Abstract
BackgroundMiscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement.ResultsIn this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to the Miscanthus genome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae, M. sinensis showed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories.ConclusionsTaken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis transcriptomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species.
Highlights
Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production
PacBio Iso-Seq sequencing of Miscanthus transcriptome To obtain a wide coverage of the Miscanthus transcriptome, high-quality mRNAs from leaves and stems of two Miscanthus sinensis genotypes (B0605 and C0542) were sequenced using the PacBio Iso-Seq Sequel platform
Our PacBio Iso-Seq dataset consisted mostly of high-quality reads of inserts (ROIs) with quality values above 0.95, which is much higher than the quality of most PacBio ROIs reported in previous studies (Fig. 1b) [18, 22]
Summary
Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. Knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement. Miscanthus sinensis Andersson (Poaceae) is considered to be one of the most promising lignocellulosic bioenergy crops owing to its high biomass yield, ability to grow on marginal land, and low fertilizer requirements [1]. As a non-model species, dedicated functional genomics and transcriptomic resources for Miscanthus are still poorly explored owing to the high heterozygosity and complex ploidy of their genomes, which becomes a bottleneck for understanding the molecular processes underlying its superior bioenergetic qualities. Understanding molecular processes underlying the basic biology of M. sinensis would enable agronomists to develop crops ideal for biomass production
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