A high-resolution haplotype pangenome uncovers somatic hybridization, recombination and intercontinental migration in oat crown rust

Henningsen, Eva C.; Lewis, David; Nazareno, Eric; Huang, Yung-Fen; Steffenson, Brian J.; Boesen, Brendan; Kianian, Shahryar F.; Stone, Eric; Dodds, Peter N.; Sperschneider, Jana; Figueroa, Melania

doi:10.1101/2024.03.27.583983

Cited by 4 publications

(2 citation statements)

References 69 publications

(158 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Beyond adding genomes to the graphs, a step further would be to create a pangenome graph that incorporates fully phased diploid or polyploid genome assemblies, thus uncovering possible variation and recombination between haplotypes (Henningsen et al, 2024). For example, oomycetes are mostly diploids, but there are various reports of whole-genome duplication in Phytophthora betacei, and aneuploidy in Phytophthora capsici and in Phytophthora cinnamomi (Seidl et al, 2012;Kasuga et al, 2016;Hu et al, 2020;Ayala-Usma et al, 2021;Engelbrecht et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Especially chromosome-level genome assemblies will be essential to achieve the necessary resolution to uncover and study highly variable regions that are enriched for pathogenicity-related genes (Fletcher and Michelmore, 2023; Westerhoven et al ., 2024). Beyond adding genomes to the graphs, a step further would be to create a pangenome graph that incorporates fully phased diploid or polyploid genome assemblies, thus uncovering possible variation and recombination between haplotypes (Henningsen et al ., 2024). For example, oomycetes are mostly diploids, but there are various reports of whole-genome duplication in Phytophthora betacei , and aneuploidy in Phytophthora capsici and in Phytophthora cinnamomi (Seidl et al ., 2012; Kasuga et al ., 2016; Hu et al ., 2020; Ayala-Usma et al ., 2021; Engelbrecht et al ., 2021).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Skiadas,

Vidal,

Dommisse

et al. 2024

Preprint

View full text Add to dashboard Cite

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens’ genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage and expand on an innovative, multi-genome method to construct, annotate, and analyse the first pangenome graph of an oomycete plant pathogen. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogenPeronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates thatP. effusagenomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, pathogenicity related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.Author SummaryPlant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies ofPeronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Skiadas,

Vidal,

Dommisse

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Characterisation of virulence ofPuccinia coronataf. sp.avenaein Australia in the 2023 growing season

Nguyen,

Henningsen,

Lewis

et al. 2024

Preprint

View full text Add to dashboard Cite

Crown rust caused by the basidiomycete fungus Puccinia coronata f. sp. avenae (Pca) results in significant crop losses worldwide. Genetic solutions to protect against this disease require disease resistance gene discovery and introduction of resistance genes into elite germplasm by breeders. To inform disease resistance breeding activities, it is paramount to monitor changes of virulence in the Pca population and link those to genotypes of the pathogen. In 2023, a collection of 37 Pca isolates from diverse regions in Australia were gathered and their infection types across a commonly used set of oat differential lines determined to assign virulence pathotypes. We compared those virulence phenotypes to data collected in previous collections. While some of the virulence phenotypes had been reported in 2022, our analysis detected new virulence or an increase in frequency for virulence on some resistance genes. Notably, some of the frequency increases in virulence were recorded in Western Australia (WA), a region of interest due to its role in oat production for milling.

show abstract

The genetic diversity of the soybean rust pathogenPhakopsora pachyrhizihas been driven by two major evolutionary lineages

Rocha,

Ferreira,

Castanho

et al. 2024

Preprint

View full text Add to dashboard Cite

Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found high levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72-1 and AU79-1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two P. pachyrhizi lineages. We observed no clear congruence between virulence levels of P. pachyrhizi isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in P. pachyrhizi. Taken together, our study offers new insights into the evolutionary history of P. pachyrhizi and demonstrates that multiple MAT genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of P. pachyrhizi.

show abstract

A high-resolution haplotype pangenome uncovers somatic hybridization, recombination and intercontinental migration in oat crown rust

Cited by 4 publications

References 69 publications

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Characterisation of virulence ofPuccinia coronataf. sp.avenaein Australia in the 2023 growing season

The genetic diversity of the soybean rust pathogenPhakopsora pachyrhizihas been driven by two major evolutionary lineages

Contact Info

Product

Resources

About