Whose Genome Has Been Sequenced? Hevea brasiliensis

de-novo-sequencingAll of us have at least once been doing experiments in the lab. And so everyone was confronted with latex gloves. And more and more of us developed a kind of latex allergy.

According to Rahman et al. “these allergies are triggered by certain proteins present in Hevea-derived natural rubber (NR). […] Hevea brasiliensis (Willd.) Muell.-Arg., also known as Pará rubber tree, is the primary commercial source for natural rubber (NR) production” (in total nearly 11 million tons in 2011 for all 2,500 rubber tree species).

Although rubber is used for > 50.000 products worldwide this is the first de novo sequencing approach. So far only transcriptome analysis studies were performed, which lack the non-coding regions of the genome.

What was sequenced?

Young leaves of Hevea brasiliensis RRIM 600. Genome size: ~ 2.15 Gb; 18 chromosomes

De novo sequencing strategy:

  1. Libraries: shotgun and mate-pair libraries (insert size: 500 bp) on HiSeq 2000; LPE libraries (insert sizes: 8 kb and 20 kb) on Roche GS FLX; Paired-end library (insert size: 2 kb) on SOLiD
  2. Coverage of all sequencing strategies together: ~ 43x (after filtering repeat-matching reads: ~ 13x = 27.86Gb)
  3. Data output: 143 scaffolds (total 1.119 Mb with N50 = 2.972 bp)
  4. Bioinformatics: CLC Workbench & Newbler assembler using different input data and different assembling strategies

Transcriptome sequencing strategy:

  1. Libraries: cDNA libraries
  2. Sequencing with Illumina HiSeq and Roche/454
  3. Bioinformatics: CLC Workbench assembler for the Illumina reads and Newbler for combining Roche and Illumina reads.

This de novo genome sequencing approach revealed that ~ 78% of the genome are repetitive regions. This study helps to improve breeding of H. brasiliensis by allowing marker assisted selection to further increase the disease resistance and minimize the allergenicity.

Read the complete publication here.

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Stephanie Engel

About Stephanie Engel

Stephie's motto: NGS rules. She is thrilled by molecular diagnostics.

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