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 C4 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.

Using γ-ray irradiation and epiphytic microbiota inoculation to separate the effects of chemical and microbial factors on fermentation quality and bacterial community of ensiled Pennisetum giganteum

“…Pennisetum giganteum (Pennisetum giganteum Z. X. Lin), a fast-growing and high-yield perennial C 4 grass, belongs to the genus Pennisetum in the Poaceae family. It is widely planted in over 80 countries in tropical, subtropical and temperate regions (Jia et al, 2020;Li et al, 2020). P. giganteum has high nutritional value and good palatability and has been developed as a source of forage.…”

Combination of Single-Molecule Long-Read Sequencing and Illumina Sequencing Revealed the Mechanism of Anthocyanins Accumulation in an Ornamental Grass, Pennisetum Setaceum ‘Rubrum’

“…The discovery of alternative splicing and translation is part of the abscisic acid reaction in Arabidopsis seedlings (Zhu et al, 2017). In Pennisetum giganteum , AS were found in both samples treated at low temperature and samples at room temperature, but the proportion of two or more subtypes of Unitransmodels was higher than that of room temperature samples, suggesting that alternative splicing events induced by low temperature stress may exist in Pennisetum giganteum (Li et al, 2020b). In this study, 5,352 transcripts were identified as natural splicing altered, accounting for 5.49% of the redundant transcripts.…”

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 ].…”