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.

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions

“…Because of its genome size and high repeat content (Lau et al, 2016; Tang et al, 2016), genetic analysis of the species represents considerable obstacles to breeding, and several methodologies must be used to better understand its organization (Fierst, 2015). …”

Pemanfaatan bioinformatika dalam bidang pertanian dan kesehatan (The utilization of bioinformatics in the field of agriculture and health)

“…Penelitian terkait sekuensing genom tanaman telah dilakukan pada padi dan jagung sejak 19 tahun yang lalu (COE 1998;Goff et al, 2002). Beberapa contoh lain genom lengkap dari spesies tanaman yang sudah disekuens dalam kurun waktu 10 tahun terakhir adalah tanaman kentang, tomat, kacang kedelai, rumput, kelapa sawit, karet, kopi dan tebu (Haas et al, 2009;Schmutz et al, 2010;Vogel et al, 2010;Xu et al, 2011;Sato et al, 2012;Singh et al, 2013;Denoeud et al, 2014;de Setta et al, 2014;Lau et al, 2016;Tang et al, 2016). Sebagian basis data terkait genom tanaman tersebut bersifat publik atau disebut open access sehingga dapat digunakan dalam penelitian lanjutan oleh para peneliti di seluruh dunia.…”

Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

“…Oleh karena itu, pendekatan in silico melalui bioinformatika dapat digunakan untuk mempercepat analisis dalam prediksi famili gen PI (Penders et al, 2008). Selain itu, informasi genom karet dari klon RRIM 600 dan Reyan 7-33-97 telah tersedia dan dapat diakses secara daring pada basis data European Nucleotide Archive (ENA) (Lau et al, 2016;Rahman et al, 2013;Tang et al, 2016).…”