A composited genome approach to analyse cistrome diversity in barley
- 1Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf, Germany
Abstract
Motivation: Functional regulatory variants are important determinants of heritable diversity, yet their systematic identification requires both genome-wide maps of transcription factor (TF) occupancy and suitable genome sequences for mapping. While chromosome-scale assemblies remain costly for large association panels, short-read sequencing data are widely available. We investigated whether draft genomes reconstructed from short reads are sufficient for comparative MOA-seq analyses of TF occupancy. Results: We generated genome-wide TF footprint maps for the barley cultivars Bowman, Morex, and Golden Promise, identifying approximately 240,000 loci per genotype. Roughly half of all footprints occurred in intergenic regions. Footprints conserved between genotypes were depleted for sequence variation and located closer to genes. Meanwhile, genotype-specific footprints were enriched for SNP-containing and gene-distal regions, highlighting the extensive diversity of regulatory landscapes among barley cultivars. We further compared two short-read-based draft genome assembly strategies: i) a SNP-replacement and ii) a Practical Haplotype Graph (PHG)-based composite genome approach, to enable MOA-seq analyses without chromosome-scale genome assemblies. Compared to the SNP-replacement strategy, the composite genome displayed 2.3-fold higher local sequence concordance for SNPs/INDELs relative to the published reference. Both draft genomes accurately reproduced MOA-seq profiles, recovering approximately 80 % of reference peak bases with per-base coverage correlations of 0.79-0.90 relative to the assembled reference. While the composite genome performed best across the genome overall, the simpler SNP-replacement strategy more accurately recovered TF occupancy within regulatory peaks due to fewer structural alignment artefacts. Availability: Pipelines consist of existing open-source tools, Bash, GAWK and Java, and are available at [zenodo; tbd].
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BibTeX
@misc{kok2026composited,
title = {{A composited genome approach to analyse cistrome diversity in barley}},
author = {A. Kok and J.-Y. Zhu and N. Bajaczyk and V. Joisten-Rosenthal and S. Mukherjee and S. Weizel and V. S. Bonthala and N. Sargheini and B. Huettel and B. Usadel and J. Engelhorn and B. Stich and T. Hartwig},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.27.762185},
url = {https://www.biorxiv.org/content/10.64898/2026.10.27.762185v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A composited genome approach to analyse cistrome diversity in barley
AU - A. Kok
AU - J.-Y. Zhu
AU - N. Bajaczyk
AU - V. Joisten-Rosenthal
AU - S. Mukherjee
AU - S. Weizel
AU - V. S. Bonthala
AU - N. Sargheini
AU - B. Huettel
AU - B. Usadel
AU - J. Engelhorn
AU - B. Stich
AU - T. Hartwig
PY - 2026
DA - 2026/10/27
PB - bioRxiv
DO - 10.64898/2026.10.27.762185
UR - https://www.biorxiv.org/content/10.64898/2026.10.27.762185v1
AB - Motivation: Functional regulatory variants are important determinants of heritable diversity, yet their systematic identification requires both genome-wide maps of transcription factor (TF) occupancy and suitable genome sequences for mapping. While chromosome-scale assemblies remain costly for large association panels, short-read sequencing data are widely available. We investigated whether draft genomes reconstructed from short reads are sufficient for comparative MOA-seq analyses of TF occupancy. Results: We generated genome-wide TF footprint maps for the barley cultivars Bowman, Morex, and Golden Promise, identifying approximately 240,000 loci per genotype. Roughly half of all footprints occurred in intergenic regions. Footprints conserved between genotypes were depleted for sequence variation and located closer to genes. Meanwhile, genotype-specific footprints were enriched for SNP-containing and gene-distal regions, highlighting the extensive diversity of regulatory landscapes among barley cultivars. We further compared two short-read-based draft genome assembly strategies: i) a SNP-replacement and ii) a Practical Haplotype Graph (PHG)-based composite genome approach, to enable MOA-seq analyses without chromosome-scale genome assemblies. Compared to the SNP-replacement strategy, the composite genome displayed 2.3-fold higher local sequence concordance for SNPs/INDELs relative to the published reference. Both draft genomes accurately reproduced MOA-seq profiles, recovering approximately 80 % of reference peak bases with per-base coverage correlations of 0.79-0.90 relative to the assembled reference. While the composite genome performed best across the genome overall, the simpler SNP-replacement strategy more accurately recovered TF occupancy within regulatory peaks due to fewer structural alignment artefacts. Availability: Pipelines consist of existing open-source tools, Bash, GAWK and Java, and are available at [zenodo; tbd].
ER -