Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Jinyu Wang, Xianran Li, Kyung Do Kim, Michael J. Scanlon, Scott A. Jackson, Nathan M Springer, Jianming Yu

Research output: Contribution to journalArticle

Abstract

Background: Plant 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. Results: Here, 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. Conclusions: The [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.

Original languageEnglish (US)
Article number74
JournalGenome biology
Volume20
Issue number1
DOIs
StatePublished - Apr 25 2019

Fingerprint

domestication
Soybeans
Zea mays
soybean
Nucleotides
genome
divergence
nucleotides
maize
Genome
soybeans
corn
Single Nucleotide Polymorphism
Base Composition
repair
mutation
genomics
Domestication
Mutation
DNA Transposable Elements

Keywords

  • Base composition
  • Domestication
  • Evolution
  • Genome divergence
  • Methylation
  • Mutation
  • Solar UV
  • UV damage repair

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. / Wang, Jinyu; Li, Xianran; Do Kim, Kyung; Scanlon, Michael J.; Jackson, Scott A.; Springer, Nathan M; Yu, Jianming.

In: Genome biology, Vol. 20, No. 1, 74, 25.04.2019.

Research output: Contribution to journalArticle

Wang, Jinyu ; Li, Xianran ; Do Kim, Kyung ; Scanlon, Michael J. ; Jackson, Scott A. ; Springer, Nathan M ; Yu, Jianming. / Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. In: Genome biology. 2019 ; Vol. 20, No. 1.
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AB - Background: Plant 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. Results: Here, 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. Conclusions: The [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.

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