Genome stability is in the eye of the beholder: CR1 retrotransposon activity varies significantly across avian diversity

Galbraith, James D., Kortschak, Robert Daniel, Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992 and Adelson, David L. (2021) Genome stability is in the eye of the beholder: CR1 retrotransposon activity varies significantly across avian diversity. Genome Biology and Evolution, 13 (12). ISSN 1759-6653

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Abstract

Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Biological Sciences
Related URLs:	https://academic.oup.com/gbe/article/doi...
Depositing User:	LivePure Connector
Date Deposited:	15 Dec 2021 09:30
Last Modified:	17 Oct 2024 00:24
URI:	https://ueaeprints.uea.ac.uk/id/eprint/82690
DOI:	10.1093/gbe/evab259

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