Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)
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Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family Dacrymycetaceae and investigations on the biosynthesis of glycolipids with potential applications in the food industry.
This evaluation refers to version 1 of the preprint
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Abstract
The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has also been used in food additives given its ability to synthesize long-chain glycolipids. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size of D. spathularia is 29.2 Mb and in high sequence contiguity and completeness, including scaffold N50 of 1.925 Mb and 92.0% BUSCO score, respectively. A total of 11,510 protein-coding genes, and 474.7 kb repeats accounting for 1.62% of the genome, were also predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology such as wood decaying capability, evolutionary relationships with other fungus, as well as their unique biology and applications in the food industry.
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Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family …
Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family Dacrymycetaceae and investigations on the biosynthesis of glycolipids with potential applications in the food industry.
This evaluation refers to version 1 of the preprint
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AbstractThe edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has also been used in food additives given its ability to synthesize long-chain glycolipids. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size of D. spathularia is 29.2 Mb and in high sequence contiguity and completeness, including scaffold N50 of 1.925 Mb and 92.0% BUSCO score, respectively. A total of 11,510 protein-coding genes, and 474.7 kb repeats accounting for 1.62% of the genome, were also predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology such as wood decaying capability, evolutionary relationships with other fungus, as well as their …
AbstractThe edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has also been used in food additives given its ability to synthesize long-chain glycolipids. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size of D. spathularia is 29.2 Mb and in high sequence contiguity and completeness, including scaffold N50 of 1.925 Mb and 92.0% BUSCO score, respectively. A total of 11,510 protein-coding genes, and 474.7 kb repeats accounting for 1.62% of the genome, were also predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology such as wood decaying capability, evolutionary relationships with other fungus, as well as their unique biology and applications in the food industry.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.120), and has published the reviews under the same license. This is part of a thematic series presenting Data Releases from the Hong Kong Biodiversity Genomics consortium (https://doi.org/10.46471/GIGABYTE_SERIES_0006). These are as follows.
Reviewer 1. Anton Sonnenberg
Is the language of sufficient quality? Yes.
Are all data available and do they match the descriptions in the paper? Yes.
Is the data acquisition clear, complete and methodologically sound? Yes.
Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes.
Figure 1E could be improved by eliminating in the pie-chart the non-repeat sequences or bar-plot the repeats. That will visualize better the frequencies of each type of repeats.
Reviewer 2. Riccardo Iacovelli
Is the language of sufficient quality? No.
There are several typos spread across the text, and some sentences are written in an unclear manner. I provide some suggestions in the attachment.
Are all data available and do they match the descriptions in the paper?
Yes, but some of the data shown is rather unclear and/or not supported by sufficient explanation. For example, what is actually Fig. 1C showing? Because the reference in the text (which contains a typo, line 197) refers to something else. What is the second set of stats in Fig. 1B? This other organism is not mentioned at all anywhere in the manuscript.
Are the data and metadata consistent with relevant minimum information or reporting standards?
No. NCBI TaxID of the sequenced species object of this work is missing.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?
No. In my opinion, some of the procedures described for the processing of the sample and library prep for sequencing are reported in an unclear way. For example, lines 100-103: no details on RNAse A treatment; how do you define chloroform:IAA (24:1) washes? how much supernatant is added to how much H1 buffer to have the final volume of 6 ml? Another example, lines 180-175: what parameters did you use for EvidenceModeler to generate the final consensus genes model? The weight given to each particular prediction set is important.
Is there sufficient data validation and statistical analyses of data quality?
No/ While sufficient data validation and statistical analyses have been carried out with respect to DNA sequencing and genome assembly, nothing is reported about DNA extraction and quality. The authors mention several times throughout the text that DNA preps are checked via NanoDrop, Qubit, gel electrophoresis, etc. But none of this is shown in the main body or in the supplementary information. Without this information, it is difficult to assess directly the efficacy of DNA extraction and preparation methods. I recommend including this type of data.
Additional Comments:
In this article, the authors report the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. In general, I find the data of sufficiently high quality for release, and I do agree with the authors in that it will prove useful to gain further insights into the ecology of the fungus, and to better understand the genetic basis of its ability to decay wood and produce valuable compounds. This can ultimately lead to discoveries with applications in biotech and other industries.
Nevertheless, during the review process I noticed several shortcomings with respect to unclear language, insufficient description of the experimental procedures and/or results presented, and missing data altogether. These are all discussed within the checklist available in the ReView portal. For minor comments line-by-line, see below:
1: Dacrymycetaceae should be italicized (throughout the whole manuscript). This follows the convention established by The International Code of Nomenclature for algae, fungi, and plants (https://www.iaptglobal.org/icn). Although not binding, this allows easy recognition of taxonomic ranks when reading an article. 49: other fungus -> other fungi 56: photodynamic injury -> UV damage/radiation (photodynamic is used with respect to light-activated therapies etc.) 60: in food industry as natural preservatives in soft drinks -> in food industry to produce natural preservatives for soft drinks 68: cultivated in industry as food additives -> cultivated in industry to produce food additives 69: isolated fungal extract -> the isolated fungal extract 71: What do you mean by Pacific? It’s unclear 71-72: the genomic resource -> genomic data/ genome sequence 72: I would remove “with translational values”, it is very vague and does not add anything to the statement 78: genomic resource -> genomic data/ genome sequence 78-81: this could be rephrased in a smoother manner: e.g. something like “the genomic data will be useful to gain a better understanding of the fungus’ ecology as well as the genetic basis of its wood-decaying ability and…” 85: fruit bodies -> fruiting bodies 88-89: Grown hyphae from >2 week-old was transferred Fungal hyphae from 2-week old colonies were transferred 90-91: validated with the DNA barcode of Translation assigned by DNA barcoding using the sequence of Translation… 95: ~ -> Approximately (sentences are not usually started with symbols or numbers) 101-3: Procedure is not clear enough (see other comments through ReView portal) 124: for further cleanup the library -> to further clean up the library / for further cleanup of the library 132: as line 95 152: as lines 95, 132 181-5: Insufficient description of methods, see comments through ReView portal 197: Figure and 1C; Table 2 -> Figure 1C and Table 2 200: average protein length of 451 bp -> average protein-coding gene length / average protein length of ~150 amino acids 211: via the fermentation process with applications in the food industry -> via the fermentation process with potential applications in the food industry
As a fungal biologist myself interested in fungal genomics and biotechnology, I would like to thank the authors for carrying out this work and the editor for the opportunity to review it. I am looking forward to reading the revised version of the manuscript.
Riccardo Iacovelli, PhD GRIP, Chemical and Pharmaceutical Biology department University of Groningen, Groningen - The Netherlands
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