The genomic ecosystem of transposable elements in maize.

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past tra...

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Autores principales:	Michelle C Stitzer, Sarah N Anderson, Nathan M Springer, Jeffrey Ross-Ibarra
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/c6b1e467813e4afc96d9a21d072dd984
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spelling	oai:doaj.org-article:c6b1e467813e4afc96d9a21d072dd9842021-12-02T20:03:31ZThe genomic ecosystem of transposable elements in maize.1553-73901553-740410.1371/journal.pgen.1009768https://doaj.org/article/c6b1e467813e4afc96d9a21d072dd9842021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009768https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.Michelle C StitzerSarah N AndersonNathan M SpringerJeffrey Ross-IbarraPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 10, p e1009768 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Michelle C Stitzer Sarah N Anderson Nathan M Springer Jeffrey Ross-Ibarra The genomic ecosystem of transposable elements in maize.
description	Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
format	article
author	Michelle C Stitzer Sarah N Anderson Nathan M Springer Jeffrey Ross-Ibarra
author_facet	Michelle C Stitzer Sarah N Anderson Nathan M Springer Jeffrey Ross-Ibarra
author_sort	Michelle C Stitzer
title	The genomic ecosystem of transposable elements in maize.
title_short	The genomic ecosystem of transposable elements in maize.
title_full	The genomic ecosystem of transposable elements in maize.
title_fullStr	The genomic ecosystem of transposable elements in maize.
title_full_unstemmed	The genomic ecosystem of transposable elements in maize.
title_sort	genomic ecosystem of transposable elements in maize.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c6b1e467813e4afc96d9a21d072dd984
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The genomic ecosystem of transposable elements in maize.

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