Abstract
BackgroundStructural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation.ResultsIn this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement.ConclusionsThese findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.
Highlights
A striking range of natural genetic diversity has been revealed at the level of SNPs, indel polymorphisms (IDPs), and structural variation [1,2,3,4]
An abnormal interaction was observed between 22 M to 25 M on chromosome 6 based on AGPv4 genome, which maps to the exact location of the largest presence-absence variations (PAVs) RegionA (Additional file 1: Figure S1c), suggesting a putative assembly error in this region
Recombination repression contributed to the preservation of large PAVs Despite the growing evidence supporting the role of PAVs in the intraspecific genome evolution, megabase-scale PAVs have been rarely characterized in plant species including maize
Summary
A striking range of natural genetic diversity has been revealed at the level of SNPs, indel polymorphisms (IDPs), and structural variation [1,2,3,4]. The prevalence of PAVs in the genome-wide context varies among species as well as individual samples. In eukaryotes in higher animals including humans, PAVs were found often with a much smaller size scale, and they predominantly consist of intergenic sequences [14, 15]. A growing number of eukaryotes, such as fungi, algae, and plant species, have been reported with large-size PAVs containing functional genes [9, 10, 16,17,18,19]. Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation
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