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PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study
Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10325485/ https://www.ncbi.nlm.nih.gov/pubmed/37410918 http://dx.doi.org/10.1093/database/baad050 |
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author | Hu, Jian Huang, Baisha Yin, Hao Qi, Kaijie Jia, Yuanyuan Xie, Zhihua Gao, Yuan Li, Hongxiang Li, Qionghou Wang, Zewen Zou, Ying Zhang, Shaoling Qiao, Xin |
author_facet | Hu, Jian Huang, Baisha Yin, Hao Qi, Kaijie Jia, Yuanyuan Xie, Zhihua Gao, Yuan Li, Hongxiang Li, Qionghou Wang, Zewen Zou, Ying Zhang, Shaoling Qiao, Xin |
author_sort | Hu, Jian |
collection | PubMed |
description | Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn |
format | Online Article Text |
id | pubmed-10325485 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103254852023-07-07 PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study Hu, Jian Huang, Baisha Yin, Hao Qi, Kaijie Jia, Yuanyuan Xie, Zhihua Gao, Yuan Li, Hongxiang Li, Qionghou Wang, Zewen Zou, Ying Zhang, Shaoling Qiao, Xin Database (Oxford) Original Article Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn Oxford University Press 2023-07-06 /pmc/articles/PMC10325485/ /pubmed/37410918 http://dx.doi.org/10.1093/database/baad050 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://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 Hu, Jian Huang, Baisha Yin, Hao Qi, Kaijie Jia, Yuanyuan Xie, Zhihua Gao, Yuan Li, Hongxiang Li, Qionghou Wang, Zewen Zou, Ying Zhang, Shaoling Qiao, Xin PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title | PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title_full | PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title_fullStr | PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title_full_unstemmed | PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title_short | PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study |
title_sort | pearmodb: a multiomics database for pear (pyrus) genomics, genetics and breeding study |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10325485/ https://www.ncbi.nlm.nih.gov/pubmed/37410918 http://dx.doi.org/10.1093/database/baad050 |
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