Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa

Abstract

Genome duplication, which results in polyploidy, is disruptive to fundamental biological processes. Genome duplications occur spontaneously in a range of taxa and problems such as sterility, aneuploidy, and gene expression aberrations are common in newly formed polyploids. In mammals, genome duplication is associated with cancer and spontaneous abortion of embryos. Nevertheless, stable polyploid species occur in both plants and animals. Understanding how natural selection enabled these species to overcome early challenges can provide important insights into the mechanisms by which core cellular functions can adapt to perturbations of the genomic environment. Arabidopsis arenosa includes stable tetraploid populations and is related to well-characterized diploids A. lyrata and A. thaliana. It thus provides a rare opportunity to leverage genomic tools to investigate the genetic basis of polyploid stabilization. We sequenced the genomes of twelve A. arenosa individuals and found signatures suggestive of recent and ongoing selective sweeps throughout the genome. Many of these are at genes implicated in genome maintenance functions, including chromosome cohesion and segregation, DNA repair, homologous recombination, transcriptional regulation, and chromatin structure. Numerous encoded proteins are predicted to interact with one another. For a critical meiosis gene, ASYNAPSIS1, we identified a non-synonymous mutation that is highly differentiated by cytotype, but present as a rare variant in diploid A. arenosa, indicating selection may have acted on standing variation already present in the diploid. Several genes we identified that are implicated in sister chromatid cohesion and segregation are homologous to genes identified in a yeast mutant screen as necessary for survival of polyploid cells, and also implicated in genome instability in human diseases including cancer. This points to commonalities across kingdoms and supports the hypothesis that selection has acted on genes controlling genome integrity in A. arenosa as an adaptive response to genome doubling.

Figure 1. Geographic locations of A. arenosa populations sampled in this study.

Geographic locations of sampled tetraploid populations from railways (red) and forested rock outcrops (green), and two diploid populations (blue). TBG = Triberg railway station, Germany; US = Upfinger Steige, Bad Urach, Germany; BGS = Berchtesgaden railway station, Germany; KA = Kasparstein castle, Austria; SN = Streçno castle, Slovakia; CA = Carpathian Mountains, Southern Tatras range, Slovakia. For genome sequencing, we sampled three plants each from TBG, US, BGS and KA.

Figure 2. The site frequency spectrum of A. arenosa.

Folded site frequency spectrum (SFS) of single nucleotide polymorphisms (SNPs) in A. arenosa protein-coding sequences. Each column indicates the abundance of SNPs that fall into a particular frequency class and columns are color-coded to indicate non-synonymous sites (red) and synonymous sites (blue). There is a significant skew toward low-frequency mutations at non-synonymous sites (red) compared to synonymous sites (dark blue) (Mann-Whitney U Test p<7×10⁻⁸).

Figure 3. Site frequency spectra and SNP frequency for NRPB1 and ASY1.

(A) Polymorphism in NRPB1. Top graph shows unfolded SFS (top graph) relative to A. lyrata. Lower graph shows SNP frequencies along the gene's length relative to A. lyrata and A. thaliana. Light blue rectangle indicates region coding for C-terminal heptad repeat tail. (B) Polymorphism in ASY1. Top graph shows unfolded SFS (top graph) relative to A. lyrata. Lower graph shows SNP frequencies along the gene's length relative to A. lyrata and A. thaliana. Light blue rectangle indicates region encoding conserved HORMA domain. Non-synonymous sites are shown in red, synonymous in dark blue, and intronic sites in grey.

Figure 4. Conservation within the HORMA domain of ASY1.

Alignment of a portion of the conserved HORMA domain of ASY1 with related sequences obtained from GenBank (Species names and GenBank numbers are given). Stars above the alignment indicate amino acids perfectly conserved among these sequences. The boxed amino acid position indicates one in which a derived allele (K>E) predominates in tetraploid A. arenosa that is rare in diploid A. arenosa and not found in other species reported in Genbank.

Figure 5. Predicted interactions among 27 putatively selected genes in A. arenosa.

Network shows connections predicted by the AtPIN database (see methods) among selected genes in A. arenosa.