title: Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.
abstract: BACKGROUND
  The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom.
  
  
  RESULTS
  We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch.
  
  
  CONCLUSIONS
  We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales.
authors.affiliation: Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany. praveen.baskaran@tuebingen.mpg.de.
authors.forename: Praveen
authors.initials: P
authors.lastname: Baskaran
authors.affiliation: Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany. christian.roedelsperger@tuebingen.mpg.de.
authors.forename: Christian
authors.initials: C
authors.lastname: Rödelsperger
authors.affiliation: Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany. neel.prabh@tuebingen.mpg.de.
authors.forename: Neel
authors.initials: N
authors.lastname: Prabh
authors.affiliation: Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany. vahan.serobyan@tuebingen.mpg.de.
authors.forename: Vahan
authors.initials: V
authors.lastname: Serobyan
authors.affiliation: Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany. gabriel.markov@tuebingen.mpg.de.
authors.forename: Gabriel V
authors.initials: GV
authors.lastname: Markov
authors.affiliation: Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin-Buch, 13125, Germany. Antje.Hirsekorn@mdc-berlin.de.
authors.forename: Antje
authors.initials: A
authors.lastname: Hirsekorn
authors.affiliation: Max-Planck Institute for Biology of Aging, Joseph-Stelzmann-Str. 9b, Köln, 50866, Germany. christoph.dieterich@age.mpg.de.
authors.forename: Christoph
authors.initials: C
authors.lastname: Dieterich
mesh_terms: D000818:Animals; D005075:Biological Evolution; D017173:Caenorhabditis elegans / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D007814:Larva / Q000254:growth & development; D005810:Multigene Family; D009348:Nematoda / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny