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02 02, 2017;7 41457.

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species.

Wirulda Pootakham, Chutima Sonthirod, Chaiwat Naktang, Panthita Ruang-Areerate, Thippawan Yoocha, Duangjai Sangsrakru, Kanikar Theerawattanasuk, Ratchanee Rattanawong, Napawan Lekawipat, Sithichoke Tangphatsornruang
Author Information
  1. Wirulda Pootakham: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  2. Chutima Sonthirod: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  3. Chaiwat Naktang: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  4. Panthita Ruang-Areerate: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  5. Thippawan Yoocha: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  6. Duangjai Sangsrakru: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
  7. Kanikar Theerawattanasuk: Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
  8. Ratchanee Rattanawong: Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
  9. Napawan Lekawipat: Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.
  10. Sithichoke Tangphatsornruang: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
PMID: 28150702 DOI: 10.1038/srep41457

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.

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MeSH Term

Alternative Splicing
Disease Resistance
Gene Duplication
Gene Ontology
Genome, Plant
Hevea
Hybridization, Genetic
Molecular Sequence Annotation
Open Reading Frames
Phylogeny
Plant Diseases
Repetitive Sequences, Nucleic Acid
Sequence Analysis, DNA
Tetraploidy
Journal Article Research Support, Non-U.S. Gov't

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