Genes for Phylogenies: Identifying Genes with Intrinsically Good Properties for Phylogenetic Estimation

系统发育基因：识别具有内在良好特性的基因以进行系统发育估计

• 批准号: 0089533
• 负责人: Gavin Naylor
• 金额: $ 20万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-07-15 至 2004-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0089533&HistoricalAwards=false
• 关键词: Genes; Phylogenies; Identifying; Intrinsically; Good

The study of phylogenetic relationships among species of vertebrate animals relies heavily at present on analyses of mitochondrial gene sequences, and less so on analyses of nuclear genes. Dr. Gavin Naylor of Iowa State University is exploring several candidate nuclear genes, presumed to be single-copy or from small families (duplications) of genes, in order to find sources of reliable characters for phylogenetic analysis of vertebrates. From initial surveys of over 7000 genes in gene-sequence databases, ten or so candidates will be selected, amplification primers constructed to extract and amplify the segments, and the genes then sequenced for several model taxa of fishes, birds, and mammals. In comparing mutational differences between gene sequences from different organisms, such properties as nucleotide base compositional evenness, the proportion of sites free to vary, the among-site rate variation, and codon usage will be evaluated in tests using a known phylogenetic tree for the model taxa. Not all genes are equally likely to yield informative results in phylogenetic analyses, but there has been little explicit testing of properties of candidate genes, to determine beforehand useful gene sources. The work to be carried out will identify genes with properties that predispose them to be phylogenetically useful and will provide empirical tests of their utility. As sequencing technology improves and as more genomes are sequenced in their entirety, bioinformatics will turn to comparative genomics to mine information that is buried in the comparison of whle-genomes. This endeavor will be greatly enhanced with an accurate understanding of the phylogenetic relationships among the genomes being compared, and in turn robust, reliable phylogenies will depend upon data drawn from several nuclear as well as mitochondrial genes.

脊椎动物动物物种之间的系统发育关系的研究目前严重依赖于线粒体基因序列的分析，而对核基因的分析较少。爱荷华州立大学的加文·纳勒（Gavin Naylor）博士正在探索几种候选核基因，这些核基因被认为是单拷贝或基因的小家族（重复），以找到可靠特征的来源，以用于脊椎动物的系统发育分析。从基因序列数据库中7000多个基因的初始调查，将选择十个候选者，构建用于提取和放大段的放大引物，然后对几种鱼类，鸟类和哺乳动物的几种模型分类群进行了测序。在比较来自不同生物体的基因序列之间的突变差异，例如核苷酸碱基组成均匀性，自由变化的位点的比例，位置速率变化和密码子使用情况将在测试中使用已知的系统发育树的测试评估。并非所有基因在系统发育分析中同样可能产生信息的结果，但是几乎没有明确测试候选基因的特性，以确定事先有用的基因源。要进行的工作将识别具有使它们具有系统发育有用的特性的基因，并将提供其实用性的经验测试。 随着测序技术的改善，随着更多的基因组的整体测序，生物信息学将转向比较基因组学，以掩盖在hle基因组比较中的信息。 通过对要比较的基因组之间的系统发育关系的准确理解，这项努力将大大增强，并且依靠稳健，可靠的系统发育将取决于从几个核和线粒体基因中获取的数据。