A composited genome approach to analyse cistrome diversity in barley

Composite genome assemblies for barley enabled MOA-seq comparisons that recovered ~80% of reference peak bases with per-base coverage correlations of 0.79–0.90.

• Why it matters: Functional regulatory variants require genome-wide TF occupancy maps and genome sequences that are feasible for large panels, yet chromosome-scale assemblies are costly.
• What they did: Genome-wide TF footprint maps were generated for Hordeum vulgare cultivars Bowman, Morex, and Golden Promise, and two short-read draft assembly strategies (SNP-replacement vs PHG-based composite) were benchmarked against a published reference.
• The result: The PHG-based composite genome showed 2.3-fold higher local sequence concordance for SNPs/INDELs, while the SNP-replacement strategy more accurately recovered TF occupancy within regulatory peaks.

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