Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes

Mbaye Tine; Heiner Kuhl; Peter R Teske; Richard Reinhardt

doi:10.1002/ece3.7507

Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes

Ecol Evol. 2021 Apr 2;11(11):6546-6557. doi: 10.1002/ece3.7507. eCollection 2021 Jun.

Authors

Mbaye Tine^{1

2}, Heiner Kuhl³, Peter R Teske⁴, Richard Reinhardt²

Affiliations

¹ UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (S2ATA) Université Gaston Berger (UGB) Saint-Louis Senegal.
² Genome Centre at the Max-Planck Institute for Plant Breeding Research Köln Germany.
³ Department of Ecophysiology and Aquaculture Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany.
⁴ Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Johannesburg South Africa.

Abstract

Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.

Keywords: Dicentrarchus labrax; European sea bass; comparative genomics; evolution; promoter; single‐exon gene.