article. The major coding gene arrangements of sea urchins and sea cucumbers are identical. The major coding gene arrangements within starfishes are also identical,and there is a long fragment inversion compared with these of sea urchins and sea cucumbers. The major coding gene arrangements of Phanogenia gracilis and Florometra serratissima(Crinoidea) are identical,compared with which there are a protein-coding genes (nad4L) translocation in Antedon mediterranea and Neogymnocrinus richeri mitochondrial genomes,respectively. The major coding gene arrangements of three families Amphiuridae,Ophiactidae and Ophiocomidae (Ophiuroidea: Ophiurida) are identical. However,there are three protein-coding genes (nad1,nad2 and cob) inversions in the mitochondrial genomes of Ophiura albida and Ophiura lutkeni,which belong to another family in the same order Ophiurida. Compared with five mitochondrial genomes from Ophiurida,there are major coding gene rearrangements in Astrospartus mediterraneus(Ophiuroidea: Euryalida) mitochondrial genome. The genetic variation analyses of main genes (13 protein coding genes) within 29 echinoderms mitochondrial genomes shown that nad5,nad4 and nad2 gene are ideal molecular markers. Tree topologies based on amino acid sequences of the protein-coding genes in 29 echinoderms mitochondrial genomes by two methods (neighbor-joining and maximum likelihood method) are identical. Phylogenetic trees based on mitochondrial genome data support that five classes (Ophiuroidea,Holothuroidea,Echinoidea,Asteroidea and Crinoidea) are monophyletic groups,and the relationship within them are (((Echinoidea+Asteroidea)+Holothuroidea)+Ophiuroidea)+Crinoidea. The class Crinoidea is the most ancient group in echinoderms,which located in the root of phylogenetic trees. Phylogenetic results support all families are monophyletic groups. Comprehensive analyses of phylogenetic trees based on the protein coding genes and major genes rearrangements support that Ophiurida is not monophyletic. The validity of the family Ophiurida is also worth further studies.
- mitochondrial genome /
- protein-coding gene /
- gene rearrangement /
- molecular marker /
- phylogeny /
- echinoderms

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参考文献(24)

Brusca R C,Brusca G J. Invertebrates[M]. Sunderland,MA: Sinauer Associates,2003.

廖玉麟,肖宁. 中国海棘皮动物的种类组成及区系特点[J]. 生物多样性,2011,19 (6): 729—736.

Matsubara M,Komatsu M,Araki T,et al. The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences[J]. Mol Phylogenet Evol,2005,36 (3): 598—605.

Smith M J,Banfield D K,Doteval K,et al. Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus[J]. J Mol Evol,1990,31 (3): 195—204.

Yasuda N,Hamaguchi M,Sasaki M,et al. Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus[J]. BMC Genomics,2006,7 (1): 17—26.

Asakawa S,Himeno H,Miura K,et al. Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome[J]. Genetics,1995,140 (3): 1047—1060.

Perseke M,Bernhard D,Fritzsch G,et al. Mitochondrial genome evolution in Ophiuroidea,Echinoidea,and Holothuroidea: insights in phylogenetic relationships of Echinodermata[J]. Mol Phylogenet Evol,2010,56 (1): 201—211.

Perseke M,Fritzsch G,Ramsch K,et al. Evolution of mitochondrial gene orders in echinoderms[J]. Mol Phylogenet Evol,2008,47 (2): 855—864.

Scouras A,Beckenbach K,Arndt A,et al. Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny[J]. Mol Phylogenet Evol,2004,31 (1): 50—65.

Smith M J,Arndt A,Gorski S,et al. The phylogeny of echinoderm classes based on mitochondrial gene arrangements[J]. J Mol Evol,1993,36 (6): 545—554.

De-Giorgi C,Martiradonna A,Lanave C,et al. Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome[J]. Mol Phylogenet Evol,1996,5 (2): 323—332.

Cantatore P,Roberti M,Rainaldi G,et al. The complete nucleotide sequence,gene organization,and genetic code of the mitochondrial genome of Paracentrotus lividus[J]. J Biol Chem,1989,264 (19): 10965—10975.

Valverde J R,Marco R,Garesse R. A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria[J]. PNAS,1994,91 (12): 5368—5371.

Sun X,Li Q,Kong L. Comparative mitochondrial genomics within sea cucumber (Apostichopus japonicus): Provide new insights into relationships among color variants[J]. Aquaculture,2010,309 (1/4): 280—285.

Shen X,Tian M,Liu Z,et al. Complete mitochondrial genome of the sea cucumber Apostichopus japonicus(Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern[J]. Gene,2009,439 (1-2): 79—86.

Fan S,Hu C,Wen J,et al. Characterization of mitochondrial genome of sea cucumber Stichopus horrens: a novel gene arrangement in Holothuroidea[J]. Sci China,2011,54 (5): 434—441.

Scouras A,Smith M J. The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: signature nucleotide bias and unique nad4L gene rearrangement within crinoids[J]. Mol Phylogenet Evol,2006,39 (2): 323—334.

Larkin M A,Blackshields G,Brown N P,et al. Clustal W and Clustal X version 2.0[J]. Bioinformatics,2007,23 (21): 2947—2948.

Librado P,Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics,2009,25 (11): 1451—1452.

Tamura K,Peterson D,Peterson N,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J]. Mol Biol Evol,2011,28 (10): 2731—2739.

Guindon S,Dufayard J F,Lefort V,et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[J]. Syst Biol,2010,59 (3): 307—321.

申欣,田美,程汉良,等. 海参纲线粒体基因组特征分析及分子标记探讨[J]. 水产科学,2011,30 (7): 400—404.

田美,申欣,孟学平,等. 海胆纲线粒体基因组特征及基因差异位点分析[J]. 水产科学,2011,30 (3): 174—176.

田美,申欣,孟学平,等. 7 个海星动物线粒体基因组比较及基因变异位点分析[J]. 台湾海峡,2012,31 (2): 189—194.

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