title: Gene ontology based characterization of expressed sequence tags (ESTs) of Brassica rapa cv. Osome.
abstract: Chinese cabbage (Brassica rapa) is widely recognized for its economic importance and contribution to human nutrition but abiotic and biotic stresses are main obstacle for its quality, nutritional status and production. In this study, 3,429 Express Sequence Tag (EST) sequences were generated from B. rapa cv. Osome cDNA library and the unique transcripts were classified functionally using a gene ontology (GO) hierarchy, Kyoto encyclopedia of genes and genomes (KEGG). KEGG orthology and the structural domain data were obtained from the biological database for stress related genes (SRG). EST datasets provided a wide outlook of functional characterization of B. rapa cv. Osome. In silico analysis revealed % 83 of ESTs to be well annotated towards reeds one dimensional concept. Clustering of ESTs returned 333 contigs and 2,446 singlets, giving a total of 3,284 putative unigene sequences. This dataset contained 1,017 EST sequences functionally annotated to stress responses and from which expression of randomly selected SRGs were analyzed against cold, salt, drought, ABA, water and PEG stresses. Most of the SRGs showed differentially expression against these stresses. Thus, the EST dataset is very important for discovering the potential genes related to stress resistance in Chinese cabbage, and can be of useful resources for genetic engineering of Brassica sp.
authors.affiliation: Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-742, Republic of Korea.
authors.forename: Senthil Kumar Thamil
authors.initials: SK
authors.lastname: Arasan
authors.forename: Jong-In
authors.initials: JI
authors.lastname: Park
authors.forename: Nasar Uddin
authors.initials: NU
authors.lastname: Ahmed
authors.forename: Hee-Jeong
authors.initials: HJ
authors.lastname: Jung
authors.forename: In-Ho
authors.initials: IH
authors.lastname: Lee
authors.forename: Yong-Gu
authors.initials: YG
authors.lastname: Cho
authors.forename: Yong-Pyo
authors.initials: YP
authors.lastname: Lim
authors.forename: Kwon-Kyoo
authors.initials: KK
authors.lastname: Kang
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
mesh_terms: D001937:Brassica / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D030541:Databases, Genetic; D020224:Expressed Sequence Tags / Q000378:metabolism*; D020869:Gene Expression Profiling; D015723:Gene Library; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D006801:Humans; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D012965:Sodium Chloride