Parkinson John, Mitreva Makedonka, Whitton Claire, Thomson Marian, Daub Jennifer, Martin John, Schmid Ralf, Hall Neil, Barrell Bart, Waterston Robert H, McCarter James P, Blaxter Mark L
Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada.
Nat Genet. 2004 Dec;36(12):1259-67. doi: 10.1038/ng1472. Epub 2004 Nov 14.
The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.
线虫门占据了从自由生活的微生物食者到人类寄生虫等广泛的生态位。我们使用来自30个物种（包括28种寄生虫）的265,494个表达序列标签序列（对应93,645个推定基因）分析了该门的基因组生物学。每个物种35%至70%的基因与模式线虫秀丽隐杆线虫的蛋白质具有显著相似性。超过一半的推定基因是该门独有的，23%是其来源物种独有的。我们尚未接近穷尽该门的基因组多样性。我们鉴定出2600多个不同的已知蛋白质结构域，其中一些在主要线虫分类群之间具有不同的丰度。我们还从线虫特异性基因中定义了4228个线虫特异性蛋白质家族：这类基因可能是物种和更高级别分类差异的基础。线虫特异性家族作为药物和疫苗靶点特别有趣。
