Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development.

Saara K Luna,Frédéric J J Chain

doi:10.3390/genes12101628

Saara K Luna, Frédéric J J Chain

Open Access

https://doi.org/10.3390/genes12101628

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Journal: Genes	Publication Date: Oct 16, 2021
Citations: 10	License type: CC BY 4.0

Affiliation: Harvard University, University of Massachusetts Lowell

Abstract

Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.

Highlights

Published: 16 October 2021Gene duplication is a common source of new genes [1]
Protein sequences were downloaded from Ensembl Protists [35] for all genomepredicted protein-coding genes in five dictyostelid species, referred to as dd: Dictyostelium discoideum, dp: Dictyostelium purpureum, df: Dictyostelium (Cavenderia) fasciculata, dl: Dictyostelium (Tieghemostelium) lacteum, and pp: Polysphondylium (Heterostelium) pallidum (Supplementary Table S1)
lineage-specific expansions (LSEs) were recovered by determining whether the species contributing the most genes to each orthogroup has disproportionately high numbers of paralogs relative to the orthogroup size

Summary

Introduction

Gene duplications occur frequently via mechanisms such as unequal crossing-over during homologous recombination, nonhomologous end joining during DNA repair, and retrotransposition [2,3]. These mutational events can result in variation in gene content across species, in part due to lineage-specific gene expansions [4]. Duplicate genes can undergo divergence from one another through the accumulation of mutations; as new mutations are likely deleterious, most duplicate genes are eventually pseudogenized or lost in the span of a few million years [5]. In particular those that arise de novo, are expected to emerge with low levels and narrow expression

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