PREreview of HarbouringStarships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi

PREreview of “Harbouring Starships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi”

Authors: Samuel O’Donnell, Gabriela Rezende, Jean-Philippe Vernadet, Alodie Snirc1, Jeanne Ropars

Posted on: bioRxiv

URL: https://www.biorxiv.org/content/10.1101/2024.07.03.601904v1

Brief summary of the study

The study investigated the presence and impact of horizontal gene transfers (HGT) of large transposons, termed Starships, in the genomes of domesticated and pathogenic fungi, particularly focusing on the genera Aspergillus and Penicillium. Their findings showed that fungi associated with human-related environments, such as food production and clinical settings, have significantly higher Starship content compared to their wild counterparts. This accumulation of Starships is proposed to facilitate rapid adaptation to the study environment.

Major comments (validity or strength of the methodology, experiments and analyses, strength of the conclusions)

• This report looks pretty good, describing quantification, great discussion of previous articles and talking about how Starship is leading to evolution.

• The study combined publicly available and newly assembled genomes of over 1,600 genome dataset. The use of long-read sequencing to identify complete Starship elements is a strength, as it mitigates the limitations of short-read assemblies. However, the reliance on the number of Captain genes as a proxy for Starship content may introduce some inaccuracies. The authors validate this proxy through correlations with genome size, which is commendable but further direct validations (e.g., experimental confirmation of gene functionality) would strengthen the conclusions.

Minor comments (clarifications to statements in the text, interpretation of the results, presentation of the data/figures)

• In the introduction, it could be helpful to provide a brief explanation of why the specific genera Aspergillus and Penicillium were chosen for this study

• The final paragraph in the introduction is a conclusion of the work, so it might be better to remove it from the introduction and add it under a conclusion subtitle

• The figures are well represented. However, to make the article interesting to read, especially for non-fungal genomic scientists, additional simpler legends or details can be added to some of the figures. For instance, the phylogenetic tree in Figure 1 is quite dense and could benefit from being split into multiple panels or provided with more detailed information to enhance clarity and comprehension.

• Some sections, such as the detailed explanation of the methodology, could be streamlined for better readability. For instance, the description of the genome-graph based pipeline could be summarized more concisely. The figures effectively illustrate the findings, but some complex graphs might benefit from additional explanatory legends or annotations to aid in interpretation for non-specialist readers.

• The methodology has some sections with complex workflows and processes, so it might be a good idea to include figures or flowcharts that visually represent the methodology, making it easier to follow and understand

Comments on reporting (information on the statistical analyses or availability of data)

• The statistical methods used to assess the significance of the differences in Starship content across different environmental settings were well-described. The resources for the genome database for the Starship extraction should be made publicly available to ensure reproducibility of the work for upcoming studies.

• The statistical methods used to correlate Captain counts with genome sizes and to compare Starship content among different environments are appropriate and well-explained. The use of BUSCO-based phylogenetic trees adds robustness to species identification.

Suggestions for future studies

• Expanding the survey to include a wider range of environmental contexts and fungal species could provide a better understanding of the ecological and evolutionary mechanism of Starship acquisition.

• I=For future studies, it is suggested to investigate the functional roles of Starship cargo genes in greater detail to elucidate their contributions to fungal adaptation.

Conflicts of interest of reviewers

• There are no conflicts of interest to declare.

Competing interests

The authors declare that they have no competing interests.