In their manuscript "A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum", Chen et al. describe a dataset that was mostly published previously in Genome Biology (Montanini et al. Genome Biology 2014, 15:411, GEO accession GSE49700). While it might be interesting for readers to get a more comprehensive description of this dataset, including information that was not already published in the Genome Biology article, there are some major issues with the present manuscript:

Major compulsory revisions:

• Most of the text is an exact copy or a rewording of descriptions that are already given in the Genome Biology paper. Neither the description of the methods nor of the biological findings are significantly different from what was already published, therefore it is not clear what additional insights the reader might gain from this manuscript. Re-publication of the dataset can only be justified if additional metadata/descriptions/methods/analyses are given that might help re-use of the data or give novel biological insights.

• The datasets summarized in Table 1 seem to be mostly identical to the ones available via GSE49700 (as judged by the read numbers, with the exception of the samples 5-aza-treated BS-seq and 5-aza untreated BS-seq, for which read numbers differ between the numbers in SRA and those given in both the Genome Biology paper and this manuscript), but any reference to the GEO resource is missing in the manuscript. Two WG-seq datasets seem not to be included in the GEO dataset even though they are mentioned in the Genome Biology paper (Table S1 in additional file 1 of this paper). These look like they are included in the present dataset on the Genome Biology repository, but they should also be submitted to SRA, ENA or another public database. If these data are indeed the new/additional data for this manuscript, this should be made clear in the text of tables and more information on the analysis should be given (if they were just not yet included in the GEO dataset for the Genome Biology paper, this could probably be addressed by adding them to the existing GEO dataset). Individual GEO/SRA numbers for each sequencing sample should be given in Table 1 to avoid confusion of this manuscript and the Genome Biology paper and corresponding GEO dataset.

• With respect to the datasets that are available on the Giga Science web site, there are several datasets for other organisms included in the submission (e.g. Neurospora, Saccharomyces, Aspergillus), for which no description or references are given in the manuscripts or in the readme file. It might be that these datasets could help researchers when re-using the data, but for this, a description and references are necessary.

In summary, this manuscript could be greatly improved by proper referencing to the original Genome Biology article and its GEO/SRA datasets, and by giving additional information not present in the Genome Biology article that might facilitate re-use of the data or offer additional insights. Currently, the reader would be much better of reading the very interesting Genome Biology article.

Level of interest An article of limited interest Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests

In their revised manuscript, Chen et al. address most of my previous concerns. Minor/discretionary comments: The Genome Biology paper that contains the comprehensive description of the biological findings is still not properly referenced in [11] (authors, year, journal etc. should be given as in the other references), and from the text (section "purpose of data acquisition", third paragraph) it does not become clear that the present manuscript builds on/describes additional data related to this paper.

To avoid confusion for readers, it would be helpful to make this clear. Level of interest An article whose findings are important to those with closely related research interests Quality of written English Acceptable

Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.