De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests

  1. Zoltan Erdos
  2. David John Studholme
  3. Ben Raymond
  4. Manmohan D. Sharma

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Abstract

The entomopathogenic fungus Akanthomyces muscarius is commonly used in agriculture to manage insect pests. Besides its use as a commercially important biological control agent, it also presents a potential model for studying host–pathogen interactions and the evolution of virulence in a laboratory setting. Here, we describe the first high-quality genome sequence for A. muscarius . We used long- and short-read sequencing to assemble a sequence of 36.1 Mb with an N 50 of 4.9 Mb. Genome annotation predicted 12347 genes, with 96.6 % completeness based on the core Hypocrealen gene set. The high-quality assembly and annotation of A. muscarius presented in this study provides an essential tool for future research on this commercially important species.

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  1. Version published to 10.1099/acmi.0.000568.v3 on Access Microbiology
  3. Version published to 10.1099/acmi.0.000568.v2 on Access Microbiology
  4. Access Microbiology

    This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. Thank you for your submission. The manuscript is in a broadly appropriate state with reviewers highlighting minor edits which would strengthen the piece. Please address these comments.

  5. Access Microbiology

    Comments to Author

    Methodological rigour, reproducibility, and availability of underlying data For this work to provide a high-quality genome assembly for Akanthomyces muscarius multiple methods have been trailed and their effectiveness reported using methods such as Quast and BUSCO. The data, both raw reads and final assembly, are given in repositories and full details are given for running of software. Presentation of results The results are presented as tables that summaries the assembly statistics of the Akanthomyces muscarius with the various methods used as well as comparison assembly statistics to organisms of the same order. This seems appropriate for the information being conveyed in this work. How the style and organization of the paper communicates and represents key findings The style and organisation are appropriate to communicate a genome announcement. Literature analysis or discussion This is limited due to the nature of the work, however the relevant research on genome assembly, trimming and quality has been cited and taken into consideration here. Any other relevant comments While I don't think it is a requirement - an interesting and useful addition to this paper could be in inclusion of Ideel (https://github.com/mw55309/ideel) analysis to add to the assessment of assembly quality. Similarly, I think it would be a useful addition to include some phylogenetic information based on this sequence perhaps showing how this genome fits within the Hypocreales or wider.

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  6. Access Microbiology

    Comments to Author

    This genome report details the sequencing of Akanthomyces muscarius using a hybrid approach. 1. Methodological rigour, reproducibility and availability of underlying data The methods are sound and the bioinformatics appears to have been performed well. The authors provide the codes used for assembly and annotation and the final genome is available in GenBank. One point that needs clarification is the number of Illumina libraries that were sequenced. The text refers to plural (libraries), but it reads as if only a single library was sequenced. 2. Presentation of results There are several instances in which I would like the writing to be clarified (please see attachment) and three instances of results that I think could be added to complete the picture. The results of the sequencing runs (i.e. the number of reads) are given in the Methods section, whereas this may be more suited to the beginning of the Results section. The authors base their section of the POLCA-corrected Flye assembly on the BUSCO scores, but they do not report the BUSCO scores for the assemblies in Table 1. These should be included. It is also important to note whether the BUSCO scores reported is the combined result of the single-copy and duplicate BUSCOs or only the single-copy. RepeatMasker was used to identify repeats in the genome. The total percentage of repeats should be added to Table 2 for easy comparison among the species. Then, instead of only mentioning which repeats were found in the text (lines 145-146), the authors should include a table of the different types and their respective contributions to the total repeat content. The conclusions mention that this is a near chromosome-level assembly. It would be valuable for the authors to search for telomere repeats in the genome to support their claim. This would also indicate whether any full-length chromosomes are contained in the assembly. 4. Literature analysis or discussion I find the discussion of the availability of other genomes in this genus or of other entomopathogenic fungi a bit lacking. Neither the introduction or conclusion mentions how many genomes are available in either of these categories. It is also, therefore, unclear how the genomes used for comparison in Table 2 were selected - are these all the other available genomes of Hypocreales entomopathogens or just a selection? And if a selection, how were they chosen? The conclusions section is only two sentences long, so there is ample opportunity for providing some more detail.

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Satisfactory

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  7. Version published to 10.1099/acmi.0.000568.v1 on Access Microbiology