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Population genetics of the highly polymorphic RPP8 gene family
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MacQueen, Alice, Tian, Dacheng, Chang, Wenhan, Holub, E. B., Kreitman, Martin and Bergelson, Joy (2019) Population genetics of the highly polymorphic RPP8 gene family. Genes, 10 (9). e691. doi:10.3390/genes10090691
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Official URL: https://doi.org/10.3390/genes10090691
Abstract
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.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QP Physiology Q Science > QR Microbiology |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) | |||||||||
| SWORD Depositor: | Library Publications Router | |||||||||
| Library of Congress Subject Headings (LCSH): | Natural immunity, Nucleotides , Leucine, Immune response -- Molecular aspects, Molecular evolution, Gene conversion , Mutation (Biology) | |||||||||
| Journal or Publication Title: | Genes | |||||||||
| Publisher: | MDPI | |||||||||
| ISSN: | 2073-4425 | |||||||||
| Official Date: | 8 September 2019 | |||||||||
| Dates: |
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| Volume: | 10 | |||||||||
| Number: | 9 | |||||||||
| Article Number: | e691 | |||||||||
| DOI: | 10.3390/genes10090691 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Publisher Statement: | ** From MDPI via Jisc Publications Router ** History: accepted 03-09-2019; pub-electronic 08-09-2019. ** Licence for this article: https://creativecommons.org/licenses/by/4.0/ | |||||||||
| Access rights to Published version: | Open Access | |||||||||
| RIOXX Funder/Project Grant: |
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