Genomics of Diploidization in Palms and Grasses

Polyploidy refers to a state in which organisms have more than two complete sets of chromosomes. Following polyploidy, short and long-term cytological and genomic changes lead polyploids to restore a diploid-like state--the process known as diploidization. The diploidization rate and mechanisms show lineage-specific differences, and there is insufficient evidence to define a clear paradigm of how different polyploid species respond to post-polyploidy changes. Here, I investigated the consequences of whole genome duplication (WGD) following an ancient event in palms and another recent event in grass species Zea mays. I generated a chromosome-level genome assembly of a mangrove palm species Nypa fruticans, characterized its variation in the structural features compared to other palm genomes, and investigated the retention of duplicated genes. I found that the N. fruticans genome differs in chromosomal rearrangements and in accumulation of transposable elements with other palm species following WGD. I also identified high retention of duplicated genes in N. fruticans. Functional enrichment analysis showed that the dosage balance hypothesis and selective pressures of adapting to a harsh intertidal environment could primarily explain the retention of the duplicated genes. Further exploration of salt-tolerant orthologous genes also supports the hypothesis. To study maize, I generated a chromosome-level monoploid genome assembly of a parental relative Vossia cuspidata and used phylogenomic approaches to detect signals of homoeologous exchange, exploring its impact on the evolutionary history of maize subgenomes following WGD. The study found that V. cuspidata is closely related to one of the maize diploid progenitors, with homoeologous exchanges potentially obscuring the ancestry of maize subgenomes. Further, through transcriptomic profiling of maize and its wild relatives, I investigated the functional differences in the flooding tolerance of these species. I identified evolutionarily conserved and species-specific genes in response to flooding stress. The findings suggest that extensive rewiring of the gene regulatory circuitry and the outcome of phenotypic plasticity resulting from the interaction with their environment might underlie the variation in flooding response in maize and its relatives. Altogether, my dissertation provides important insights into the dynamics and complexity of diploidization and suggests that understanding the lineage-specific differences requires further investigations.