Evolution of the Largest Mammalian Genome

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 5 Ma. 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.

Genome diversity and species richness in mammals

“…The smallest diploid mammalian karyotype is found in the Indian muntjac deer (2n = 6-7) (Yang, Carter et al 1995). The largest, not surprisingly, is found in the red viscacha rat (2n = 102) (Evans, Upham et al 2017). Hence, karyotype diversity is an order of magnitude larger than genome size diversity in mammals.…”

“…Different animal taxa typically have characteristic ranges of genome size that can vary substantially between lineages and among groups. Salamanders, for example, have genome sizes ranging between 15 pg in the Desmognathus clade and 120 pg in the Necturus clade (Sessions 2008), whereas mammals have genome sizes ranging from 1.6 pg in bats to 9.2 pg in the red viscacha rat (Tympanoctomys barrerae) (Bromham 2011, Evans, Upham et al 2017, Kapusta, Suh et al 2017.…”

Meiotic drive shapes rates of karyotype evolution in mammals

“…The one possible exception is the red viscacha rat (Tympanoctomys barrerae) from Argentina. However, the evidence for and against polyploidy in this species is arguably inconclusive (Gallardo et al 1999;Svartman et al 2005;Teta et al 2014;Evans et al 2017). We chose to exclude this species from our dataset for three reasons.…”

Genetic mapping in polyploids

“…Polyploidy is also sometimes artificially induced in animals, for example in Pacific oysters (Crassostreae gigas) (Benabdelmouna and Ledu, 2015) or the silkmoth (Bombyx mori L.) (Rasmussen and Holm, 1979). There continues to be debate about whether any polyploid mammals exist, with the initial claim that the Argentinian red vizcacha rat (Tympanoctomys barrerae) is tetraploid (Gallardo et al, 1999) being more recently challenged in light of new data (Svartman et al, 2005;Evans et al, 2017).…”