Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum

• Published in: Plant molecular biology 2022-05, Vol.109 (1-2), p.159-175
• Main Authors: Liu, Lingyun, Teng, Ke, Fan, Xifeng, Han, Chao, Zhang, Hui, Wu, Juying, Chang, Zhihui
• Format: Article
• Language: English
• Subjects: Accumulation; Alternative splicing; Analysis; Anthocyanin; Anthocyanins; Anthocyanins - metabolism; Biochemistry; Biomedical and Life Sciences; DNA sequencing; Flavonoids; Flowers & plants; Gene Expression Profiling; Genes; Genomes; Grasses; High-Throughput Nucleotide Sequencing; Landscaping; Life Sciences; Molecular biology; Molecular modelling; Next-generation sequencing; Non-coding RNA; Nucleotide sequencing; Open reading frames; Pennisetum - genetics; Pennisetum setaceum; Plant Breeding; Plant Pathology; Plant Sciences; RNA; RNA, Long Noncoding - genetics; Transcription factors; Transcriptome; Transcriptomes; Transcriptomics
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-022-01264-x

Key message Combination analysis of single-molecule long-read and Illumina sequencing provide full-length transcriptome information and shed new light on the anthocyanin accumulation mechanism of Pennisetum setaceum cv. ‘Rubrum’. Pennisetum setaceum cv. ‘Rubrum’ is an ornamental grass with purple leaves widely used in landscaping. However, the current next-generation sequencing (NGS) transcriptome information of this species is not satisfactory due to the difficulties in obtaining full-length transcripts. Furthermore, the molecular mechanisms of anthocyanin accumulation in P. setaceum have not been thoroughly studied. In this study, we used PacBio full-length transcriptome sequencing (SMRT) combined with NGS technology to build and improve the transcriptomic datasets and reveal the molecular mechanism of anthocyanin accumulation in P. setaceum cv. ‘Rubrum’. Therefore, 280,413 full-length non-chimeric reads sequences were obtained using the SMRT technology. We obtained 97,450 high-quality non-redundant transcripts and identified 5352 alternative splicing events. In addition, 93,066 open reading frames (ORFs), including 57,457 full ORFs and 2910 long non-coding RNA (lncRNAs) were screened out. Furthermore, 10,795 differentially expressed genes were identified using NGS. We also explored key genes, synthesis pathways, and detected lncRNA involved in anthocyanin accumulation, providing new insights into anthocyanin accumulation in P. setaceum cv. ‘Rubrum’. To our best knowledge, we provided the full-length transcriptome information of P. setaceum cv. ‘Rubrum’ for the first time. The results of this study will provide baseline information for gene function studies and pave the way for future P. setaceum cv. ‘Rubrum’ breeding projects.