Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor

Setsuko Shimada, Yuko Makita, Tomoko Kuriyama-Kondou, Mika Kawashima, Yoshiki Mochizuki, Hideki Hirakawa, Shusei Sato, Tetsuro Toyoda, Minami Matsui

    Research output: Contribution to journalArticlepeer-review

    2 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)485-493
    Number of pages9
    JournalDNA Research
    Volume22
    Issue number6
    DOIs
    Publication statusPublished - 2015 Jun 17

    Keywords

    • Full-length cDNA
    • RNA-Seq
    • Sorghum bicolor
    • Transcriptome

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

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