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Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species

BACKGROUND: Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS: We developed the software easy-to-annotate Helitron (EAHelitron), a...

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Autores principales: Hu, Kaining, Xu, Kai, Wen, Jing, Yi, Bin, Shen, Jinxiong, Ma, Chaozhi, Fu, Tingdong, Ouyang, Yidan, Tu, Jinxing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591975/
https://www.ncbi.nlm.nih.gov/pubmed/31234777
http://dx.doi.org/10.1186/s12859-019-2945-8
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author Hu, Kaining
Xu, Kai
Wen, Jing
Yi, Bin
Shen, Jinxiong
Ma, Chaozhi
Fu, Tingdong
Ouyang, Yidan
Tu, Jinxing
author_facet Hu, Kaining
Xu, Kai
Wen, Jing
Yi, Bin
Shen, Jinxiong
Ma, Chaozhi
Fu, Tingdong
Ouyang, Yidan
Tu, Jinxing
author_sort Hu, Kaining
collection PubMed
description BACKGROUND: Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS: We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes. CONCLUSION: EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2945-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-65919752019-07-08 Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species Hu, Kaining Xu, Kai Wen, Jing Yi, Bin Shen, Jinxiong Ma, Chaozhi Fu, Tingdong Ouyang, Yidan Tu, Jinxing BMC Bioinformatics Research Article BACKGROUND: Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS: We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes. CONCLUSION: EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2945-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-06-24 /pmc/articles/PMC6591975/ /pubmed/31234777 http://dx.doi.org/10.1186/s12859-019-2945-8 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Hu, Kaining
Xu, Kai
Wen, Jing
Yi, Bin
Shen, Jinxiong
Ma, Chaozhi
Fu, Tingdong
Ouyang, Yidan
Tu, Jinxing
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title_full Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title_fullStr Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title_full_unstemmed Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title_short Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
title_sort helitron distribution in brassicaceae and whole genome helitron density as a character for distinguishing plant species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591975/
https://www.ncbi.nlm.nih.gov/pubmed/31234777
http://dx.doi.org/10.1186/s12859-019-2945-8
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