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Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches
BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cu...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780850/ https://www.ncbi.nlm.nih.gov/pubmed/29363422 http://dx.doi.org/10.1186/s12864-017-4333-y |
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author | Makita, Yuko Kawashima, Mika Lau, Nyok Sean Othman, Ahmad Sofiman Matsui, Minami |
author_facet | Makita, Yuko Kawashima, Mika Lau, Nyok Sean Othman, Ahmad Sofiman Matsui, Minami |
author_sort | Makita, Yuko |
collection | PubMed |
description | BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS: A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. CONCLUSION: The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4333-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5780850 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57808502018-02-06 Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches Makita, Yuko Kawashima, Mika Lau, Nyok Sean Othman, Ahmad Sofiman Matsui, Minami BMC Genomics Research BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS: A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. CONCLUSION: The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4333-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-19 /pmc/articles/PMC5780850/ /pubmed/29363422 http://dx.doi.org/10.1186/s12864-017-4333-y Text en © The Author(s). 2018 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 Makita, Yuko Kawashima, Mika Lau, Nyok Sean Othman, Ahmad Sofiman Matsui, Minami Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title | Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title_full | Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title_fullStr | Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title_full_unstemmed | Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title_short | Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
title_sort | construction of pará rubber tree genome and multi-transcriptome database accelerates rubber researches |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780850/ https://www.ncbi.nlm.nih.gov/pubmed/29363422 http://dx.doi.org/10.1186/s12864-017-4333-y |
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