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 nongenic 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 timescale with peaks at ∼16 and 300 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.

中文翻译：

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大单倍型凸显了玉米泛基因组内复杂的年龄结构

玉米和其他真核生物的基因组在低重组区域包含稳定的单倍型。这些区域，包括着丝粒、长异色块和 rDNA 阵列，其多样性和起源很难分析。现在已经有了极大改进的基因组组装，可以在这些和其他非基因空间上进行比较基因组学。使用 26 个完整的玉米基因组，我们开发了比对基因间序列同时排除基因和调控区域的方法。着丝粒单倍型 (cenhaps) 在功能着丝粒区域两侧延伸出巨型碱基，并显示为进化层，单倍型分歧/合并时间可追溯到 45 万年前 (kya)。将相同的方法应用于其他低重组区域（异色旋钮和 rDNA）和所有基因间空间表明，深度合并时间在玉米全基因组中普遍存在。分歧估计在很宽的时间尺度上变化，峰值在~16和300 kya，反映了不同种群之间基因流动的复杂历史以及与驯化相关的种群规模的变化。Cenhaps 和其他长单倍型生动地展示了这种古老的多样性。