Long-term balancing selection drives evolution of immunity genes in Capsella

ELife
Daniel KoenigDetlef Weigel

Abstract

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

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Citations

Jun 30, 2019·The New Phytologist·Jörg A BachmannTanja Slotte
Feb 19, 2020·Molecular Biology and Evolution·Paul D BlischakRyan N Gutenkunst
May 18, 2020·Genetics·Tuomas Hämälä, Peter Tiffin
Aug 30, 2020·Nature Reviews. Genetics·Dieter Ebert, Peter D Fields
Sep 20, 2019·Ecology and Evolution·Tiina M MattilaTanja Slotte
Sep 25, 2020·The New Phytologist·Wei-Lin WanEunyoung Chae
Feb 13, 2021·Heredity·J Grey MonroePádraic J Flood
Apr 7, 2021·Nature Ecology & Evolution·Daehan LeeErik C Andersen
Mar 7, 2021·Evolution; International Journal of Organic Evolution·Sylvain Glémin
Apr 15, 2021·Molecular Plant-microbe Interactions : MPMI
Apr 2, 2021·The Plant Cell·A Cristina Barragan, Detlef Weigel
Jun 19, 2021·Fungal Biology·Sandra HilárioArtur Alves
Sep 10, 2021·Nature·Rory N PruittThorsten Nürnberger
Oct 3, 2021·Journal of Molecular Biology·Asen Daskalov, N Louise Glass
Nov 20, 2021·Evolution; International Journal of Organic Evolution·Amanda Kyle Gibson

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Methods Mentioned

BETA
PCA
Illumina sequencing

Software Mentioned

bwa
Fastsimcoal
Falcon
SnpEff
freebayes
AliView
BEAGLE
GenomeMapper
EIGENSTRAT
vcftools

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