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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa
GigaByte, Vol.2024
08/10/2024
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Abstract
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.
Details
- Title
- CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa
- Creators
- Locedie Mansueto - Southern Cross University, Faculty of Science and EngineeringKenneth L. McNally - International Rice Research InstituteTobias Kretzschmar - Southern Cross University, Military Road, Lismore New South Wales 2480, AustraliaRamil Mauleon - Southern Cross University, Military Road, Lismore New South Wales 2480, Australia, International Rice Research Institute, Pili Drive, Los Baños Laguna 4031, Philippines
- Publication Details
- GigaByte, Vol.2024
- Publisher
- GigaScience Press
- Grant note
- This study was funded by the Australian Research Council (ARC) Linkage project LP210200606. In addition, first author LM received a stipend from Southern Cross University (SCU). The ICGRC and CannSeek web servers are hosted and funded by SCU.
- Identifiers
- 991013225677002368
- Academic Unit
- Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article