LsRTDv1, a reference transcript dataset for accurate transcript-specific expression analysis in lettuce.

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Accurate gene and transcript expression quantification is vital for understanding biological processes.
• Alignment-free RNA sequencing analysis requires a high-quality reference transcriptome.
• Existing lettuce transcriptome data has limitations in isoform resolution.

Purpose of the Study:

• To generate a comprehensive and high-confidence reference transcript dataset for lettuce (cv. Saladin).
• To improve the accuracy and efficiency of gene expression analysis in lettuce.
• To facilitate the study of transcriptional and alternative splicing regulation in response to stimuli.

Main Methods:

• Combined long- and short-read sequencing data for lettuce.
• Integrated publicly available transcriptome annotations.
• Filtered transcripts for high-confidence splice junctions and transcriptional start/end sites to create LsRTDv1.

Main Results:

• LsRTDv1 increases the average number of transcript isoforms per gene from 1.4 to 2.7.
• LsRTDv1 significantly improves RNA-seq data mapping rates.
• LsRTDv1 enables detection of novel genes (primarily long non-coding RNAs) and infection-responsive alternative splicing events.

Conclusions:

• LsRTDv1 is a valuable genomic resource for lettuce research.
• The improved reference dataset enhances the analysis of gene expression and alternative splicing.
• This resource aids in understanding lettuce responses to biotic stress, such as Botrytis cinerea infection.