The rubber tree genome reveals new insights into rubber production and species adaptation

Abstract

The Para rubber tree (Hevea brasiliensis) is an economically important tropical tree species that produces natural rubber, an essential industrial raw material. Here we present a high-quality genome assembly of this species (1.37 Gb, scaffold N50 = 1.28 Mb) that covers 93.8% of the genome (1.47 Gb) and harbours 43,792 predicted protein-coding genes. A striking expansion of the REF/SRPP (rubber elongation factor/small rubber particle protein) gene family and its divergence into several laticifer-specific isoforms seem crucial for rubber biosynthesis. The REF/SRPP family has isoforms with sizes similar to or larger than SRPP1 (204 amino acids) in 17 other plants examined, but no isoforms with similar sizes to REF1 (138 amino acids), the predominant molecular variant. A pivotal point in Hevea evolution was the emergence of REF1, which is located on the surface of large rubber particles that account for 93% of rubber in the latex (despite constituting only 6% of total rubber particles, large and small). The stringent control of ethylene synthesis under active ethylene signalling and response in laticifers resolves a longstanding mystery of ethylene stimulation in rubber production. Our study, which includes the re-sequencing of five other Hevea cultivars and extensive RNA-seq data, provides a valuable resource for functional genomics and tools for breeding elite Hevea cultivars.

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

“…6, the results from sequencing‐based expression analyses were broadly similar to the qPCR results at least one time point post treatment. The RNA‐seq data were also verified by our published analyses 38, 49. Above all, we can verify that the results of the RNA‐seq analyses on HbCPK genes are authentic.…”

“…M. esculenta, R. communis A. thaliana, P. trichocarpa , and O. sativa . In the case of H. brasiliensis , two sets of Solexa sequencing data were used, one from the NCBI SRA database (http://www.ncbi.nlm.nih.gov/nuccore/448814761) and the other from our own data 38. As shown in Fig.…”

“…The genome and protein sequences of A. thaliana , O. sativa , P. trichocarpa , M. esculenta , and R. communis were downloaded from Phytozome v10 (http://www.phytozome.net/). The H. brasiliensis genome and transcriptome data were obtained from GenBank (http://www.ncbi.nlm.nih.gov/nuccore/448814761) and our own data 38. Local BLAST alignment was performed using published CDPK and CRK sequences form A. thaliana , P. trichocarpa , and O. sativa as queries to search against the deduced proteome of each species for the candidate CDPK s and CRK s from H. brasiliensis , A. thaliana, O. sativa, P. trichocarpa, M. esculenta , and R. communis .…”

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).…”

“…Pra-perlakuan sekuen genom utuh dan sortasi scaffold pada tanaman karet Genom tanaman karet (H. brasiliensis) klon Reyan 7-33-97 telah berhasil dipetakan oleh Tang et al (2016). Perakitan genom tanaman karet sebesar 1,37 Gb melingkupi 93,8% dari total ukuran genom karet (1,46 Gb), diketahui memiliki jumlah scaffold sebanyak 7453 scaffold (N50 scaffold = 1,28 Mb), jumlah contig sebanyak 84.285 contig (N50 contig = 30,6 kb), dan jumlah gen sebanyak 43.792 gen.…”