A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to...

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Main Authors:	Gao, Dongying, Chen, Jinfeng, Chen, Mingsheng, Meyers, Blake C., Jackson, Scott
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281118/

id	pubmed-3281118
recordtype	oai_dc
spelling	pubmed-32811182012-02-22 A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes Gao, Dongying Chen, Jinfeng Chen, Mingsheng Meyers, Blake C. Jackson, Scott Research Article LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 50–80 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass. Public Library of Science 2012-02-16 /pmc/articles/PMC3281118/ /pubmed/22359654 http://dx.doi.org/10.1371/journal.pone.0032010 Text en Jackson et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Gao, Dongying Chen, Jinfeng Chen, Mingsheng Meyers, Blake C. Jackson, Scott
spellingShingle	Gao, Dongying Chen, Jinfeng Chen, Mingsheng Meyers, Blake C. Jackson, Scott A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
author_facet	Gao, Dongying Chen, Jinfeng Chen, Mingsheng Meyers, Blake C. Jackson, Scott
author_sort	Gao, Dongying
title	A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
title_short	A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
title_full	A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
title_fullStr	A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
title_full_unstemmed	A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
title_sort	highly conserved, small ltr retrotransposon that preferentially targets genes in grass genomes
description	LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 50–80 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281118/
_version_	1611506618959134720

A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

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