Summary
Publication
Tang, C., Yang, M., Fang, Y., Luo, Y., Gao, S., Xiao, X., . . . Huang, H. (2016). The rubber tree genome reveals new insights into rubber production and species adaptation. Nature Plants, 2(6), 16073. doi:10.1038/nplants.2016.73
Name
Hevea brasiliensis - Reference Genome
Resource Type
Genome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Hevea brasiliensis

Genomic DNA was prepared from leaves of six Hevea cultivars using the CTAB method. For genome sequencing, paired-end libraries (<600 bp) and mate-paired libraries (800 bp to 10 kb) were constructed by the standard A-tailing Illumina protocol and by the modified SOLiD mate-pair library preparation protocol. Raw reads were pre-processed by an in-house perlscript, and then proofread by a module in SOAPdenovo package. Raw RNA-seq reads were processed and the clean reads were then mapped to the Hevea genome using GSNAP54 and to compute the transcripts expression levels Cufflinks55 was used . SOAPdenovo assembled the pre-processed paired-end reads and SSPACE was using to construct the scaffolds for the mate-pair reads. Repeat sequences were annotated using RepeatMasker on de novo. BLASTP program was used to identify the homolog pairs and the MCscan program60 was used to search for collinearity blocks.

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

Details
Program, Pipeline, Workflow or Method Name
SOAPdenovo
Program Version
r241 (H.brasiliensis)
Date Performed
Monday, October 29, 2018 - 16:13
Data Source
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