Utility of PacBio Iso-Seq for transcript and gene discovery in Hevea latex

Full-length cDNA libraries (< 1 kb, 1–2 kb, 2–3 kb, 3–6 kb size ranges) were generated from latex of a Hevea brasiliensis tree clone, RRIM 600, for PacBio Iso-Seq sequencing. The total number of high-quality consensus sequences obtained from nearly 20 Gb of raw reads was 207,943 having an average length of 1823 bp and N50 of 2538 bp. Mapping of high-quality consensus sequences to the published Reyan 7-33-97 genome sequence produced 37,224 Iso-Seq transcripts with an average length of 2030 bp and N50 of 2529 bp. These represented 14,999 genic loci. Comparison with the Reyan 7-33-97 gene models indicated that 50.75% of Iso-Seq transcripts were potentially novel gene isoforms. Subsequently, we also demonstrate the application of Iso-Seq in identifying previously unknown alternatively spliced transcripts based on three case studies of candidate rubber genes of interest. Findings from this study support the usefulness of PacBio Iso-Seq as transcriptome resources for gene family characterisation and genome annotation in Hevea.