De novo reconstruction of transcriptomes of ten Oryza sativa cultivars using PacBio Single-Molecule Real-Time sequencing

We sequenced transcriptomes of ten rice cultivars of the subspecies aus, indica and japonica on the PacBio Sequel I platform. RNA was isolated from different tissues of plants grown under control and abiotic stress conditions in climate chambers and in the field. De novo reference transcriptomes were reconstructed resulting in 38,900 to 54,500 high-quality isoforms per cultivar.The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding that are not present in the reference transcriptome/genome. In addition, our approach provides a general, cost-effective alternative to genome sequencing for the identification of candidate genes in highly stress tolerant "exotic" genotypes.