Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.

ABSTRACT: While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating protein-coding gene annotations across pangenomes in a single 'pangene set' remains challenging, both because of methodological inconsistency and biological presence-absence variation (PAV). Here, we review and experimentally evaluate the root of genome annotation and pangene set inconsistency using two polyploid plant pangenomes: cotton and soybean, which were chosen because of their existing diverse high-quality genomic resources and the known importance of gene PAV in their respective breeding programs. We first demonstrate that building pangene sets across different genome resources is highly error prone: PAV calculated directly from the genome

SUBMITTER: Bruna T 

PROVIDER: S-EPMC12856356 | biostudies-literature | 2026 Mar

REPOSITORIES: biostudies-literature