Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0466-2) contains supplementary material, which is available to authorized users.

Adult influence on juvenile phenotypes by stage-specific pheromone production

“…29, 2018; ( Supplementary Fig. 2) 30 , the most downstream enzyme in the β-oxidation pathway of 104 ascaroside synthesis 17 . Finally, we profiled the endo-metabolome of eggs, but find only 105 appreciable amounts of Asc#1,#9, #12, and Pasc#9, and little to no traces of the more complex 106 ascaroside derivatives ( Supplementary Fig.…”

The Regulation of Developmental Diapause is Coordinated with Molting and Olfaction

“…PPA10139 shares 89% 371 similarity with C. elegans HSD-2, which encodes one of three hydroxysteroid 372 dehydrogenases in C. elegans involved in the biosynthesis of dafachronic acids 373 [73]. Consistent with its potential role in repressing dauer formation, PPA10139 374 transcripts are significantly lower in DL than in the J2, J3, J4, and adult stages 375 (gene prediction Contig6-snapTAU.237) [74]. To confirm that the deletion of Ppa-376 hsd is solely responsible for the Daf-c phenotype of csu60, we made a construct 377 containing a ~2 kb promoter of PPA10139 driving its full-length cDNA to rescue 378 the csu60 deletion by transgene complementation.…”

“…To determine if the 414 mutated coding sequence is represented in the transcripts, we amplified and 415 sequenced mixed-stage tu391 cDNA for a few candidates, including the patched-416 related protein PPA21795 (Ppa-ptr-4), and confirmed the point mutation in the 417 transcript predicted to result in an amino acid substitution (Met>Lys). PPA21795 418 transcripts are also expressed at significantly lower levels in DL than in J2 and J3 419 larvae [74]. However, given the complexity of the PPA21795 exon-intron structure 420 (33 exons), we did not pursue transgenic rescue experiments to test if it is 421 responsible for the tu391 phenotypes.…”

“…Microarray and RNA-seq studies have shown substantial divergence of 542 dauer-specific genes between P. pacificus and C. elegans, as well as more 543 upregulated dauer-specific genes in P. pacificus than in C. elegans [74,86]. In P. 544 pacificus, the DAF-12/∆7-DA module is a shared regulatory target for both dauer 545 entry and mouth form dimorphism [37,87].…”

Comparative transcriptomics across nematode life cycles reveal gene expression conservation and correlated evolution in adjacent developmental stages

“…Although the LCE estimation revealed 336 strong concerted evolution between individual larval stages, an alternative explanation may 337 be the imperfect synchronization of worm culture in non-model organisms. For instance, the 338 staging protocol in P. pacificus was observed in major developmental transcriptome 339 clustering with a mixture of early larvae, late larvae, and adult (Baskaran et al 2015). 340…”