GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.

Contreras-Moreira, Bruno, Saraf, Shradha, Naamati, Guy, Casas, Ana M, Amberkar, Sandeep S, Flicek, Paul, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Dyer, Sarah (2023) GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome biology, 24 (1). p. 223.

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Official URL: http://dx.doi.org/10.1186/s13059-023-03071-z

Abstract

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 recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .

Item Type:	Article
Uncontrolled Keywords:	Genome, Plant, Software
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	13 Oct 2023 09:11
Last Modified:	30 Oct 2023 03:32
DOI:	10.1186/s13059-023-03071-z
Open Access URL:	https://genomebiology.biomedcentral.com/articles/1...
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3173684