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P-MITE: a database for plant miniature inverted-repeat transposable elements

Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MIT...

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Detalles Bibliográficos
Autores principales: Chen, Jiongjiong, Hu, Qun, Zhang, Yu, Lu, Chen, Kuang, Hanhui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964958/
https://www.ncbi.nlm.nih.gov/pubmed/24174541
http://dx.doi.org/10.1093/nar/gkt1000
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author Chen, Jiongjiong
Hu, Qun
Zhang, Yu
Lu, Chen
Kuang, Hanhui
author_facet Chen, Jiongjiong
Hu, Qun
Zhang, Yu
Lu, Chen
Kuang, Hanhui
author_sort Chen, Jiongjiong
collection PubMed
description Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MITE-Hunter and/or Repetitive Sequence with Precise Boundaries (RSPB). MITEs were found in all, but one (Cyanidioschyzon merolae), species. Combined with the MITEs identified previously from the rice genome, >2.3 million sequences from 3527 MITE families were obtained from 41 plant species. In general, higher plants contain more MITEs than lower plants, with a few exceptions such as papaya, with only 538 elements. The largest number of MITEs is found in apple, with 237 302 MITE sequences. The number of MITE sequences in a genome is significantly correlated with genome size. A series of databases (plant MITE databases, P-MITE), available online at http://pmite.hzau.edu.cn/django/mite/, was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used to study the origin and amplification of MITEs, MITE-derived small RNAs and roles of MITEs on gene and genome evolution.
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spelling pubmed-39649582014-03-25 P-MITE: a database for plant miniature inverted-repeat transposable elements Chen, Jiongjiong Hu, Qun Zhang, Yu Lu, Chen Kuang, Hanhui Nucleic Acids Res VII. Plant databases Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MITE-Hunter and/or Repetitive Sequence with Precise Boundaries (RSPB). MITEs were found in all, but one (Cyanidioschyzon merolae), species. Combined with the MITEs identified previously from the rice genome, >2.3 million sequences from 3527 MITE families were obtained from 41 plant species. In general, higher plants contain more MITEs than lower plants, with a few exceptions such as papaya, with only 538 elements. The largest number of MITEs is found in apple, with 237 302 MITE sequences. The number of MITE sequences in a genome is significantly correlated with genome size. A series of databases (plant MITE databases, P-MITE), available online at http://pmite.hzau.edu.cn/django/mite/, was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used to study the origin and amplification of MITEs, MITE-derived small RNAs and roles of MITEs on gene and genome evolution. Oxford University Press 2014-01-01 2013-10-29 /pmc/articles/PMC3964958/ /pubmed/24174541 http://dx.doi.org/10.1093/nar/gkt1000 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle VII. Plant databases
Chen, Jiongjiong
Hu, Qun
Zhang, Yu
Lu, Chen
Kuang, Hanhui
P-MITE: a database for plant miniature inverted-repeat transposable elements
title P-MITE: a database for plant miniature inverted-repeat transposable elements
title_full P-MITE: a database for plant miniature inverted-repeat transposable elements
title_fullStr P-MITE: a database for plant miniature inverted-repeat transposable elements
title_full_unstemmed P-MITE: a database for plant miniature inverted-repeat transposable elements
title_short P-MITE: a database for plant miniature inverted-repeat transposable elements
title_sort p-mite: a database for plant miniature inverted-repeat transposable elements
topic VII. Plant databases
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964958/
https://www.ncbi.nlm.nih.gov/pubmed/24174541
http://dx.doi.org/10.1093/nar/gkt1000
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