GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.
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ABSTRACT:
SUBMITTER: Contreras-Moreira B
PROVIDER: S-EPMC10552430 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
Publications
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.
Contreras-Moreira Bruno B Saraf Shradha S Naamati Guy G Casas Ana M AM Amberkar Sandeep S SS Flicek Paul P Jones Andrew R AR Dyer Sarah S
Genome biology 20231005 1
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapit ...[more]
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