Researchers Use Illumina Platform for Transcriptome Sequencing and De Novo Analysis of Youngia Japonica

Jun 03, 2014     Email"> PrintText Size

Youngia japonica L. (Oriental false hawksbeard) is a weed species originated in Asia, but is now world-widely distributed. Youngia japonica is used as a Chinese traditional medicine, because of its guaiane-type sesquiterpene and other constituents that exhibit strong antiallergic, antioxidant, and antitumor activities. However, studies about the DNA or protein sequences of this species are limited.  

Prof. PENG Yulan of Biodiversity research group in Chengdu Institute of Biology, Chinese Academy of Sciences, aimed to study this taxon. De nov transcriptome sequencing was conducted for the first time for the comprehensive analysis of the genetic diversity of Y. japonica. The Y. japonica transcriptome was sequenced using Illumina paired-end sequencing technology. 

Meanwhile, a total of 51,850 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 41,752 were annotated in the Swiss-Protdatabase. Researchers mapped 9,125 unigenes onto 163 pathways using the KyotoEncyclopedia of Genes and Genomes Pathway database. 

In addition, 3,648 simple sequence repeats (SSRs) were detected. The data provide the most comprehensive transcriptome resource currently available for Y. japonica. C4 photosynthesis unigenes were found in the biological process of Y. japonica. There are 5596 unigenes were found to be related to defense response and 1344 related to signal transduction mechanisms. These data provide insights into the genetic diversity of Y. japonica. Numerous SSRs contributed to the development of novel markers. These data may serve as a new valuable resource for genomic studies on Youngia and, more generally, Cichoraceae.

A large number of candidate genes potentially involved in growth, development, flowering, plant hormone and defense responses are worthy of further investigation. The results were published in PLoS ONE.