Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genot...

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Autores principales:	Eddie K. H. Ho, Emily S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, Sarah Schaack
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/10eba345c52943858b3e0ecd4ed9c09e
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spelling	oai:doaj.org-article:10eba345c52943858b3e0ecd4ed9c09e2021-11-25T05:51:20ZEngines of change: Transposable element mutation rates are high and variable within Daphnia magna1553-73901553-7404https://doaj.org/article/10eba345c52943858b3e0ecd4ed9c09e2021-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594854/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10−5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome. Author summary Transposable elements (TEs) are a significant portion of most eukaryotic genomes, yet our understanding of their rates of mobility and their patterns of accumulation remain very limited. Here, we estimate genome-wide rates of gain and loss of TEs in Daphnia magna, a well-studied model organism in ecology, and compare these rates of mutation to the long-term accumulation of TEs in the genome. Rates vary remarkably among genotypes and populations, and between different types of TEs within the same lineage. Despite this variation, over long time periods, TE content in the genome is extremely similar across genotypes within the species. We compare our results to the few estimates available from other taxa, and argue that TEs are an important source of mutagenesis in the genome worthy of further investigation.Eddie K. H. HoEmily S. BellisJaclyn CalkinsJeffrey R. AdrionLeigh C. Latta IVSarah SchaackPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Eddie K. H. Ho Emily S. Bellis Jaclyn Calkins Jeffrey R. Adrion Leigh C. Latta IV Sarah Schaack Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
description	Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10−5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome. Author summary Transposable elements (TEs) are a significant portion of most eukaryotic genomes, yet our understanding of their rates of mobility and their patterns of accumulation remain very limited. Here, we estimate genome-wide rates of gain and loss of TEs in Daphnia magna, a well-studied model organism in ecology, and compare these rates of mutation to the long-term accumulation of TEs in the genome. Rates vary remarkably among genotypes and populations, and between different types of TEs within the same lineage. Despite this variation, over long time periods, TE content in the genome is extremely similar across genotypes within the species. We compare our results to the few estimates available from other taxa, and argue that TEs are an important source of mutagenesis in the genome worthy of further investigation.
format	article
author	Eddie K. H. Ho Emily S. Bellis Jaclyn Calkins Jeffrey R. Adrion Leigh C. Latta IV Sarah Schaack
author_facet	Eddie K. H. Ho Emily S. Bellis Jaclyn Calkins Jeffrey R. Adrion Leigh C. Latta IV Sarah Schaack
author_sort	Eddie K. H. Ho
title	Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
title_short	Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
title_full	Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
title_fullStr	Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
title_full_unstemmed	Engines of change: Transposable element mutation rates are high and variable within Daphnia magna
title_sort	engines of change: transposable element mutation rates are high and variable within daphnia magna
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/10eba345c52943858b3e0ecd4ed9c09e
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Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

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