Genome evolution in the carnivorous plant Utricularia gibba

We performed several investigations related to the nuclear genome of U. gibba, which was sequenced as part of this study. Despite having a much smaller genome size, the U. gibba genome accommodates more genes than several well-known plant species, such as grape, coffee or papaya. The main difference between U. gibba and other known plant genomes is in the dramatic reduction of non-coding DNA. A transient expression assay of some compact promoters from U. gibba suggested their possible functionality for downstream gene regulation. Our results suggest that only a small fraction of non-coding DNA is sufficient to regulate the processes essential for both the development and reproduction of a complex, specialized plant species. Second, we found evidence that at least three rounds of whole genome duplication (WGD) have occurred during the evolution of U. gibba's genome since the time it diverged from a common ancestor with tomato and grape. Our study on the duplicate gene turnover rate of U. gibba has suggested that the gene death rate is significantly higher in U. gibba than for four other plant species included in the study. Interestingly, the gene gain rate is also significantly higher, likely reflecting the occurrence of multiple WGD events and possibly also small-scale genome duplications. Taking together, the compact U. gibba genome not only drastically reduced its non-coding DNA content, but also dynamically gained and shed newly duplicated coding genes very rapidly, the latter of which applied constraint on its total gene number. Statistical analysis of functional categories assigned to gene families in U. gibba and four other plant species revealed several functions to be strongly associated with U. gibba-specific gene families, gene singletons or gene families specifically expanded in U. gibba as compared to the other species. These results suggested important roles for these functions in U. gibba evolution, given that they survived deletion pressure during its genome evolution. Last, phylogenetic analysis of MADS-box genes from 7 angiosperms revealed gene subfamily expansions and contractions in different plant species, and the observed dynamics among gene subfamilies were proposed to have potential functional significance for these species, especially U. gibba. Evolutionary models were proposed based on the investigation of syntenic relationships among genomic blocks containing MADS-box genes from clades that show interesting subfamily expansions in U. gibba. Our results suggested that shared or taxon-specific WGDs and tandem duplications, together with protein functional changes, could further shape gene subfamily architecture in eudicots.