Comparative genomics in the chestnut blight fungus Cryphonectria parasitica reveals large chromosomal rearrangements and a stable genome organization
Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus
About twenty-five years after the sequencing of the first fungal genome and a dozen years after the first plant pathogenic fungi genomes were sequenced, unprecedented international efforts have led to an impressive collection of genomes available for the community of mycologists in international databases (Goffeau et al. 1996, Dean et al. 2005; Spatafora et al. 2017). For instance, to date, the Joint Genome Institute Mycocosm database has collected more than 2,100 fungal genomes over the fungal tree of life (https://mycocosm.jgi.doe.gov). Such resources are paving the way for comparative genomics, population genomics and phylogenomics to address a large panel of questions regarding the biology and the ecology of fungal species. Early on, population genomics applied to pathogenic fungi revealed a great diversity of genome content and organization and a wide variety of variants and rearrangements (Raffaele and Kamoun 2012, Hartmann 2022). Such plasticity raises questions about how to choose a representative genome to serve as an ideal reference to address pertinent biological questions.
Cryphonectria parasitica is a fungal pathogen that is infamous for the devastation of chestnut forests in North America after its accidental introduction more than a century ago (Anagnostakis 1987). Since then, it has been a quarantine species under surveillance in various parts of the world. As for other fungi causing diseases on forest trees, the study of adaptation to its host in the forest ecosystem and of its reproduction and dissemination modes is more complex than for crop-targeting pathogens. A first reference genome was published in 2020 for the chestnut blight fungus C. parasitica strain EP155 in the frame of an international project with the DOE JGI (Crouch et al. 2020). Another genome was then sequenced from the French isolate YVO003, which showed a few differences in the assembly suggesting possible rearrangements (Demené et al. 2019). Here the sequencing of a third isolate ESM015 from the native area of C. parasitica in Japan allows to draw broader comparative analysis and particularly to compare between native and introduced isolates (Demené et al. 2022).
Demené and collaborators report on a new genome sequence using up-to-date long-read sequencing technologies and they provide an improved genome assembly. Comparison with previously published C. parasitica genomes did not reveal dramatic changes in the overall chromosomal landscapes, but large rearrangements could be spotted. Despite these rearrangements, the genome content and organization – i.e. genes and repeats – remain stable, with a limited number of genes gains and losses. As in any fungal plant pathogen genome, the repertoire of candidate effectors predicted among secreted proteins was more particularly scrutinized. Such effector genes have previously been reported in other pathogens in repeat-enriched plastic genomic regions with accelerated evolutionary rates under the pressure of the host immune system (Raffaele and Kamoun 2012). Demené and collaborators established a list of priority candidate effectors in the C. parasitica gene catalog likely involved in the interaction with the host plant which will require more attention in future functional studies. Six major inter-chromosomal translocations were detected and are likely associated with double break strands repairs. The authors speculate on the possible effects that these translocations may have on gene organization and expression regulation leading to dramatic phenotypic changes in relation to introduction and invasion in new continents and the impact regarding sexual reproduction in this fungus (Demené et al. 2022).
I recommend this article not only because it is providing an improved assembly of a reference genome for C. parasitica, but also because it adds diversity in terms of genome references availability, with a third high-quality assembly. Such an effort in the tree pathology community for a pathogen under surveillance is of particular importance for future progress in post-genomic analysis, e.g. in further genomic population studies (Hartmann 2022).
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Sebastien Duplessis (2022) Comparative genomics in the chestnut blight fungus Cryphonectria parasitica reveals large chromosomal rearrangements and a stable genome organization. Peer Community in Genomics, 100013. https://doi.org/10.24072/pci.genomics.100013
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/2021.03.09.434572
Version of the preprint: 4
Author's Reply, 17 Jun 2022
Decision by Sebastien Duplessis, 24 Jan 2022
After reading in full the latest version of your manuscript, I can see that the remarks from the two reviewers were carefully considered to generate this version, which now reads very well. The revised version of Table 1 with the metrics, now presented for the isolate ESM015, makes the data clearer for the reader.
I only have a final minor concern regarding one of the comments from the second reviewer:
Please explain the following: “EffectorP identified 1,117 models with a putative signal peptide,…pp.”. I don’t think effectorP predicts signal peptides please clarify. This section needs corrections as it is the wrong usage of EffectorP. EffectorP should only be applied on the secretome as mentioned in both original papers. This section says there are 88 high confidence CSEPs. Latter analysis talks about effectors e.g S5 how are all these related?
I had the exact same comment after reading the previous version of the article and unfortunately, this point does not seem to be fully resolved.
EffectorP indeed applies to the secretome, which should be first defined. I am not discussing the best method for secretome prediction, whatever the tools, it remains a prediction from the proteome and any investigator can choose a preferred tool or combination of tools for this. SignalP being one.
Here, I read and understand that SignalP was used on one side and EffectorP on the other one, then the overlap of the two sets is defining the set of high confidence effectors. It is somehow confusing.
One would expect to see i) SignalP applied to the proteome then ii) EffectorP applied onto the predicted secretome, then selection of candidate effectors for further investigation.
Also, in line 1431 the caption for Figure S5 indicates ... Effectors predicted by EffectorP or predicted by SignalP (SP) ... In the latter, they should not be claimed as "effectors" but rather as Predicted Secreted Proteins. This also adds to the confusion as pointed out by the same reviewer.
Finally, on the terms "high confidence effectors". EffectorP remains a prediction tool and high confidence could be gained only by complementary approaches (expression during host-interaction, homology with bona fide effectors, ...). "Selected candidate effectors" would be a more cautious naming. For your information, there is a new version of the EffectorP tool available (if applied, it may confirm the previously unraveled candidates, ... this is not mandatory or a request).
Minor point, CSEP acronym is defined on line 554 and should be used in plain again on line 724.
If the process of selection of your candidates could be clarified, it will be my pleasure to recommend this study in PCIgenomics.
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2021.03.09.434572
Version of the preprint: 3
Author's Reply, None
Decision by Sebastien Duplessis, 02 Jul 2021
I am happy to send my decision based on the reports from two reviewers who are experts in fungal genomics.
I am sincerely sorry for the too long delay in sending this decision. I was counting on the advices from a third reviewer with strong expertise in the field of forest pathogenomics. Unfortunately, I had to drop my hopes after a long period of silence with no more answers from this colleague. I hope there was no trouble on this reviewer’s side.
After I received the comments from the two reviewers, I went through your manuscript again and I concur with their constructive remarks and I am sure considering these will help strengthen and reshape the manuscript into a great article that I would be happy to recommend to the community!
With my best regards,