title: Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans.
abstract: Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters from first- and infective third-stage larva (L1, L3i) of the parasitic nematode Strongyloides stercoralis and compared the results to Caenorhabditis elegans, a species that has an L3i-like dauer stage. In the comparison of S. stercoralis clusters with stage-specific expression to C. elegans homologs expressed in either dauer or nondauer stages, matches between S. stercoralis L1 and C. elegans nondauer-expressed genes dominated, suggesting conservation in the repertoire of genes expressed during growth in nutrient-rich conditions. For example, S. stercoralis collagen transcripts were abundant in L1 but not L3i, a pattern consistent with C. elegans collagens. Although a greater proportion of S. stercoralis L3i than L1 genes have homologs among the C. elegans dauer-specific transcripts, we did not uncover evidence of a robust conserved L3i/dauer 'expression signature.' Strikingly, in comparisons of S. stercoralis clusters to C. elegans homologs with RNAi knockouts, those with significant L1-specific expression were more than twice as likely as L3i-specific clusters to match genes with phenotypes. We also provide functional classifications of S. stercoralis clusters.
authors.affiliation: Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA. mmitreva@watson.wstl.edu
authors.forename: Makedonka
authors.initials: M
authors.lastname: Mitreva
authors.forename: James P
authors.initials: JP
authors.lastname: McCarter
authors.forename: John
authors.initials: J
authors.lastname: Martin
authors.forename: Mike
authors.initials: M
authors.lastname: Dante
authors.forename: Todd
authors.initials: T
authors.lastname: Wylie
authors.forename: Brandi
authors.initials: B
authors.lastname: Chiapelli
authors.forename: Deana
authors.initials: D
authors.lastname: Pape
authors.forename: Sandra W
authors.initials: SW
authors.lastname: Clifton
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Nutman
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development; D003001:Cloning, Molecular; D016000:Cluster Analysis; D003470:Culture Media / Q000737:chemistry / Q000378:metabolism; D018509:DNA, Helminth / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D017238:Genes, Helminth / Q000235:genetics; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D010641:Phenotype; D034622:RNA Interference / Q000502:physiology; D018510:RNA, Helminth / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D017171:Strongyloides stercoralis / Q000235:genetics* / Q000254:growth & development; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D003470:Culture Media; D018509:DNA, Helminth; D018510:RNA, Helminth