ConTEdb: a comprehensive database of transposable elements in conifers

Conifers are the largest and most ubiquitous group of gymnosperms and have significant ecological significance and economic importance. However, the huge and complex genomes have hindered the sequencing and mining of conifer genomes. In this study, we identified 413 423 transposable elements (TEs) f...

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Detalles Bibliográficos
Autores principales: Yi, Fei, Ling, Juanjuan, Xiao, Yao, Zhang, Hanguo, Ouyang, Fangqun, Wang, Junhui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Original Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301336/
https://www.ncbi.nlm.nih.gov/pubmed/30576494
http://dx.doi.org/10.1093/database/bay131
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author Yi, Fei
Ling, Juanjuan
Xiao, Yao
Zhang, Hanguo
Ouyang, Fangqun
Wang, Junhui
author_facet Yi, Fei
Ling, Juanjuan
Xiao, Yao
Zhang, Hanguo
Ouyang, Fangqun
Wang, Junhui
author_sort Yi, Fei
collection PubMed
description Conifers are the largest and most ubiquitous group of gymnosperms and have significant ecological significance and economic importance. However, the huge and complex genomes have hindered the sequencing and mining of conifer genomes. In this study, we identified 413 423 transposable elements (TEs) from Picea abies, Picea glauca and Pinus taeda using a combination of multiple approaches and classified them into 11 133 families. A comprehensive web-based database, ConTEdb, was constructed and served for researchers. ConTEdb enables users to browse, retrieve and download the TE sequences from the database. Several analysis tools are integrated into ConTEdb to help users mine the TE data easily and effectively. In summary, ConTEdb provides a platform to study TE biology and functional genomics in conifers.
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spelling pubmed-63013362018-12-27 ConTEdb: a comprehensive database of transposable elements in conifers Yi, Fei Ling, Juanjuan Xiao, Yao Zhang, Hanguo Ouyang, Fangqun Wang, Junhui Database (Oxford) Original Article Conifers are the largest and most ubiquitous group of gymnosperms and have significant ecological significance and economic importance. However, the huge and complex genomes have hindered the sequencing and mining of conifer genomes. In this study, we identified 413 423 transposable elements (TEs) from Picea abies, Picea glauca and Pinus taeda using a combination of multiple approaches and classified them into 11 133 families. A comprehensive web-based database, ConTEdb, was constructed and served for researchers. ConTEdb enables users to browse, retrieve and download the TE sequences from the database. Several analysis tools are integrated into ConTEdb to help users mine the TE data easily and effectively. In summary, ConTEdb provides a platform to study TE biology and functional genomics in conifers. Oxford University Press 2018-12-17 /pmc/articles/PMC6301336/ /pubmed/30576494 http://dx.doi.org/10.1093/database/bay131 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Yi, Fei
Ling, Juanjuan
Xiao, Yao
Zhang, Hanguo
Ouyang, Fangqun
Wang, Junhui
ConTEdb: a comprehensive database of transposable elements in conifers
title ConTEdb: a comprehensive database of transposable elements in conifers
title_full ConTEdb: a comprehensive database of transposable elements in conifers
title_fullStr ConTEdb: a comprehensive database of transposable elements in conifers
title_full_unstemmed ConTEdb: a comprehensive database of transposable elements in conifers
title_short ConTEdb: a comprehensive database of transposable elements in conifers
title_sort contedb: a comprehensive database of transposable elements in conifers
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301336/
https://www.ncbi.nlm.nih.gov/pubmed/30576494
http://dx.doi.org/10.1093/database/bay131
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