Přehled o publikaci

The cyclic process of polyploidization and diploidization is fundamental to the evolution of plant genomes. Post-polyploid diploidization (PPD) results in variation in karyotype structures and genomic sequences, which can vary in intensity and be accompanied by speciation events. It remains unclear how and to what extent chromosomal diploidization, including descending dysploidy, i.e., reduction in chromosome number, is associated with diploidization at the sequence level. Our previous work has demonstrated two-speed (fast vs. slow) chromosomal diploidization in genomes of different subclades of the monophyletic crucifer tribe Microlepidieae, endemic to Australia and New Zealand. These meso-allotetrapolyploid genomes originated via a shared hybridization followed by long-distance dispersal (LDD) to Australasia. In this presentation, I will describe our recent work investigating the PPD process in genomes of representative species of the Microlepidieae and the closely related tribe Hemilophieae. We have generated chromosome-level genome assemblies for six species with a 3.5-fold variation in chromosome number (n = 4 to n = 14) and a 4.3-fold variation in genome size (0.4 to 1.7 Gbp). The expansion of genome size was mainly caused by the accumulation of LTR retrotransposons, especially Athila elements. Despite evolutionary genome reshuffling during PPD, we were able to identify subgenome-specific genomic regions based on different gene fractionation and gene tree topologies, as well as shared karyotype structures with closely related diploid genomes. While we observed comparably high levels of gene retention in the dominant subgenomes, we found biased genome fractionation in the submissive subgenomes, with the extent of gene loss varying across genomes. Subgenome-aware phylogenomics revealed a shared ancestry of the Microlepidieae and Hemilophieae tribes. Whereas the maternal subgenomes (n = 8) were sister to the Crucihimalayeae, the paternal subgenome (n = 6) has karyotype identical to extant genomes of the tribe Yinshanieae. Therefore, our genomic evidence indicates that the most common ancestor of the Microlepidieae (n = 14) most likely originated in the Himalaya–Hengduan Mountains, where the Hemilophieae species are endemic. Despite the lack of correlation between diploidization at the chromosomal and sequence levels, we posit that the differential extent of PPD in the Microlepidieae genomes may be related to eco-physiological adaptations after LDD. We are currently inspecting the functional relevance of gene loss and retention across species. In addition, we are comparing whole-genome methylation profiles between genomes and subgenomes to investigate their epigenetic divergence during PPD at different rates. Using the Microlepidieae species as a model system, our results provide new insights into the PPD process in plants.