Comparative genomics reveals expansion of the FLC region in the genus Arabidopsis

Population history in Arabidopsis halleri using multilocus analysis

A. halleri is a psuedometallophyte with a patchy distribution in Europe and is often spread by human activity. To determine the population history and whether this history is consistent with potential human effects, we surveyed nucleotide variation using 24 loci from 12 individuals in a large A. halleri population. The means of total and silent nucleotide variation (theta(W)) are within the range expected for the species. The population genetic neutrality tests Tajima's D and Wall's B had significant composite results rejecting panmixia, and Approximate Bayesian Computation analysis revealed that a subdivision model better explained the variation than the standard neutral model, refugia (or admixture), bottleneck or change of population size models. A categorical regression analysis further supports the subdivision model, and under the subdivision model, the neutrality tests are no longer significant. The best support was for two source populations, a situation consistent with the mixing of two populations possibly mediated by human activity. This scenario might limit the genetic diversity and adaptive potential of the population. The non-neutral population variation described here should be considered in bioinformatic searches for adaptation.

Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana

We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.