title: The rubber tree genome shows expansion of gene family associated with rubber biosynthesis.
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.
authors.affiliation: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.|Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Nyok-Sean
authors.initials: NS
authors.lastname: Lau
authors.affiliation: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.affiliation: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Mika
authors.initials: M
authors.lastname: Kawashima
authors.affiliation: Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Todd D
authors.initials: TD
authors.lastname: Taylor
authors.affiliation: Transdisciplinary Research Integration Center, National Institute of Polar Research, Tachikawa, Tokyo 190-8518, Japan.
authors.forename: Shinji
authors.initials: S
authors.lastname: Kondo
authors.affiliation: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.|School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
authors.forename: Ahmad Sofiman
authors.initials: AS
authors.lastname: Othman
authors.affiliation: Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.|School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
authors.forename: Alexander Chong
authors.initials: AC
authors.lastname: Shu-Chien
authors.affiliation: Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Minami
authors.initials: M
authors.lastname: Matsui
mesh_terms: D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D028482:Hevea / Q000235:genetics*; D007840:Latex / Q000096:biosynthesis*; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012408:Rubber / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome / Q000235:genetics
chemical_list: D007840:Latex; D010940:Plant Proteins; D018749:RNA, Plant; D012408:Rubber