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.
Highlights
Signalling pathways underlie development, behaviour and pathology
While the pathways controlling the dauer transition are generally well-conserved, we identify an evolutionary path of gene duplication and pathway co-option that leads from the ancestral nematode to C. elegans
For each C. elegans protein that seeded a search, we carried out a manual inspection for both positive and negative results
Summary
Signalling 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. While there are a limited number of pathway types, they can vary in terms of membership and can be strung together to form complex interactions [1]. Given their role in development and in human disease, understanding how these pathways evolve is an important, outstanding question. The surge of metazoan genomes has created the temptation to search for orthologous genes involved in a pathway of interest and to offer some biological interpretations. Such comparisons are a routine feature of publications announcing new genomes. This is an important pitfall for comparative genomics and molecular biology analyses; the non-
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