Sexual reproduction is the null hypothesis for life cycles of rust fungi

Hemileia vastatrix in Coffea spp.: Distribution of Urediniospores Grouped by Size and Insights into Morphological Structures

Hemileia vastatrix coffee leaf rust reduces Mexican coffee production by 51%. We aimed to analyze the size and distribution of H. vastatrix urediniospores among coffee plantations, as well as the morphological structures of the uredinium. In 2015, 65 leaf samples with rust symptoms were collected from 17 coffee cultivars grown at various altitudes (229-1649 m) under different environmental conditions in 14 regions of four Mexican states. A total of 30 spores per sample were measured and grouped using the Ward centroid method, and the group distribution was analyzed. Uredinia morphology was examined via electron microscopy, and the identity of the rust was confirmed. We identified eight significant spore groups. Groups 8h and 3a had the smallest and largest spores, respectively, which were distributed in two and one state, respectively, at different altitudes. The spores in groups 1b-7f were variable within the intermediate size range, and their distribution was at least one group per state under temperate, warm, and humid conditions. The uredinium had double-cell walls in the pedicels and urediniospores, a split septum, spores with hilum and protuberances, and an oval spore shape; anastomosis was detected on vegetative hyphae and haustoria. These findings may reflect gaps in knowledge in the biological cycle of this rust.

Segmental duplications drive the evolution of accessory regions in a major crop pathogen

Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.

Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.

Current Status and Future Perspectives of Genomics Research in the Rust Fungi

Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.