Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome.

ABSTRACT: Seabuckthorn (Hippophaerhamnoides L.) is known for its medicinal, nutritional and environmental importance since ancient times. However, very limited efforts have been made to characterize the genome and transcriptome of this wonder plant. Here, we report the use of next generation massive parallel sequencing technology (Illumina platform) and de novo assembly to gain a comprehensive view of the seabuckthorn transcriptome. We assembled 86,253,874 high quality short reads using six assembly tools. At our hand, assembly of non-redundant short reads following a two-step procedure was found to be the best considering various assembly quality parameters. Initially, ABySS tool was used following an additive k-mer approach. The assembled transcripts were subsequently subjected to TGICL suite. Fin

SUBMITTER: Ghangal R 

PROVIDER: S-EPMC3749127 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature