title: Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.
abstract: Sorghum bicolor is one of the most important crops for food and bioethanol production. Its small diploid genome and resistance to environmental stress make sorghum an attractive model for studying the functional genomics of the Saccharinae and other C4 grasses. We analyzed the domain-based functional annotation of the cDNAs using the gene ontology (GO) categories for molecular function to characterize all the genes cloned in the full-length cDNA library of sorghum. The sorghum cDNA library successfully captured a wide range of cDNA-encoded proteins with various functions. To characterize the protein function of newly identified cDNAs, a search of their deduced domains and comparative analyses in the Oryza sativa and Zea mays genomes were carried out. Furthermore, genes on the sense strand corresponding to antisense transcripts were classified based on the GO of molecular function. To add more information about these genes, we have analyzed the expression profiles using RNA-Seq of three tissues (spikelet, seed and stem) during the starch-filling phase. We performed functional analysis of tissue-specific genes and expression analysis of genes of starch biosynthesis enzymes. This functional analysis of sorghum full-length cDNAs and the transcriptome information will facilitate further analysis of the Saccharinae and grass families.
authors.affiliation: Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Setsuko
authors.initials: S
authors.lastname: Shimada
authors.affiliation: Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.affiliation: Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Kuriyama-Kondou
authors.affiliation: Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Mika
authors.initials: M
authors.lastname: Kawashima
authors.affiliation: RIKEN Advanced Center for Computing and Communication (ACCC), Wako, Saitama 351-0198, Japan.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.affiliation: RIKEN Advanced Center for Computing and Communication (ACCC), Wako, Saitama 351-0198, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.affiliation: Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan minami@riken.jp.
authors.forename: Minami
authors.initials: M
authors.lastname: Matsui
mesh_terms: D018076:DNA, Complementary / Q000032:analysis / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D023281:Genomics; D012275:Oryza / Q000235:genetics*; D045868:Sorghum / Q000235:genetics*; D013213:Starch / Q000096:biosynthesis / Q000235:genetics; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D013213:Starch
keywords: RNA-Seq; Sorghum bicolor; full-length cDNA; transcriptome