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The rubber tree genome shows expansion of gene family associated with rubber biosynthesis

Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity...

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Autores principales: Lau, Nyok-Sean, Makita, Yuko, Kawashima, Mika, Taylor, Todd D., Kondo, Shinji, Othman, Ahmad Sofiman, Shu-Chien, Alexander Chong, Matsui, Minami
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008842/
https://www.ncbi.nlm.nih.gov/pubmed/27339202
http://dx.doi.org/10.1038/srep28594
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author Lau, Nyok-Sean
Makita, Yuko
Kawashima, Mika
Taylor, Todd D.
Kondo, Shinji
Othman, Ahmad Sofiman
Shu-Chien, Alexander Chong
Matsui, Minami
author_facet Lau, Nyok-Sean
Makita, Yuko
Kawashima, Mika
Taylor, Todd D.
Kondo, Shinji
Othman, Ahmad Sofiman
Shu-Chien, Alexander Chong
Matsui, Minami
author_sort Lau, Nyok-Sean
collection PubMed
description Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.
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spelling pubmed-50088422016-09-08 The rubber tree genome shows expansion of gene family associated with rubber biosynthesis Lau, Nyok-Sean Makita, Yuko Kawashima, Mika Taylor, Todd D. Kondo, Shinji Othman, Ahmad Sofiman Shu-Chien, Alexander Chong Matsui, Minami Sci Rep Article Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree. Nature Publishing Group 2016-06-24 /pmc/articles/PMC5008842/ /pubmed/27339202 http://dx.doi.org/10.1038/srep28594 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Lau, Nyok-Sean
Makita, Yuko
Kawashima, Mika
Taylor, Todd D.
Kondo, Shinji
Othman, Ahmad Sofiman
Shu-Chien, Alexander Chong
Matsui, Minami
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title_full The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title_fullStr The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title_full_unstemmed The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title_short The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
title_sort rubber tree genome shows expansion of gene family associated with rubber biosynthesis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008842/
https://www.ncbi.nlm.nih.gov/pubmed/27339202
http://dx.doi.org/10.1038/srep28594
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