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Slow DNA loss in the gigantic genomes of salamanders

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dc.contributor.authorSun, Cheng, author
dc.contributor.authorArriaza, José R. López, author
dc.contributor.authorMueller, Rachel Lockridge, author
dc.contributor.authorOxford University Press, publisher
dc.date.accessioned2007-01-03T05:34:21Z
dc.date.available2007-01-03T05:34:21Z
dc.date.issued2012
dc.descriptionAll data used in this study were obtained from public databases.
dc.description.abstractEvolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ~1-30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes - the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis, Danio rerio, Gallus gallus, Homo sapiens, and Xenopus tropicalis. Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.
dc.description.sponsorshipPublished with support from the Colorado State University Libraries Open Access Research and Scholarship Fund.
dc.format.mediumborn digital
dc.format.mediumarticles
dc.identifier.bibliographicCitationSun, Cheng, José R. López Arriaza, and Rachel Lockridge Mueller, Slow DNA Loss in the Gigantic Genomes of Salamanders. Genome Biology and Evolution 4, no. 12 (2012): 1340-1348. http://dx.doi.org/10.1093/gbe/evs103
dc.identifier.doihttps://dx.doi.org/10.1093/gbe/evs103
dc.identifier.urihttp://hdl.handle.net/10217/79233
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartofOpen Access Research and Scholarship Fund (OARS)
dc.rights.licenseThis article is open access and distributed under the terms and conditions of the Creative Commons Attribution 3.0 Unported (CC BY 3.0).
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectgenome size
dc.subjectmutation
dc.subjectindel spectrum
dc.subjectdeletion
dc.subjectinsertion
dc.subjecttransposable element
dc.titleSlow DNA loss in the gigantic genomes of salamanders
dc.typeText

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