title: Comparative transcriptomics of the nematode gut identifies global shifts in feeding mode and pathogen susceptibility.
abstract: BACKGROUND
  The nematode Pristionchus pacificus has been established as a model for comparative studies using the well known Caenorhabditis elegans as a reference. Despite their relatedness, previous studies have revealed highly divergent development and a number of morphological differences including the lack of a pharyngal structure, the grinder, used to physically lyse the ingested bacteria in C. elegans.
  
  
  RESULTS
  To complement current knowledge about developmental and ecological differences with a better understanding of their feeding modes, we have sequenced the intestinal transcriptomes of both nematodes. In total, we found 464 intestine-enriched genes in P. pacificus and 724 in C. elegans, of which the majority (66%) has been identified by previous studies. Interestingly, only 15 genes could be identified with shared intestinal enrichment in both species, of which three genes are Hedgehog signaling molecules supporting a highly conserved role of this pathway for intestinal development across all metazoa. At the level of gene families, we find similar divergent trends with only five families displaying significant intestinal enrichment in both species. We compared our data with transcriptomic responses to various pathogens. Strikingly, C. elegans intestine-enriched genes showed highly significant overlaps with pathogen response genes whereas this was not the case for P. pacificus, indicating shifts in pathogen susceptibility that might be explained by altered feeding modes.
  
  
  CONCLUSIONS
  Our study reveals first insights into the evolution of feeding systems and the associated changes in intestinal gene expression that might have facilitated nematodes of the P. pacificus lineage to colonize new environments. These findings deepen our understanding about how morphological and genomic diversity is created during the course of evolution.
authors.affiliation: Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstr. 35-39, Tübingen, Germany. james.lightfoot@tuebingen.mpg.de.
authors.forename: James W
authors.initials: JW
authors.lastname: Lightfoot
authors.affiliation: Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Boots Science Building, Nottingham, UK. veeren.chauhan@nottingham.ac.uk.
authors.forename: Veeren M
authors.initials: VM
authors.lastname: Chauhan
authors.affiliation: Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Boots Science Building, Nottingham, UK. jon.aylott@nottingham.ac.uk.
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Aylott
authors.affiliation: Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstr. 35-39, Tübingen, Germany. christian.roedelsperger@tuebingen.mpg.de.
authors.forename: Christian
authors.initials: C
authors.lastname: Rödelsperger
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000382:microbiology; D017124:Conserved Sequence; D004926:Escherichia coli / Q000254:growth & development; D005247:Feeding Behavior / Q000502:physiology; D041981:Gastrointestinal Tract / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D017238:Genes, Helminth; D053823:Hedgehog Proteins / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics* / Q000382:microbiology; D015398:Signal Transduction; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D053823:Hedgehog Proteins