A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology

Moolhuijzen, Paula; See, Pao Theen; Shi, Gongjun; Powell, Harold R.; Cockram, James; Jørgensen, Lise Nistrup; Benslimane, Hamida; Strelkov, Stephen E.; Turner, Judith A.; Liu, Zhaohui; Moffat, Caroline S.

doi:10.1099/mgen.0.000872

Cited by 10 publications

(8 citation statements)

References 88 publications

(148 reference statements)

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“…We obtained the set of 27 P. tritici-repentis genomes [15] used to benchmark Parsnp v1 in a recent study [11] and ran Parsnp v2 without partitioning. While most the metrics of Parsnp v2 remain the same as those reported in [11], the memory usage dropped from 57Gb to 8.4Gb.…”

Section: Resultsmentioning

confidence: 99%

Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets

Kille,

Nute,

Huang

et al. 2024

Preprint

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Motivation:Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014.Results:To address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4x and reduce runtime by over 2x, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes.

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Section: Resultsmentioning

confidence: 99%

Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets

Kille,

Nute,

Huang

et al. 2024

Preprint

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“…The latter could be detected by first identifying mChr and other accessory genomic elements, and then comparing them with the core genome. Studies of this nature have recently detected cases of horizontal introgression in other fungal pathogens (Moolhuijzen et al 2022; Petersen et al 2023). In addition to these approaches, the integration of artificial intelligence to distinguish between core chromosomes and mChr using short-read sequencing data presents a timely and innovative approach (Gyawali et al 2023).…”

Section: Discussionmentioning

confidence: 99%

Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages

Barragan,

Latorre,

Malmgren

et al. 2024

Preprint

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Crop disease pandemics are often driven by clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb supernumerary mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.

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“…Gene PAV plays an important role in fungal pan-genome evolution [2][3][4][5]. To improve our understanding of these events, we designed a robust pipeline to identify orthogroups experiencing PAV in M. oryzae.…”

Section: Discussionmentioning

confidence: 99%

“…While bacteria typically gain and lose genes in the form of large horizontal gene transfer events [1], the accessory portion of fungal pan-genomes, which is defined in contrast to the conserved set of genes found in all members of a species, are typically shaped by small gene duplication and deletion events, which contribute to gene presence-absence variation (PAV) [2]. Previous fungal pan-genome studies have focused on the roles and functions of core and accessory genes [2][3][4][5], but our knowledge of which genomic and epigenomic features shape fungal pangenomes remains limited. Some studies have highlighted an association of accessory genes with subterminal chromosomal regions and transposable elements (TEs) [2,3], but it is uncertain whether these associations are strong enough to be predictive of gene PAV.…”

Section: Introductionmentioning

confidence: 99%

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Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen

Joubert

Krasileva

2023

Preprint

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Background: Fungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts. Results: We analyzed gene PAV in the rice and wheat blast fungus, Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infecting M. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes of M. oryzae differed in their number and their genomic context. Conclusions: Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.

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A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology

Cited by 10 publications

References 88 publications

Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets

Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets

Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages

Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen

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