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.

A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans

“…3). Of all P. penetrans clusters with homologies, the majority (62.6%) matched sequences in all three databases, as has been observed in previous studies (McCarter et al 2003a;Mitreva et al 2004). Many gene products in this category are conserved across metazoans, and are involved in core biological processes.…”

“…Many gene products in this category are conserved across metazoans, and are involved in core biological processes. In contrast to our prior studies of M. incognita (McCarter et al 2003a) and S. stercoralis (Mitreva et al 2004), the C. elegans genome alone was no longer the best source for P. penetrans sequence homologies (78.9%), as 95.5% of the clusters matched nematode sequences from species other than C. elegans. The prominence of matches to Fig.…”

“…Based on the identified clusters, this project generated sequence data for 420 genes, corresponding to a new gene discovery rate of 22% (420/ 1928). Fragmentation, whereby one gene is represented by multiple non-overlapping clusters (Mitreva et al 2004), was not observed for this P. penetrans dataset, most probably because the use of an SL1 primer in Fig. 1 Histogram showing the distribution of P. penetrans ESTs by cluster size library construction ensured that the sequenced clones extended to the 5¢ ends of the mature transcripts.…”

“…The completed cluster assembly, NemaGene Pratylenchus penetrans v 1.0, was used as the basis for all subsequent analysis and is available for searching and acquisition by FTP at http://www.nematode.net. ''Fragmentation'', defined as the representation of a single gene by multiple non-overlapping clusters, was estimated by examining P. penetrans clusters with homology to C. elegans (Mitreva et al 2004). Overall representation of P. penetrans genes is based on a theoretical gene number of 21,712, comparable to that of C. elegans (Wormpep v. 104).…”

“…Sequencing, EST processing and clustering were performed as described previously (McCarter et al 2003a;Mitreva et al 2004). Submissions were deposited in GenBank in June and July 2002.…”