title: Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention.
abstract: Hybridization and polyploidy followed by genome-wide diploidization had a significant impact on the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization affected post-polyploid gene retention. Sixteen species representing 10 Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for the tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of genomic data for Brassicaceae indicate that extant chromosome number variation in many plant groups, and especially monophyletic taxa with multiple base chromosome numbers, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests of the predictability of patterns of post-polyploid genome evolution.
authors.affiliation: Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
authors.forename: Terezie
authors.initials: T
authors.lastname: Mandáková
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Barker
authors.affiliation: Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Lysak
mesh_terms: D019607:Brassicaceae / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011123:Polyploidy
chemical_list: D010940:Plant Proteins
keywords: Brassicaceae; biased gene retention/loss; chromosomal rearrangement; chromosome number variation; descending dysploidy; mesopolyploidy; post-polyploid diploidization; whole-genome duplication