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

Abstract

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 noncoding 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 fastgrowing 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.

Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

“…We uncovered differences in flavonoid metabolism, unsaturated fatty metabolism and TCA cycle between KL and RB under the no-freezing condition (0 h at −25°C). Flavonoid metabolites, acting as antioxidants to remove ROS, can increase FT ( Li et al, 2019 ), while unsaturated fatty metabolism, by enhancing the cell membrane fluidity, can increase plant resistance to cold ( Li et al, 2020 ). The TCA cycle represents energy metabolism, while energy metabolism meant that plant dormancy was weak ( Wang et al, 2021 ).…”

“…Both genotypes were cold acclimated to a maximum FT through the natural cooling of the field during the winter before treating them at −25 • C. We uncovered differences in flavonoid metabolism, unsaturated fatty metabolism and TCA cycle between KL and RB under the no-freezing condition (0 h at −25 • C). Flavonoid metabolites, acting as antioxidants to remove ROS, can increase FT (Li et al, 2019), while unsaturated fatty metabolism, by enhancing the cell membrane fluidity, can increase plant resistance to cold (Li et al, 2020).…”

Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals

“…Temperature-dependent alternative splicing might therefore function as a "thermometer" in plants to measure changes in ambient temperature [16,23,25,27]. In Arabidopsis, tea plants and Jujuncao, RT-PCR and RNA sequence analyses revealed that alternative splicing of a variety of genes is changed dramatically during cold acclimation [100][101][102][103]. The findings suggest that alternative splicing events play an important regulatory role in response to cold stress [100][101][102][103][104].…”

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

“…With the continuous upgrading and application of sequencing technologies, transcript reconstruction and annotation based on full-length transcript sequencing, followed by mining gene function at the molecular level, have gradually become research hotspots for species with no or difficult-to-assemble reference genomes, e.g., Cistanche tubulosa [ 23 ], Panax japonicus [ 24 ], Cinnamomum porrectum [ 25 ], Pennisetum giganteum [ 26 ], Portulaca oleracea [ 27 ], Nitraria sibirica Pall [ 28 ]. We conducted the first systematic full-length transcriptome analysis of the above-ground tissues of swamp reeds and dune reeds, revealing the alternative splicing pattern of low complexity in long-term adaptation to complex desert adversity.…”