Abstract:
As the global population approaches 10 billion, the challenge of ensuring food security becomes increasingly urgent. Rice, a staple crop for much of the world, and its wild relatives in the Oryza genus hold significant promise for crop improvement. My PhD defense seminar will explore how leveraging high-quality genomic resources from wild Oryza species, particularly the autotetraploid HHJJ genome types O. ridleyi and O. longiglumis, provides crucial insights into the evolutionary dynamics of these genomes, allowing for the reconstruction and study of ancestral genomes, as well as the analysis of gene fractionation and the contribution of transposable elements (TEs) to genome size expansion.

I will introduce the concept of Platinum-Standard Reference Sequences (PSRefSeq), presenting the first PSRefSeqs for polyploid O. ridleyi and O. longiglumis. These resources establish a new standard for genome assembly in crop wild relatives and provide a foundation for a wide range of evolutionary studies offering a deeper understanding of the structural and functional evolution of plant genomes.

Next, my research will further explore the evolutionary dynamics of both genes and transposable elements (TEs) in polyploids, focusing on gene fractionation and how nested TE insertions have driven the expansion of the HH subgenome, making it approximately 1.5 times larger than the JJ subgenome in both species. This expansion has significant implications for evolutionary processes. I will also characterize TEs in terms of their phylogeny and insertion times, as well as analyze fractionated genes for Gene Ontology (GO) term enrichment.

Additionally, I will present the ancestral genome reconstruction of the subgenome HH and JJ genomes as well as the ancestor of HHJJ species, generated using the Progressive Cactus alignment tool. These reconstructed sequences provide insights into genome evolution over the past ~9.8 million years, enabling a detailed study of the rapid turnover of transposable elements (TEs) and the identification of fixed TEs, along with the selective pressures acting upon them.

In conclusion, my talk provides key insights into the evolutionary dynamics of transposable elements and genome evolution in the Oryza HHJJ genome wild relatives, laying the groundwork for deepening our understanding of plant genome evolution with an emphasis on TEs over millions of years. Finally, I will consolidate these findings, emphasizing the potential of Oryza wild relatives and their genomic diversity in efforts to improve rice crops and contribute to global food security solutions.

Bio:
Saule Mussurova completed her BSc in Genetics at University College London in 2014, followed by a MSc in Plant Genetics and Crop Improvement at the University of East Anglia in 2017. She has briefly worked as a junior researcher (Nazarbayev University, Astana, Kazakhstan) and a start-up consultant (Nazarbayev University – Colorado State University) before following her passion for science, outreach and food sustainability by pursuing a PhD in Plant Science at KAUST in Professor Rod A. Wing's laboratory. Her PhD thesis topic explored the genome biology and evolution of two wild relative of rice – Oryza ridleyi and Oryza longiglumis thereby, laying the foundation for their use in the improvement of cultivated rice, neodomestication and conservation.