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PmiREN2.0: from data annotation to functional exploration of plant microRNAs
Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide use...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728213/ https://www.ncbi.nlm.nih.gov/pubmed/34554254 http://dx.doi.org/10.1093/nar/gkab811 |
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author | Guo, Zhonglong Kuang, Zheng Zhao, Yongxin Deng, Yang He, Hao Wan, Miaomiao Tao, Yihan Wang, Dong Wei, Jianhua Li, Lei Yang, Xiaozeng |
author_facet | Guo, Zhonglong Kuang, Zheng Zhao, Yongxin Deng, Yang He, Hao Wan, Miaomiao Tao, Yihan Wang, Dong Wei, Jianhua Li, Lei Yang, Xiaozeng |
author_sort | Guo, Zhonglong |
collection | PubMed |
description | Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants. |
format | Online Article Text |
id | pubmed-8728213 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87282132022-01-05 PmiREN2.0: from data annotation to functional exploration of plant microRNAs Guo, Zhonglong Kuang, Zheng Zhao, Yongxin Deng, Yang He, Hao Wan, Miaomiao Tao, Yihan Wang, Dong Wei, Jianhua Li, Lei Yang, Xiaozeng Nucleic Acids Res Database Issue Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants. Oxford University Press 2021-09-23 /pmc/articles/PMC8728213/ /pubmed/34554254 http://dx.doi.org/10.1093/nar/gkab811 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Guo, Zhonglong Kuang, Zheng Zhao, Yongxin Deng, Yang He, Hao Wan, Miaomiao Tao, Yihan Wang, Dong Wei, Jianhua Li, Lei Yang, Xiaozeng PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title | PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title_full | PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title_fullStr | PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title_full_unstemmed | PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title_short | PmiREN2.0: from data annotation to functional exploration of plant microRNAs |
title_sort | pmiren2.0: from data annotation to functional exploration of plant micrornas |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728213/ https://www.ncbi.nlm.nih.gov/pubmed/34554254 http://dx.doi.org/10.1093/nar/gkab811 |
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