Family size and turnover rates among several classes of small non-protein-coding RNA genes in caenorhabditis nematodes

Paul Po Shen Wang, Ilya Ruvinsky*

*Corresponding author for this work

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

It is important to understand the forces that shape the size and evolutionary histories of gene families. Here, we investigated the evolution of non-protein-coding RNA genes in the genomes of Caenorhabditis nematodes. We specifically focused on nested arrangements, that is, cases in which an RNA gene is entirely contained in an intron of another gene. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. Two distinct patterns are evident in the data. Genes encoding small nuclear RNAs (snRNAs) and transfer RNAs form large families, which have persisted since before the common ancestor of Metazoa. Yet, individual genes die relatively rapidly, with few orthologs having survived since the divergence of Caenorhabditis elegans and Caenorhabditis briggsae. In contrast, genes encoding small nucleolar RNAs (snoRNAs) are either single-copy or form small families. Individual snoRNAs turn over at a relatively slow rate - most C. elegans genes have clearly identifiable orthologs in C. briggsae. We also found that in Drosophila, genes from larger snRNA families die at a faster rate than their counterparts from single-gene families. These results suggest that a relationship between family size and the rate of gene turnover may be a general feature of genome evolution.

Original languageEnglish (US)
Pages (from-to)565-574
Number of pages10
JournalGenome biology and evolution
Volume4
Issue number4
DOIs
StatePublished - Sep 24 2012

Keywords

  • Birth-and-death
  • C. elegans
  • Evolution
  • Gene family
  • Nested genes
  • Small RNA

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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