De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species.
Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range "Chicago" technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree's 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Wirulda
W
Pootakham
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Chutima
C
Sonthirod
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Chaiwat
C
Naktang
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Panthita
P
Ruang-Areerate
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Thippawan
T
Yoocha
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Duangjai
D
Sangsrakru
Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
Kanikar
K
Theerawattanasuk
Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
Ratchanee
R
Rattanawong
Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
Napawan
N
Lekawipat
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
Sithichoke
S
Tangphatsornruang
D017398:Alternative Splicing / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D020440:Gene Duplication; D063990:Gene Ontology; D018745:Genome, Plant; D028482:Hevea / Q000235:genetics*; D006824:Hybridization, Genetic; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D057891:Tetraploidy