Transcriptome de novo assembly and differentially expressed genes related to cytoplasmic male sterility in kenaf (Hibiscus cannabinus L.)

Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce functional pollen during anther development; it plays a key role in hybrid seed production. CMS in kenaf (Hibiscus cannabinus L.) was first found by our group, but little is known about its molecular mechanism. To reveal the possible mechanism, a comparative transcriptome analysis of kenaf anthers from a CMS line and its maintainer was conducted using Solexa sequencing. We obtained 29,656,489 and 30,712,685 raw paired-end reads from the CMS and maintainer lines, respectively. These reads were eventually assembled into 54,563 unigenes with a mean size of 1,015 bp. As a result, 45,930 (84 %) sequences were annotated against the nr protein database. 15,977 (29 %) sequences were assigned to 286 kyoto encyclopedia of genes and genomes (KEGG) pathways, 20,289 (37 %) sequences have Clusters of Orthologous Groups classifications, and 38,611 unigenes (71 %) have at least one gene ontology (GO) term assigned and could be categorized into 50 functional groups. By using the digital gene expression (DGE) method, 4,584 transcripts were detected with at least twofold differences between CMS and maintainer lines. A total of 838 genes were increased and 528 genes decreased by at least fivefold in the CMS line. We performed GO and KEGG pathway enrichment analysis of differentially expressed genes (DEGs). The DEGs were assigned to 155 GO terms and enriched to 74 KEGG pathways. Twenty-eight genes were randomly selected and their expression levels were confirmed by quantitative real-time PCR, and 22 of them showed expression patterns consistent with the DGE data. The results provide a comprehensive foundation for understanding anther development and the CMS mechanism in kenaf.