Cannabis Expression Atlas: a comprehensive resource for integrative analysis of Cannabis sativa L. gene expression

Abstract

Cannabis sativa L., a plant originating from Central Asia, is a versatile crop with applications spanning textiles, construction, pharmaceuticals, and food products. This study aimed to compile and analyze publicly available Cannabis RNA-Seq data and develop an integrated database tool to help advance Cannabis research in various topics such as fiber production, cannabinoid biosynthesis, sex determination, and plant development. We identified 515 publicly available RNA-Seq samples that, after stringent quality control, resulted in a high-quality dataset of 394 samples. Utilizing the Jamaican Lion genome as reference, we constructed a comprehensive database and developed the Cannabis Expression Atlas (https://cannatlas.venanciogroup.uenf.br/), a web application for visualization of gene expression, annotation, and functional classification. Key findings include the quantification of 27,640 Cannabis genes and their classification into seven expression categories: not-expressed, low-expressed, housekeeping, tissue-specific, group-enriched, mixed, and expressed-in-all tissues. The study revealed substantial variability and coherence in gene expression across different tissues and chemotypes. We found 2,382 tissue-specific genes, including 177 transcription factors.. The Cannabis Expression Atlas constitutes a valuable tool for exploring gene expression patterns and offers insights into Cannabis biology, supporting research in plant breeding, genetic engineering, biochemistry, and functional genomics.