Transcriptomics: Open Access
Open Access
ISSN: 2329-8936
ISSN: 2329-8936
Bin He
Accepted Abstracts: Transcriptomics
Oryza meyeriana (O. meyeriana), a GG genome type (2n=24), accumulated plentiful excellent characteristics with respect to tolerance to shade, blast and bacterial blight. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq. We obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, we found there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (O. sativa) genome revealed similar rate of alignment across different plant species, however 13% of the O. meyeriana contigs had not been detected as expressed in O. sativa. Furthermore, the enrichment of the plant-pathogen interaction pathway in O. meyeriana showed difference with O. sativa, including the similarity of these aligned candidate genes and the absence of candidate genes involved in the plant-pathogen interaction pathway. In addition, we identified 52 contigs as disease resistance protein which was not existed in O. sativa. Taken together, there are significant differences between O. meyeriana and O. sativa in disease resistance. This information provides a foundation for future investigations into the discovery of a huge amount of novel genes which will facilitate gene mining and provides a basis for comparative studies within the genus Oryza.
Bin He is studying at Sichuan University of Life Science Institute as a PhD student. His research concerns the transcriptome and genome of wild rice, including Oryza meyeriana, Oryza officinalis and Oryza rufipogon. He is committed to mining new resistant resource; apply new elite resistant genes to improve the resistance of rice. He has published several papers in some journals, such as BMC genomics.