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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 ISSN 2073-4425.

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Official URL: https://doi.org/10.3390/genes10090691

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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
Subjects: Q Science > QH Natural history
Q Science > QP Physiology
Q Science > QR Microbiology
Divisions: Faculty of Science, Engineering and Medicine > 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:
DateEvent
8 September 2019Published
3 September 2019Accepted
Volume: 10
Number: 9
Article Number: e691
DOI: 10.3390/genes10090691
Status: Peer Reviewed
Publication Status: Published
Reuse Statement (publisher, data, author rights): ** 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 (Creative Commons)
Date of first compliant deposit: 12 September 2019
Date of first compliant Open Access: 12 September 2019
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
GM083068National Institutes of Healthhttp://dx.doi.org/10.13039/100000002
Graduate Research Fellowships Program National Science Foundationhttp://dx.doi.org/10.13039/501100008982
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