High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features

Sutherland, Chandler A.; Prigozhin, Daniil M.; Monroe, J. Grey; Krasileva, Ksenia V.

doi:10.1038/s44319-024-00122-9

High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features

Journal Article · Mon Mar 25 04:00:00 EDT 2024 · EMBO Reports

DOI:https://doi.org/10.1038/s44319-024-00122-9· OSTI ID:2470735

^[1]; Prigozhin, Daniil M. ^[2]; ^[3]; ^[1]

University of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
University of California, Davis, CA (United States)

Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low-variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen-recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Institutes of Health (NIH); Gordon and Betty Moore Inventor Fellowship

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2470735

Journal Information:: EMBO Reports, Journal Name: EMBO Reports Journal Issue: 5 Vol. 25; ISSN 1469-3178

Publisher:: EMBO PressCopyright Statement

Country of Publication:: United States

Language:: English

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Dataset for "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features" Sutherland, Chandler A.; Prigozhin, Daniil M.; Monroe, J. Grey Zenodo https://doi.org/10.5281/zenodo.10530531	dataset	January 2024
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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Cell Biology
Evolution
Genomic Features
Immunity
Nucleotide-binding Leucine-rich-repeat Receptors (NLRs)

High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features

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