Graph construction method impacts variation representation and analyses in a bovine super-pangenome

Area of Science:

• Comparative genomics
• Bioinformatics
• Population genetics

Background:

• Pangenome construction methods are emerging, but their effects on variant representation and downstream analyses remain unclear.
• Understanding these impacts is crucial for accurate genomic analysis across diverse populations.

Purpose of the Study:

• To evaluate and compare three pangenome construction tools: pggb, cactus, and minigraph.
• To assess their performance in representing structural variations (SVs) and variable number tandem repeats (VNTRs) across multiple bovine species.

Main Methods:

• Creation of multi-species super-pangenomes using pggb, cactus, and minigraph.
• Incorporation of the Bos taurus taurus reference sequence and eleven haplotype-resolved assemblies.
• Analysis of recovered structural variations (SVs) and variable number tandem repeats (VNTRs).

Main Results:

• 221k nonredundant SVs were recovered, with 61% common across all three methods.
• Pggb and cactus showed high agreement (95%) with assembly-derived small variant calls, improving realignment.
• 63% of VNTRs had identical repeat counts across graphs, though minigraph showed coordinate system limitations.

Conclusions:

• The three pangenome methods demonstrate good consensus but possess distinct strengths and weaknesses.
• Method selection should consider the specific variant types (SVs, VNTRs) and downstream analysis goals.