title: De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes.
abstract: Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant-pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future.
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. hebin.li@foxmail.com.
authors.forename: Bin
authors.initials: B
authors.lastname: He
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. yinghonggu@gmail.com.
authors.forename: Yinghong
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China. taoxiang180@gmail.com.
authors.forename: Xiang
authors.initials: X
authors.lastname: Tao
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. xiaoxiaojie1991@foxmail.com.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. hantanheying@126.com.
authors.forename: Changhe
authors.initials: C
authors.lastname: Wei
authors.affiliation: Biotechnology &amp; Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650223, China. fugein@aliyun.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Fu
authors.affiliation: Biotechnology &amp; Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650223, China. czquan-99@163.com.
authors.forename: Zaiquan
authors.initials: Z
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. yizzhang@scu.edu.cn.
authors.forename: Yizheng
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D060467:Disease Resistance / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D053858:Metabolic Networks and Pathways; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics*; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors
keywords: Oryza officinalis; de novo assembly; disease-resistant genes; transcriptome