Exploring intra- and intergenomic variation in haplotype-resolved pangenomes.

ABSTRACT: With advances in long-read sequencing and assembly techniques, haplotype-resolved (phased) genome assemblies are becoming more common, also in the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for polyploid genomes, are currently limited. Here we describe a new strategy adopting a pangenome approach. To analyse both intra- and intergenomic variation in phased genome assemblies, we have made the software package PanTools ploidy-aware by updating the pangenome graph representation and adding several novel functionalities to assess synteny and gene retention, profile repeats and calculate synonymous and nonsynonymous mutation rates. Using PanTools, we constructed and analysed a pangenome comprising of one diploid and four tetraploid pot

SUBMITTER: Jonkheer EM 

PROVIDER: S-EPMC11869183 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature