Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes

Abstract

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid Arabidopsis kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to ∼90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.

Using runs of homozygosity and machine learning to disentangle sources of inbreeding and infer self-fertilization rates

“…Our results show that self-compatible NT1 is a mixed mater with outcrossing still occurring, while MW7S showed higher degrees of selfing. These selfcompatible lineages with intermediate selfing rates would allow for frequent admixture events, consistent with the analyses of Kolesnikova et al . (2023), which detected a considerable amount of contemporary gene flow between selfing and outcrossing populations.…”

“…In A. lyrata , we found two mixed mating populations (NT1, MW7S) matching published populations that gained self-compatibility (Kolesnikova et al . 2023).…”

“…2019; Zeitler et al . 2023) and six populations of Arabidopsis lyrata (Kolesnikova et al . 2023), as well as two highly selfing species, with four populations from the model plant Arabidopsis thaliana (Alonso-Blanco et al .…”

“…2011; Buehler et al . 2012) for A. alpina and (Kolesnikova et al . 2023) for A. lyrata ) or as a empirical control of highly selfing organisms A. thaliana and C. briggsae .…”

“…2023). For A. lyrata we used the same biallelic SNPs as described in the demographic modeling section of Kolesnikova et al . (2023) kindly provided by the authors.…”