title: Digital gene expression profiling of the Phytophthora sojae transcriptome.
abstract: The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3'-tag digital gene-expression protocol. More than 90 million clean sequence tags were generated and compared with the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes' expression patterns suggested four groups: i) mycelia and zoosporangia, ii) zoospores and cysts, iii) germinating cysts, and iv) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression?pattern clusters were obtained and the top 16 clusters, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and noncoding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis-related gene families revealed that most were infection induced but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database has been established.
authors.affiliation: Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
authors.forename: Wenwu
authors.initials: W
authors.lastname: Ye
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wang
authors.forename: Kai
authors.initials: K
authors.lastname: Tao
authors.forename: Yuping
authors.initials: Y
authors.lastname: Lu
authors.forename: Tingting
authors.initials: T
authors.lastname: Dai
authors.forename: Suomeng
authors.initials: S
authors.lastname: Dong
authors.forename: Daolong
authors.initials: D
authors.lastname: Dou
authors.forename: Mark
authors.initials: M
authors.lastname: Gijzen
authors.forename: Yuanchao
authors.initials: Y
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015870:Gene Expression / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D056426:Genetic Loci / Q000235:genetics; D016678:Genome / Q000235:genetics; D020407:Internet; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010838:Phytophthora / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D010935:Plant Diseases / Q000382:microbiology*; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA; D013997:Time Factors; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger