Abstract
BackgroundPlant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized.ResultsHere, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways.ConclusionsThe [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.
Highlights
Plant domestication provides a unique model to study genome evolution
These SNPs are designated as common SNP sets to compute the genome-wide base-composition across polymorphic sites without concerning about sampling issues due to low minor allele frequency (MAF) or high missing rate [5]
These findings indicate the presence of common underlying mechanisms that drive the domesticated accessions to build their genomes with more A and T nucleotides
Summary
Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Recent studies documented the base-composition difference and mutation rate difference between populations separated by either domestication or demographic bottleneck event, which provide novel insights on genome evolution [5,6,7]. Further investigation in DNA base composition, mutation spectrum, and the potential relationship between them is necessary to advance our understanding of genome changes. A conserved base-composition pattern, modern accessions having significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from their wild relatives, was discovered with natural populations across multiple species [5]. It would be interesting to study the regional variation of genome change pattern, captured by base composition summarized from polymorphic sites
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