Table 1 Advantages and limitations of three pangenome construction methods

De novo assembly and comparison

Whole genome alignment

Enables precise detection of structural variants (SVs) between high-quality genome assemblies

Assembling population-level accessions with long-read sequencing remains computationally intensive and costly.

Gene annotation comparison

For orphan crops with complex genomes, focusing on gene-centric comparisons can help simplify this complexity

May miss key structural variations like tandem duplications or inversions in non-coding regions

Reference-based iterative assembly

Mapping and assembly

Uses low-coverage short-read sequencing, making it cost-effective for larger sample sizes

Short-read assemblies struggle with complex repeat regions and lose positional information for genetic variants in new contigs

Assembly and mapping

Cost-effective for short-read data, accurately locating insertions with PSVCP for single-reference applications

Cannot detect complex structural variations like inversions and has difficulty representing them in a linear format

Graph pangenomes

Genetic variation graph

Capture genetic diversity, enhance structural variation representation, improve alignment, and reveal heritability

Lack of mature bioinformatics tools, difficulty in interpretation, and high computational demands