生物
单倍型
基因组
进化生物学
遗传学
基因间区
基因组学
着丝粒
异染色质
人口
溯祖理论
驯化
基因
系统发育树
染色体
等位基因
人口学
社会学
作者
Jianing Liu,R. Kelly Dawe
出处
期刊:Genome Research
[Cold Spring Harbor Laboratory]
日期:2023-02-28
卷期号:33 (3): 359-370
标识
DOI:10.1101/gr.276705.122
摘要
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.
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