Originally released 11/25/13
By a News Reporter-Staff News Editor at Biotech Business Week — Investigators discuss new findings in Life Science Research. According to news originating from New Delhi, India, by NewsRx correspondents, research stated, “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.”
Our news journalists obtained a quote from the research from Guru Gobind Singh Indraprastha University, “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. Finally, de novo short read assembly yielded 88,297 transcripts (>100 bp), representing about 53 Mb of seabuckthorn transcriptome. The average length of transcripts was 610 bp, N50 length 1198 BP and 91% of the short reads uniquely mapped back to seabuckthorn transcriptome. A total of 41,340 (46.8%) transcripts showed significant similarity with sequences present in nr protein databases of NCBI (E-value
According to the news editors, the research concluded: “The seabuckthorn transcriptome data generated here provide a valuable resource for gene discovery and development of functional molecular markers.”
For more information on this research see: Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome. Plos One, 2013;8(8):e72516. (Public Library of Science -www.plos.org; Plos One – www.plosone.org)
The news correspondents report that additional information may be obtained from R. Ghangal, University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India. Additional authors for this research include S. Chaudhary, M. Jain, R.S. Purty and P. Chand Sharma (see also Life Science Research).
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