Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species—Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana

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Abstract
Comparative mapping in cruciferous plants is ongoing, and recently two additional genetic maps of diploid Capsella and Arabidopsis lyrata subsp. petraea have been presented. We compared both maps with each other using the sequence map and genomic data resources from Arabidopsis thaliana as a reference. The ancestors of the species pair Capsella–Arabidopsis diverged from one another approximately 10–14 million years ago (mya), whereas Arabidopsis thaliana and Arabidopsis lyrata have been separated since roughly 5–6 mya. Our analysis indicated that among diploid Capsella and Arabidopsis lyrata all eight genetic linkage groups are totally colinear to each other, with only two inversions significantly differentiating these two species.By minimizing the number of chromosomal rearrangements during genome evolution, we presented a model of chromosome evolution involving all three species. From this scenario, it is obvious that Arabidopsis thaliana underwent a dramatic genome reconstruction, with a base chromosome number reduction from five to eight and with approximately 1.3 chromosomal rearrangements per million years. In contrast, the terminal lineage leading to Capsella has only undergone less than 0.09 rearrangements per million years. This is the same rate as calculated for Arabidopsis lyrata since its separation from the Capsella lineage 10–14 mya. These results are in strong contrast to all overestimated rates calculated from comparisons of the systems Arabidopsis thaliana and Brassica, and our data demonstrate the problematic nature of both model systems.