Content of review 1, reviewed on November 01, 2013

Parrots are an important group that can develop in a new model group, specifically for brain and vocalization among other things. The genome sequence of the parakeet is important, because it will increase avian data representation. The current dataset is large; containing three different assemblies performed on reads originating from different machines at deep coverage.

Below are a number of issues I would like the authors to address:

  1. These assemblies have been produced during the Assemblathon, and at least one of them are currently available on UCSC website and the GigaDB. The authors are making it easier to access the data by presenting it in the same article. It is not clear to from the article, why the authors have published only three assemblies, especially when referring to the rank of their assembly in the competition. It needs to be clarified that the data release concerns only the outcomes form one of the groups in Assemblathon paper, not all the data available on this species.

  2. Authors mention SOAPdenovo assemblies, but actually reference SOAPdenovo2. It is not clear which one was used. The links for the assemblers are not indicated either.

  3. It is not clear also if protocol used for optical mapping has been used previously, and Germinate and Grow is not referenced when first mentioned.

  4. The accession number for ENA is provided, but the NCBI archive (SRA) is not provided in the paper. Authors should think about making a more standardized way for listing sources and repositories. I would suggest adding a row of links to the Table 2.

  5. It would be a good idea to provide links to the other data from the Assembathon. If the most useful utility of this paper is to provide a single hub to access the budgerigar genome, it should do so. I would suggest that a table with links to each dataset available for the species, not only the three assemblies released by this group.

  6. The data has been generated in a competition, and has been evaluated previously in Assemblathon2 paper. The authors mention ranks of two of the assemblies, but not third.

  7. The comparisons to other genomes seem a little random. It is unclear why the three other genomes were selected for comparison. There is data for two other parrot species (macaw and amazon) are already available, that are not mentioned, and they are closer to budgerigar than the falcon, so the justification for the inclusion of that species is unclear.

  8. Needs to have a more clear indication to which versions of software have been used, and provide the appropriate links (see above).

  9. It is not clear what was the rationale of choosing the specific combinations of different technologies presented in the paper (as in 454+Illumina, PacBio + Illumina, etc).

  10. It is not clear if this is a paper or a data note. Currently the size exceeds the limit and does not comply, but can be shortened by half to make it meet the Data Note requirements. The writing should be edited to improve readability and remove redundancies and lengthy descriptions. Tenses should be synchronized in the lists (see Optical map assisted assemblies). Some of the informal language should be formalized. It would help the edit, if the manuscript is submitted double-spaced with page and line numbers so that minor issues in writing can be addressed and corrected.

  11. The number of references is too much for a data note, and it might be hard to put all of the analysis and discussion in the main text without quoting less than a few dozen papers. Alternatively, a number of supplemental files can be set up to remove the excess of references into the supplement. Perhaps some of the verbose text could be converted into tables.

Level of interest:

An article of importance in its field

Quality of written English:

Not suitable for publication unless extensively edited

Statistical review:

No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests:

i dont have any competing interests

Source

    © 2013 the Reviewer (CC-BY 3.0 - source).

Content of review 2, reviewed on April 21, 2014

The authors have answered all comments to my satisfaction. Looking forward to the publication of this paper.

Level of interest:

An article of importance in its field

Quality of written English:

Acceptable

Statistical review:

No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests:

I do not have competing ineterest

Source

    © 2014 the Reviewer (CC-BY 3.0 - source).

References

    Ganeshkumar, G., T., H. J., M., W. J., Jianwen, L., Bo, L., Yingrui, L., Yingqi, X., Yong, Z., Shiguo, Z., C., S. D., Michael, S., Robert, A., Olivier, F., Lisa, B., Ty, W., Greg, W., Isabelle, R., Roger, W., R., K. J., Sergey, K., C., W. W., Guojie, Z., M., P. A., D., J. E. 2014. High-coverage sequencing and annotated assemblies of the budgerigar genome. GigaScience.