New bioinformatics resources from The International Cannabis Genome Research Consortium
Authors: Mansueto Locedie , Edmunds Scott C 
Published: October 2024

The International Cannabis Genome Research Consortium (ICGRC) has taken up the task of providing an authoritative source of rigorous and peer-reviewed scientific information relating to Cannabis genetics, genomics and phenotyping. Just out in GigaByte are papers presenting two of these outputs, the CannSeek database bringing together the many genomics datasets, and a community-driven bioinformatics platform to facilitate Cannabis multi-omics research. The papers promoting these resources, providing details on how to use them, and most importantly providing insight into how they were put together. To provide even more insight we are hosting an online seminar with the authors of these papers. Providing an opportunity to get firsthand insight from the authors on why these platforms are important, how you can use them, and the technical details on how they were developed. Also providing an opportunity to ask directly questions to them directly.

CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa

A growing interest in Cannabis sativa uses for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once-prohibited plant. Cannabis research uses Next Generation Sequencing technologies for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to the discovery of alleles for important traits, this is absent for cannabis. The CannSeek web portal aims to address this gap. Single nucleotide polymorphism datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying trait data are hosted in the CannSeek web application, built using the Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service Application Programming Interface. The tools built into the portal allow phylogenetic analyses, varietal grouping and identifications, and favorable haplotype discovery for cannabis accessions using public sequencing data.
Availability and implementation

The CannSeek portal is available at <https://icgrc.info/cannseek>, and <https://icgrc.info/genotype_viewer>.

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research

Global changes in Cannabis legislation after decades of stringent regulation, and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host Cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing.

The Tripal platform was used to host public genome assemblies, gene annotations, QTL and genetic maps, gene and protein expression, metabolic profile and their sample attributes. SNPs were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service API, developed on top of existing Tripal modules, returns generic tables of sample, property, and values. Use-cases demonstrate the API’s utility for various -omics analyses, enabling researchers to perform multi- omics analyses efficiently.

Q&A: everything you've ever wanted to know about cannabis genomics and bioinformatics* (*but were too afraid to ask).

Please bring questions for the seminar, or leave them in the chat.