Evolution of the largest mammalian genome

Ben J. Evans, Nathan S. Upham, Goeffrey B. Golding, Ricardo A. Ojeda, Agustina A. Ojeda

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae.

Original languageEnglish (US)
Pages (from-to)1711-1724
Number of pages14
JournalGenome biology and evolution
Volume9
Issue number6
DOIs
StatePublished - Jun 2017
Externally publishedYes

Keywords

  • Caviomorpha
  • Mammals
  • Octodontidae
  • Repetitive DNA
  • Rodentia
  • Whole genome duplication

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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