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Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Publication ,  Journal Article
Wang, B; Mojica, JP; Perera, N; Lee, C-R; Lovell, JT; Sharma, A; Adam, C; Lipzen, A; Barry, K; Rokhsar, DS; Schmutz, J; Mitchell-Olds, T
Published in: Genome biology
June 2019

Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species.Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms.Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.

Duke Scholars

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Published In

Genome biology

DOI

EISSN

1474-760X

ISSN

1474-7596

Publication Date

June 2019

Volume

20

Issue

1

Start / End Page

126

Related Subject Headings

  • Selection, Genetic
  • Polymorphism, Genetic
  • Genome, Plant
  • Disease Resistance
  • Brassicaceae
  • Bioinformatics
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences
 

Citation

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Wang, B., Mojica, J. P., Perera, N., Lee, C.-R., Lovell, J. T., Sharma, A., … Mitchell-Olds, T. (2019). Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biology, 20(1), 126. https://doi.org/10.1186/s13059-019-1729-9
Wang, Baosheng, Julius P. Mojica, Nadeesha Perera, Cheng-Ruei Lee, John T. Lovell, Aditi Sharma, Catherine Adam, et al. “Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.Genome Biology 20, no. 1 (June 2019): 126. https://doi.org/10.1186/s13059-019-1729-9.
Wang B, Mojica JP, Perera N, Lee C-R, Lovell JT, Sharma A, et al. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome biology. 2019 Jun;20(1):126.
Wang, Baosheng, et al. “Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.Genome Biology, vol. 20, no. 1, June 2019, p. 126. Epmc, doi:10.1186/s13059-019-1729-9.
Wang B, Mojica JP, Perera N, Lee C-R, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome biology. 2019 Jun;20(1):126.

Published In

Genome biology

DOI

EISSN

1474-760X

ISSN

1474-7596

Publication Date

June 2019

Volume

20

Issue

1

Start / End Page

126

Related Subject Headings

  • Selection, Genetic
  • Polymorphism, Genetic
  • Genome, Plant
  • Disease Resistance
  • Brassicaceae
  • Bioinformatics
  • 08 Information and Computing Sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences