Cannabis art

Table Descriptions

Assembly Stats This table contains information on the assembly statistics of various Cannabis cultivars and samples. It includes the following columns:

  • Abv: Abbreviation of the cultivar/sample.
  • Cultivar/Sample: Name of the cannabis cultivar or sample.
  • NPGS Accession: National Plant Germplasm System accession identifier if available.
  • Chemotype: Chemical profile, typically referring to the primary cannabinoids present (e.g., THC/CBD ratio).
  • Sex (chr X/Y): Chromosomal information about the sex of the plant and assembly (X/Y).
  • Assembly Type: Type of genome assembly.
  • Total Length: Total length of the assembly in base pairs.
  • Contig N50: N50 value for contigs
  • Scaffold N50: N50 value for scaffolds
  • Gaps: Number of gaps in the assembly.

Assembly Files This table includes links to download genome assemblies:

  • Abv: Abbreviation of the cultivar/sample.
  • Genome: Link to the genome assembly fasta.
  • Archive: Archive link including gene predictions and the assembly.

Genes V2: This table provides updated version 2 gene models and annotations for the Cannabis genomes, with the following columns:

  • Abv: Abbreviation of the cultivar/sample.
  • CDS: Coding sequence information.
  • GFF3: Gene Feature Format file with genomic annotations.
  • mRNA: mRNA sequences.
  • Proteins: Protein sequences derived from the coding sequences.
  • mRNA Table: Information on mRNA sequences including eggnogmapper results.

Genes V1: This table provides information on Version 1 gene models and annotations. Columns include:

  • Abv: Abbreviation of the cultivar/sample.
  • CDS: Coding sequence fasta.
  • Proteins: Protein sequences derived from the coding sequences.
  • GFF3: Gene Feature Format file with genomic annotations.
  • RepeatMasker: RepeatMasker data for identifying repetitive elements.
  • mRNA Table: Information on genes, including eggnogmapper results.

Genes V1 primary A simplified version of the Version 1 gene models including only primary transcripts, containing:

  • Abv: Abbreviation of the cultivar/sample.
  • CDS: Coding sequence information.
  • GFF3: Gene Feature Format file with genomic annotations.
  • Proteins: Protein sequences derived from the coding sequences.

Graph Pangenomes Input and output files for PGGB and Minigraph-Cactus graph pangenomes.

  • Graph building method: PanGenome Graph Builder or Minigraph-Cactus
  • Orientation of input assemblies: Each graph pangenome has been generated twice -- once with the fasta files provided in the Assembly Files table (mixed) and once with fasta files in which the sequences have been oriented to match the plus strand of the corresponding homologous chromosome in EH23a (consistent with EH23a) .
  • Region(s) represented by file: Some files contain data for just one chromosome while others represent data from all autosomal chromosomes, just sex chromosomes, or the entire genome -- as indicated in this column
  • Assembly coordinate(s) represented in file: Certain file formats represent data with respect to the indicated assembly coordinates
  • File type: See this description of different output files

Assembly Types

  • Hifiasm_HiC : HiFi reads assembled with hifiasm along with HiC reads for phasing, then scaffolded with Juicer+3ddna.
  • Hifiasm_Trio_RagTag: HiFi reads assembled with hifiasm along with parametal reads for phasing then scaffolded using ragtag against reference cannabis genomes
  • Hifiasm_RagTag: HiFi reads assembled with hifiasm then scaffolded using ragtag against reference cannabis genomes
  • Hifiasm: HiFi reads assembled with hifiasm
  • Public: Pre-existing genomes available on NCBI
  • CCS: Circular Consensus pac bio reads assembled using HiCanu
  • CLR: Pac Bio long reads assembled using Falcon

Table Download Links

Salk Cannabis Pangenome Assemblies and Data