Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.

Area of Science:

• Genomics and Molecular Biology
• Plant Science
• Biotechnology

Background:

• Cannabis sativa exhibits significant genetic and phenotypic diversity due to extensive domestication.
• Growing medical and recreational use of cannabinoids (THC, CBD) necessitates advanced genomic tools.
• Specialized metabolites in cannabis glandular trichomes are key targets for research.

Purpose of the Study:

• To create and characterize PacBio Iso-Seq-based transcriptome assemblies for THC- and CBD-dominant cannabis chemotypes.
• To identify novel transcribed loci and alternative splicing events.
• To explore gene expression patterns related to nutrient acquisition and their chemotype-specific differences.

Main Methods:

• PacBio Iso-Seq sequencing technology was employed for transcriptome assembly.
• Assemblies were generated for two contrasting cannabis chemotypes (THC-dominant and CBD-dominant).
• Bioinformatic analyses were performed to identify novel transcripts, alternative splicing events, and gene expression patterns.

Main Results:

• Transcriptome assemblies covered approximately 60% of the cs10 reference genome, identifying 1145 novel transcribed loci.
• Each assembly defined over 50,000 transcripts and 15,000 alternative splicing events.
• Novel cis-regulatory long non-coding RNA and isoform-specific expression patterns for nutrient regulation (SPX DOMAIN 4) were characterized, showing chemotype differences.

Conclusions:

• The developed transcriptome assemblies are a valuable resource for functional genomics in Cannabis sativa.
• Novel findings include previously unidentified transcribed loci and extensive alternative splicing.
• Isoform-specific expression patterns suggest novel regulatory mechanisms for nitrogen and phosphate acquisition in cannabis.