Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual—a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

“…1c), as reported for Gh 25 , except for a few small inversions in D10 of Gt-Gm and Gm-Gb and D12 of Gd-Gt-Gm. This level of structural conservation is similar to some polyploids such as wheat 7 and Arabidopsis suecica 34 , but is different from others such as B. napus 10 , peanut 35 and T. miscellus 11 , which show rapid homoeologous shuffling.…”

Healthy Roots and Leaves: Comparative Genome Structure of Horseradish and Watercress

“…The available data on postpolyploid evolution in other crucifer allopolyploids suggest that the polyploid chromosome numbers and structure of parental subgenomes can be remarkably stable for up to a few hundred thousand years. The allopolyploid Arabidopsis suecica (2n = 26) show the stability of both parental subgenomes (Comai et al, 2003) since its origin after the last glacial maximum 22,000 years ago (Novikova et al, 2017). A comparable level of subgenome stasis is anticipated for Capsella bursa-pastoris (2n = 32), an allotetraploid genome formed during the past 100,000 to 300,000 years (Douglas et al, 2015), and the three subgenomes of the allohexaploid Camelina sativa (2n = 40; Kagale et al, 2014).…”

Competition of Parental Genomes in Plant Hybrids

“…For this reason, we focus here on allopolyploids and provide only several known examples of chromosome rearrangements in artificial homoploid hybrids. Allopolyploid hybrids possess three or more chromosome sets from two or more species, e.g., A. suecica (Novikova et al, 2017). Assuming that the basic chromosome number is the same in both parents, each chromosome in an allopolyploid can pair either with its homolog or with one of the two homoeologs.…”