An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
J. L. Steenwyk et al. "An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function" Science Advances 8 (2022) [DOI: 10.1126/sciadv.abn0105]
The evolutionary rates of functionally related genes often covary. We present a gene coevolution network inferred from examining nearly 3 million orthologous gene pairs from 332 budding yeast species spanning ~400 million years of evolution. Network modules provide insight into cellular and genomic structure and function. Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker’s yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity. Mapping the network onto the chromosomes of S. cerevisiae and Candida albicans revealed that coevolving orthologous genes are not physically clustered in either species; rather, they are often located on different chromosomes or far apart on the same chromosome. The coevolution network captures the hierarchy of cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as a linked ensemble of genes.
A web application, The budding yeast coevolution network is available on GitHub. All data (including single gene phylogenies used to examine coevolution and Pearson covariation coefficients among relative evolutionary rates for all pairwise combinations of orthologous groups of genes) and code (including the code of the web application The budding yeast coevolution network) can be found on figshare.