The Long and Short of the Sugarcane Transcriptome

Analysis of the sugarcane transcriptome is complicated by the highly polyploid genome. Assembly of transcripts from short reads is especially difficult for long transcripts from closely related genes. Our objective was to establish a reference transcriptome for the key tissues of sugarcane. We used PacBio isoform sequencing (Iso-Seq) of RNA from leaf, internode and root, at different developmental stages, from 22 varieties. The transcriptome included a total of 107,598 unique transcript isoforms, representing about 71% (~25,000 genes) of the total number of predicted sugarcane genes. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode showed that the Iso-Seq method captured more full-length transcript isoforms, at a higher N50 and average length of the largest 1,000 proteins. The RNA-Seq recovered more RNA diversity. This data set will support expression studies in sugarcane and improve gene prediction models.