Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

Abstract

BackgroundSignalling pathways underlie development, behaviour and pathology. To understand patterns in the evolution of signalling pathways, we undertook a comprehensive investigation of the pathways that control the switch between growth and developmentally quiescent dauer in 24 species of nematodes spanning the phylum.ResultsOur analysis of 47 genes across these species indicates that the pathways and their interactions are not conserved throughout the Nematoda. For example, the TGF-β pathway was co-opted into dauer control relatively late in a lineage that led to the model species Caenorhabditis elegans. We show molecular adaptations described in C. elegans that are restricted to its genus or even just to the species. Similarly, our analyses both identify species where particular genes have been lost and situations where apparently incorrect orthologues have been identified.ConclusionsOur analysis also highlights the difficulties of working with genome sequences from non-model species as reliance on the published gene models would have significantly restricted our understanding of how signalling pathways evolve. Our approach therefore offers a robust standard operating procedure for genomic comparisons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2770-7) contains supplementary material, which is available to authorized users.

Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages

“…Given that gene absence in a transcriptome might be simply due to expression changes, we performed an analysis (see STAR Methods) combining transcriptomic and genome data for P. pacificus [11] and P. exspectatus [12] as well as the transcriptome assembly of P. arcanus to test whether predicted losses in P. pacificus and P. exspectatus lacked orthologous sequences in genomic data. Even though further analysis will be needed to confirm gene losses in individual cases [13,14], our genome-wide analysis shows that 80% of predicted gene losses were indeed supported by genomic data ( Figure 1C). Thus, our phylotranscriptomic analysis strongly supports the conclusion of an overall higher rate of gene loss in hermaphroditic lineages as originally observed in Caenorhabditis [4,5,15].…”

Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes

“…Consistent with the phylogeny that underlies our study design, longer branches between extant taxa and more ancestral inner nodes (Susoy et al 2016) show higher numbers of species-specific duplications and gene losses. Because it can be difficult to differentiate true losses from missing evidence (Gilabert et al 2016;Rödelsperger 2018), the numbers of species-specific gene losses within most of the sampled Pristionchus species seem to be rather stable and only increase in the two outgroups (Fig. 1C).…”

A nematode retrotransposon in the common shrew: horizontal transfer between parasite and host

“…Within the mammals, our searches showed that RTE1 Sar is found only in S. araneus. We have previously shown that mis-assembly of the genome can be responsible for the perceived absence of a gene [23], which can also be the case for a transposon if only few, old or fragmented copies exist. Therefore, we searched for RTE1 Sar in the short sequence reads for species of the order of Eulipotyphla, for which genome projects are available: the European hedgehog Erinaceus europaeus, the Hispaniolan solenodon Solenodon paradoxus woodi and the star-nosed mole Condylura cristata, each representing a different family within the Eulipotyphyla.…”