Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
Genome Res. 2023 Mar;33(3):359-370. doi: 10.1101/gr.276705.122. Epub 2023 Feb 28.
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.
玉米和其他真核生物的基因组在低重组区域含有稳定的单倍型。这些区域包括着丝粒、长异染色质块和 rDNA 阵列，它们的多样性和起源一直难以分析。现在可以获得大大改进的基因组组装，从而能够在这些区域和其他非基因空间进行比较基因组学研究。利用 26 个完整的玉米基因组，我们开发了方法来对齐基因间序列，同时排除基因和调控区域。着丝粒单倍型（cenhaps）在功能着丝粒区域的两侧延伸了兆碱基，呈现出进化层，单倍型分歧/融合时间可以追溯到 45 万年前。将相同的方法应用于其他低重组区域（异染色质结和 rDNA）和所有基因间空间，结果表明，深合并时间在整个玉米泛基因组中普遍存在。分歧估计值在一个广泛的时间尺度上变化，峰值在 16 和 300 千年前，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大小变化。cenhaps 和其他长单倍型生动地展示了这种古老的多样性。
