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06 24, 2016;6 28594.

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

Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu-Chien, Minami Matsui
Author Information
  1. Nyok-Sean Lau: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.
  2. Yuko Makita: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
  3. Mika Kawashima: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
  4. Todd D Taylor: Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
  5. Shinji Kondo: Transdisciplinary Research Integration Center, National Institute of Polar Research, Tachikawa, Tokyo 190-8518, Japan.
  6. Ahmad Sofiman Othman: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.
  7. Alexander Chong Shu-Chien: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.
  8. Minami Matsui: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
PMID: 27339202 DOI: 10.1038/srep28594

Abstract

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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Grants

  1. UL1 TR001863/NCATS NIH HHS

MeSH Term

Genome, Plant
Genomics
Hevea
Latex
Plant Proteins
RNA, Plant
Rubber
Sequence Analysis, RNA
Transcriptome

Chemicals

Latex
Plant Proteins
RNA, Plant
Rubber
Journal Article Research Support, Non-U.S. Gov't

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