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

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…

• UD
  U.S. Department of Energy

  Awards: -AC02-05CH11231, 05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
• UD
  U.S. Department of Agriculture

  Award: DE-AC02-05CH11231
• CI
  Cotton Incorporated

  Award: 18-753
• JG
  Joint Genome Institute

  Awards: DE-AC02-05CH11231, AC02-05CH11231
• NI
  National Institute of Food and Agriculture
• OO
  Office of Science

  Awards: AC02-05CH11231, -AC02-05CH11231, DE-AC02