PS Seminar Series: PhD Exit Seminar: Phylogenomics and population genetics of global lineages of the wheat stripe rust pathogen Puccinia striiformis

Abstaract  - Wheat stripe rust, also known as yellow rust, is one of the most devastating diseases of wheat worldwide. It is caused by a complex basidiomycete fungus, Puccinia striiformis (PST). Genetic resistance has provided the most effective means of controlling the disease, but the appearance of PST races that overcome widely deployed R genes has led to destructive pandemics. In recent years, concerns over stripe rust have increased with the emergence of highly aggressive PST races (PST-S1/S2 and PST-S7/8) that have expanded virulence profiles and are well adapted to warmer temperatures compared to previous races. Rust researchers have been trying to understand the cause of this sudden resurgence of highly aggressive isolates. Microsatellite-based population genetic studies have suggested that the modern pandemic was led by the incursions of PST isolates of North Eastern Africa origin and sexually recombined isolates believed to be originated from the Himalayan region. However, more detailed analysis of the global PST isolates is required to truly understand the scale of diversity in worldwide populations. Apart from the periodic incursion/outbreak of new isolates, PST also has a remarkable ability to quickly evolve new pathotypes, rendering the widely deployed resistance gene effective. This remarkably fast evolution rate in the absence of sexual recombination has been linked to its dikaryotic lifestyle (two independently evolving nuclei) and somatic hybridization (somatic hyphal fusion of two genetically diverse isolates leading to nuclei swapping). However, conclusive evidence that these processes contribute to PST evolution is yet lacking.

I attempted to understand the worldwide population structure of PST and find evidence for the existence of somatic hybrids in the PST population by analysis of the nuclear and mitochondrial genomes of 120 global isolates. I also established methods for high purity high molecular weight DNA extraction from PST urediniospores, and produced highly contiguous genome assemblies of PST isolates, Pst-S0 and Pst-S1, the predominant races in Australia, using Oxford Nanopore sequencing technology. I developed methods for high purity high molecular weight DNA extraction from PST urediniospores which is a prerequisite for Oxford Nanopore Technologies (ONT) long-read sequencing. The ONT sequencing produces very long reads enabling highly contiguous genome assemblies. These highly contiguous assemblies help to separate the individual nuclei genomes, enabling a better understanding of inter-haplome variation. To study variation in the PST mitochondrial genome, I de novo assembled mt-genome of three major lineages (Pst-S0, Pst-S1 and Pst-S7) using long PacBio reads. The PST mt-genome is ~102 Kb in size, and its coding regions are highly interspersed with AT-rich repeats. The variation in the mitochondrial genes nad5 and nad6 differentiates the three major lineages, Pst-S0, Pst-S1, Pst-S7/8 and a forma specialis of PST, Puccinia striiformis f. sp. hordei (PSH). For diversity analysis at the nuclear genome level, I used whole-genome genotyping by sequencing (GBS) to genotype 120 PST isolates from different geographical locations. The GBS analysis recapitulates the known phylogenetic relationships between the major PST lineages (PstS0, PstS1, Pst-S2, Pst-S7 and Pst-S8). The microsatellite-based diversity analysis done at the Global Rust Reference Center in Denmark predicts 10 PST groups globally, whereas my analysis which is based on whole genome comparisons describes 5 major lineages. Genetic admixture analysis showed extensive genetic admixture in the asexual lineages of Canadian origin (Pst-CA1 and Pst-CA2) and forma specialis isolates, suggesting somatic hybridization in the history of these isolates.

Biography  - I did a Bachelor of Science (Honours) in Agricultural Science (B.Sc. (Hons.) Ag) from the Rajasthan Agriculture University, Bikaner, Rajasthan, India (1999 to 2003). I did a Master of Biotechnology (MSc) in Plant Science from Himachal Pradesh Agricultural University, Palampur, India (2003-2006). I then got a Scientist position at the National Institute of Plant Biotechnology, New Delhi (joined in 2010 and worked there until Nov 2015). I got leave from my institute to study for the PhD degree at ANU in Dec 2015. I joined the Rathjen laboratory for the PhD in Dec 2015.