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Population Genetics of the Highly Polymorphic RPP8 Gene Family

Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210008, China
Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA
School of Life Sciences, Wellesbourne Innovation Campus, University of Warwick, Wellesbourne CV359EF, UK
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 691;
Received: 29 July 2019 / Revised: 31 August 2019 / Accepted: 3 September 2019 / Published: 8 September 2019
(This article belongs to the Special Issue NLR gene evolution in plants)
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity. View Full-Text
Keywords: NLR gene; molecular evolution; intergenic gene conversion; gene duplication; copy number variation NLR gene; molecular evolution; intergenic gene conversion; gene duplication; copy number variation
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MacQueen, A.; Tian, D.; Chang, W.; Holub, E.; Kreitman, M.; Bergelson, J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes 2019, 10, 691.

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