Evolution of regulatory networks associated with traits under selection in cichlids.

Autor: Mehta TK; Earlham Institute (EI), Norwich, UK., Koch C; Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA., Nash W; Earlham Institute (EI), Norwich, UK., Knaack SA; Wisconsin Institute for Discovery (WID), Madison, USA., Sudhakar P; Earlham Institute (EI), Norwich, UK.; Quadram Institute, Norwich, UK., Olbei M; Earlham Institute (EI), Norwich, UK.; Quadram Institute, Norwich, UK., Bastkowski S; Earlham Institute (EI), Norwich, UK.; Quadram Institute, Norwich, UK., Penso-Dolfin L; Earlham Institute (EI), Norwich, UK., Korcsmaros T; Earlham Institute (EI), Norwich, UK.; Quadram Institute, Norwich, UK., Haerty W; Earlham Institute (EI), Norwich, UK., Roy S; Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA. sroy@biostat.wisc.edu.; Wisconsin Institute for Discovery (WID), Madison, USA. sroy@biostat.wisc.edu.; Department of Computer Sciences, UW Madison, Madison, USA. sroy@biostat.wisc.edu., Di-Palma F; Earlham Institute (EI), Norwich, UK. F.Di-Palma@uea.ac.uk.; Norwich Medical School, University of East Anglia, Norwich, UK. F.Di-Palma@uea.ac.uk.; School of Biological Sciences, University of East Anglia, Norwich, UK. F.Di-Palma@uea.ac.uk.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2021 Jan 08; Vol. 22 (1), pp. 25. Date of Electronic Publication: 2021 Jan 08.
DOI: 10.1186/s13059-020-02208-8
Abstrakt: Background: Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence.
Results: To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait-the visual system-for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids.
Conclusions: Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.
Databáze: MEDLINE
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