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Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome

Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. Brassica nigra L. (B-genome) is one of three Brassica diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding....

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Autores principales: Perumal, Sampath, James, Brian, Tang, Lily, Kagale, Sateesh, Robinson, Stephen J., Yang, Tae-Jin, Parkin, Isobel A. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7385995/
https://www.ncbi.nlm.nih.gov/pubmed/32793262
http://dx.doi.org/10.3389/fpls.2020.01104
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author Perumal, Sampath
James, Brian
Tang, Lily
Kagale, Sateesh
Robinson, Stephen J.
Yang, Tae-Jin
Parkin, Isobel A. P.
author_facet Perumal, Sampath
James, Brian
Tang, Lily
Kagale, Sateesh
Robinson, Stephen J.
Yang, Tae-Jin
Parkin, Isobel A. P.
author_sort Perumal, Sampath
collection PubMed
description Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. Brassica nigra L. (B-genome) is one of three Brassica diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding. Two new high copy hAT MITE families (BniHAT-1 and BniHAT-2) from the B-genome were characterized and their prevalence assessed in the genomes of the related diploids, rapa L. (A) and Brassica oleracea L. (C). Both novel MITE families were present at high copy numbers in the B-genome with 434 and 331 copies of BniHAT-1 and BniHAT-2, respectively. Yet less than 20 elements were identified in the genome assemblies of the A, and C -genomes, supporting B-genome specific proliferation of these MITE families. Although apparently randomly distributed across the genome, 68 and 70% of the B-genome MITEs were present within 2 kb flanking regions of annotated genes suggesting they might influence gene expression and/or function. In addition, MITE derived microRNAs and transcription factor binding sites suggested a putative role in gene regulation. Age of insertion analysis revealed that the major proliferation of these elements occurred during 2–3 million years ago. Additionally, site-specific polymorphism analyses showed that 44% MITEs were undergoing active amplification into the B-genome. Overall, this study provides a comprehensive analysis of two high copy MITE families, which were specifically amplified in the B-genome, suggesting a potential role in shaping the Brassica B-genome.
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spelling pubmed-73859952020-08-12 Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome Perumal, Sampath James, Brian Tang, Lily Kagale, Sateesh Robinson, Stephen J. Yang, Tae-Jin Parkin, Isobel A. P. Front Plant Sci Plant Science Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. Brassica nigra L. (B-genome) is one of three Brassica diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding. Two new high copy hAT MITE families (BniHAT-1 and BniHAT-2) from the B-genome were characterized and their prevalence assessed in the genomes of the related diploids, rapa L. (A) and Brassica oleracea L. (C). Both novel MITE families were present at high copy numbers in the B-genome with 434 and 331 copies of BniHAT-1 and BniHAT-2, respectively. Yet less than 20 elements were identified in the genome assemblies of the A, and C -genomes, supporting B-genome specific proliferation of these MITE families. Although apparently randomly distributed across the genome, 68 and 70% of the B-genome MITEs were present within 2 kb flanking regions of annotated genes suggesting they might influence gene expression and/or function. In addition, MITE derived microRNAs and transcription factor binding sites suggested a putative role in gene regulation. Age of insertion analysis revealed that the major proliferation of these elements occurred during 2–3 million years ago. Additionally, site-specific polymorphism analyses showed that 44% MITEs were undergoing active amplification into the B-genome. Overall, this study provides a comprehensive analysis of two high copy MITE families, which were specifically amplified in the B-genome, suggesting a potential role in shaping the Brassica B-genome. Frontiers Media S.A. 2020-07-21 /pmc/articles/PMC7385995/ /pubmed/32793262 http://dx.doi.org/10.3389/fpls.2020.01104 Text en Copyright © 2020 Perumal, James, Tang, Kagale, Robinson, Yang and Parkin http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Perumal, Sampath
James, Brian
Tang, Lily
Kagale, Sateesh
Robinson, Stephen J.
Yang, Tae-Jin
Parkin, Isobel A. P.
Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title_full Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title_fullStr Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title_full_unstemmed Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title_short Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome
title_sort characterization of b-genome specific high copy hat mite families in brassica nigra genome
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7385995/
https://www.ncbi.nlm.nih.gov/pubmed/32793262
http://dx.doi.org/10.3389/fpls.2020.01104
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