LsRTDv1, a reference transcript dataset for accurate transcript-specific RNA-seq analysis in lettuce

We present LsRTDv1, the Lettuce Reference Transcript Dataset version 1, to improve our understanding of the lettuce transcriptome. Current GenBank and RefSeq annotations do not capture its complexity. LsRTDv1 combines long-read Iso-seq and short-read RNA-seq data from the Saladin lettuce cultivar, enhancing its comprehensiveness. It includes Iso-seq RTD and RNA-seq RTD transcript datasets. To ensure completeness, we integrate these with existing GenBank and RefSeq annotations. This dataset aids researchers in exploring lettuce's intricate transcriptome.
In our experimental design, we grew lettuce (Lactuca sativa cv. Saladin) under controlled conditions with specific light, temperature, and humidity. We sampled twenty-three different tissues representing various developmental stages and responses to abiotic stressors (chilling, heat-shock, waterlogging, drought, and wounding) applied to 6-week-old plants. Additionally, we introduced a biotic stressor, Botrytis cinerea, by inoculating detached leaves. Samples were rapidly frozen in liquid nitrogen and stored at -80 degree before RNA extraction. RNA was purified, assessed for quality, and pooled into seven libraries for PacBio Iso-seq and Illumina short-read RNA-seq. Both sequencing processes were conducted by Novogene (UK), with PacBio Sequel II for Iso-seq and Illumina for short-read sequencing.

This submission encompasses the raw RNA-seq data obtained from the Illumina platform and the circular consensus sequencing (CCS) read of the PacBio Iso-seq data.