Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

Abstract Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources this species relatively limited, which considerably hampers further work on its biology and improvement. Results In study, through analyzing transcriptome mixed samples leaves stems using latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report first full-length dataset M. total 58.21 Gb clean data. An average 15.75 reads each sample were obtained from system, doubled data size (6.68 Gb) HiSeq platform. The integrated analyses PacBio- Illumina-based transcriptomic uncovered 408,801 non-redundant transcripts an length 1,685 bp. Of those, 189,406 commonly identified by both methods, 169,149 619 bp uniquely 51,246 2,535 Iso-Seq. Approximately 96 % final mapped back to genome, reflecting high quality coverage our results. When comparing genomes four Andropogoneae, showed closest relationship sugarcane up 93 mapping ratios, followed sorghum 80 indicating conservation orthologs in these three genomes. Furthermore, 306,228 successfully annotated against public databases including cell wall related genes transcript factor families, thus providing many new insights into gene functions. also helped identify 3,898 alternative splicing events 2,963 AS isoforms within 10 function categories. Conclusions Taken together, present study provides rich set greatly enriches understanding resources, facilitating improvement molecular studies species.