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De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
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Document Title
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
Author
Pootakham W., Sonthirod C., Naktang C., Ruang-Areerate P., Yoocha T., Sangsrakru D., Theerawattanasuk K., Rattanawong R., Lekawipat N., Tangphatsornruang S.
Name from Authors Collection
Scopus Author ID
56030033100
Affiliations
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand; Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand
Type
Article
Source Title
Scientific Reports
ISSN
20452322
Year
2017
Volume
7
Open Access
All Open Access, Gold, Green
Publisher
Nature Publishing Group
DOI
10.1038/srep41457
Format
Abstract
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. © 2017 The Author(s).
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
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Rights
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Publication Source
Scopus