Tempo and mode of gene duplication in mammalian ribosomal protein evolution.

Asav P Dharia,Matthew D Gajdosik,Ajay Obla,Amanda Simon,Craig E Nelson,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0111721

Abstract

Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism.

Highlights

Gene Duplication and Genome Evolution In 1970, Susumu Ohno hypothesized that gene duplication provided the raw material required for the diversification of gene function
76 Ribosomal Protein Family Member Analyses The first step of our pipeline identified all detectable duplicates of ribosomal protein (RP) genes in eight mammalian genomes
As we found significant association between species (p = 6.07e-17, two-way chi square test, Figure2B), all species were grouped for subsequent analyses

Summary

Introduction

Gene Duplication and Genome Evolution In 1970, Susumu Ohno hypothesized that gene duplication provided the raw material required for the diversification of gene function. A WGD is believed to have occurred in yeast [7], and several have been inferred in the teleost lineage [8]; while the last WGD believed to have occurred in the mammalian lineage took place before the emergence of modern mammals [9,10] Compared to these very large scale and rare events, duplicative transpositions and tandem duplications are likely to drive much of the duplication and loss giving rise to complex gene families. These are DNA-mediated processes that preserve varying amounts of the source gene’s intron-exon structure [4]. Recent interest in retrotransposition is highlighted by the identification of several functional retrogenes, such as Fgf and c1orf37-dup in mammals [16,17], and suggests that retroduplicaton may be a more important force in the evolution of complex gene families than has been widely appreciated

Methods

Results

Conclusion