title: A transcriptomic analysis of the phylum Nematoda.
abstract: 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.
authors.affiliation: Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada. jparkin@sickkids.ca
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
authors.forename: Makedonka
authors.initials: M
authors.lastname: Mitreva
authors.forename: Claire
authors.initials: C
authors.lastname: Whitton
authors.forename: Marian
authors.initials: M
authors.lastname: Thomson
authors.forename: Jennifer
authors.initials: J
authors.lastname: Daub
authors.forename: John
authors.initials: J
authors.lastname: Martin
authors.forename: Ralf
authors.initials: R
authors.lastname: Schmid
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.forename: Bart
authors.initials: B
authors.lastname: Barrell
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
authors.forename: James P
authors.initials: JP
authors.lastname: McCarter
authors.forename: Mark L
authors.initials: ML
authors.lastname: Blaxter
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D014644:Genetic Variation; D016678:Genome; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity