Large haplotypes highlight a complex age structure within the maize pan-genome
Open accessPreprint — published as 10.1101/gr.276705.122
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks and rDNA arrays have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other non-genic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad time scale with peaks at ∼300 kya and 16 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
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In a pan-genome for 26 diverse maize lines assembled de novo using long-read technology, the total pan-genome length was 3.7 times larger than an individual genome and only 4.9% of the pan-genome was conserved in all individuals while the rest was segregating.
“They found that the total pan-genome length was 3.7 times larger than an individual genome and that only 4.9% of the pan-genome was conserved in all individuals while the rest was segregating.”
From Genomics of plant speciation (2023) · cites this paper as Liu and Dawe (2022)
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Bock, D. G., Cai, Z., Elphinstone, C., González-Segovia, E., Hirabayashi, K., Huang, K., Keais, G. L., Kim, A., Owens, G. L., & Rieseberg, L. H. (2023) · Plant Communications · doi:10.1016/j.xplc.2023.100599 · Cited by 84 · see citing works
- Authors
- Liu, J., & Dawe, R. K.
- Affiliations
- University of Georgia (US)
- Corresponding author
- Dawe, R. Kelly
- Venue
- Genome Research
- Publisher
- openRxiv
- Published
- 2022-02-23
- Volume
- 33
- Issue
- 3
- Pages
- 359-370
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC10078284
- OpenAlex
- W4322622511
- Cited by
- 8
- References
- 0
- Citations by year
- 2026: 2 · 2025: 2 · 2023: 4
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (2040218)
- Division of Integrative Organismal Systems (IOS-174400, IOS-2040218)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- maize, pan-genome, heterochromatin, ribosomal DNA, haplotype divergence, coalescence time, gene flow, population size change, domestication
- MeSH terms
- Centromere, Zea mays, Haplotypes, Genome, Plant, Genomics
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