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Background   Pennisetum giganteum , an abundant, fast-growing perennial C 4  grass that belongs to the genus  Pennisetum , family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a source of forage for cattle and sheep, and as a tool to remedy soil erosion. However, having a chilling-sensitive nature,  P. giganteum  seedlings need to be protected while overwintering in most temperate climate regions.    Results  To elucidate the cold stress responses of  P. giganteum , we carried out comprehensive full-length transcriptomes from leaf and root tissues under room temperature (RT) and chilling temperature (CT) using PacBio Iso-Seq long reads. We identified 196,124 and 140,766 full-length consensus transcripts in the RT and CT samples, respectively. We then systematically performed functional annotation, transcription factor identification, long non-coding RNAs (lncRNAs) prediction, and simple sequence repeat (SSR) analysis of those full-length transcriptomes. Isoform analysis revealed that alternative splicing events may be induced by cold stress in  P. giganteum , and transcript variants may be involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in  P. giganteum . Furthermore, the fatty acid composition determination and gene expression level analysis supported that C18 unsaturated fatty acid biosynthesis and metabolism pathways may play roles during cold stress in  P. giganteum .    Conclusions  We provide the first comprehensive full-length transcriptomic resource for the abundant and fast-growing perennial grass  Pennisetum giganteum . Our results provide a useful transcriptomic resource for exploring the biological pathways involved in the cold stress responses of  P. giganteum .

bmc genomics

SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum