学术
硬骨鱼类线粒体基因系统发育信息效率分析
陈姝君[1,2] 赫崇波[2] 木云雷[2] 刘卫东[2] 周遵春[2] 高祥刚[2] 丛林林[1,2]
[1]辽宁师范大学生命科学学院,辽宁大连116029 [2]辽宁省海洋水产科学研究院,辽宁省海洋水产分子生物学重点实验室,辽宁省应用海洋生物技术开放实验室,辽宁大连116023
摘 要:
采用PCR产物直接测序法获得圆斑星鲽（Verasper variegatus）和条斑星鲽（V．moseri）线粒体基因组的全部基因序列，并从GenBank中下载已知分类地位相关鱼类的线粒体基因的核苷酸序列和蛋白质氨基酸序列，用蛙、鸡、牛做外群，采用NJ和MP法，重建鱼类的系统发育树。通过计算各个基因在重建系统发育树时的准确率，估算该基因所含有的系统发育信息。结果表明，从氨基酸序列和核苷酸序列以及在目、科、属综合分析，这些基因的系统发育信息大致分为好（16S rRNA、ND2、ND4、12S rRNA、ND6、ND5）、中（Cytb、COII、COIII、ND1、COI）和差（ND3、ND4L、ATP6、ATP8）3个组。在目阶元，当用核苷酸序列分析时，12SrRNA、16SrRNA、COII、ND4、ND5和ND6最好，COI、COIII、Cytb、ND1和ND2为中等，而ND3、ATPase6、ATPase8和ND4L最差。当用氨基酸序列分析时，ND4和ND5最好，ND1、ND2、Cytb、ND6、COI、COII和ND4L为中等，ND3、ATPase6、COIII和ATPase8最差。在科阶元，当用核苷酸序列时，12SrRNA、16SrRNA、ND2和ND6系统发育信息最好；用氨基酸序列时，Cytb和ND2最好。在属阶元，所有基因的核苷酸序列都具有很好的系统发育信息，而COII、ND4L、ND1和ND3的氨基酸序列系统发育信息最差。本研究结果有助于进一步利用线粒体基因研究分析鱼类系统进化关系。[著者文摘]
文章出处:
《中国水产科学》-2008年1期 -12-21页
栏目信息:
分 类 号:
文献标识码:
A
文章编号:
1005-8737-（2008）01-0012-10
Informative efficiencies of mitochondrial genes in phylogenetic analysis of teleostean
CHEN Shu-junh, HE Chong-bo, MU Yun-lei, LIU Wei-dong, ZHOU Zunchun, GAO Xiang-gang, CONG Linqin （1. College of Life Science, Liaoning Normal University, Dalian 116029, China; 2. Liaoning Ocean and Fisheries Science Research Institute, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Open Laboratory of Applied Marine Bioteclmology, Dalian 116023, China）
Abstract:
A large number of studies in evolutionary biology utillize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among teleostean lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes and ribosomal RNA genes to recover the expected phylogenies of teleostean. We sequenced the complete mitochondrial genome of Verasper variegatus and Verasper moseri using PCR direct sequencing method and reconstructed the phylogenetic trees by Neighbor- Joining （NJ） and Maximum Parsimony （MP） method with the nucleotide and amino acid sequences of all the protein-coding genes and ribosomal RNA genes of teleostean species download from GenBank, using Bos Taurus, Gallus gallus gallus, Mantella madagascariensis as outgroups and then calculated and analyzed the accuracy of the phylogenetic trees reconstructed. The results showed that the mitochondrial protein-coding genes and ribosomal RNA genes can be roughly classified into three groups of good （16S rRNA, ND2, ND4, 12S rRNA, ND6 and ND5）, medium （Cytb, COIl, COIII, ND1 and CO1）, and poor （ND3, ND4L, ATPase6 and ATPase8） phylogenetic performers in recovering these expected trees among the seven orders of telstean fishes. At the level of Order, 12S rRNA, 16S rRNA, COIl, ND4, ND5 and ND6 are of good groups, COI, COIII, Cytb, ND1 and ND2 are of medium, and ND3, ATPase6, ATPase8 and ND4L are of poor when using nucleotide sequence; ND4 and ND5 belong to good groups; ND1, ND2, Cytb, ND6, COI, COIl and ND4L are medium, and ND3, ATPase6, COIII and ATPase8 are poor using amino acid sequence. When aligned by nucleotide sequence in family, 12S rRNA, 16S rRNA, ND2 and ND6 are in good groups; Cyt b and ND2 are in good group when aligned by amino acid sequence; in genera, all sequences are in good groups when aligned by nucleotide sequence; COIl, ND4L, ND1 and ND3 are not in good groups when aligned by amino acid sequence. [Journal of Fishery Sciences of China, 2008, 15 （1） ： 12-21 ][著者文摘]
Key words:
Verasper variegatus; Verasper moseri; teleostean; mtDNA; phylogeny
基金资助:
国家自然科学基金项目资助（30571410）;海洋经济实施科技推进平台与运行项目（2005-2007年）
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