Review of: RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening biosynthesis of bioactive compounds and stage-specific alternative splicing The paper describes RNA-Seq data from the fruit development stages largely from a tetraploid southern highbush blueberry cultivar O’Neal.

Major items which need amendment/clarification etc. Item 1. The manuscript refers to a ‘blueberry draft genome assembly (page 7, line 4; page 11, line 23), and ‘genome data’ (page 4, line 27). This blueberry genome assembly is not referenced or identified. Item 2. Cultivated highbush blueberry is an autotetraploid. No mention is made of the ploidy nor its possible impact on results. For example are four alleles expressed? In the attempt to quantify expression, would all four alleles contribute equally? Item 3. No mention is made of cranberry a close relative to blueberry. BMC Plant Biol. 2014 Jun 13;14:165. doi: 10.1186/1471-2229-14-165

Item 4. Little or no mention of blueberry ESTs are mentioned.

Item 5. Page 6, lines 18-26. What was the purpose to include these other cultivars at another location. No mention is made of these data with those of O’Neal at the Salisbury location? Were the data statistically different?

Item 6. Statistical methods/description woefully lacking in the differential gene expression analysis. (page 18, line 30). These should be described in the materials and methods section. No mention is made of how many pairwise comparisons were made. There would be quite of few false positives, even at 0.001 by chance probability, if all possible 19,000 genes were analyzed this way. How many comparisons were made?

Item 7. The discussion has materials and methods repeated frequently, and discussion needs to be condensed.

Level of interest An article of importance in its field

Quality of written English Acceptable

Statistical review Yes, but I do not feel adequately qualified to assess the statistics.

Declaration of competing interests I declare that I have no competing interests

Review of: RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening biosynthesis of bioactive compounds and stage-specific alternative splicing

Item 1. The manuscript should be carefully edited for typo errors. E,g. Page 25, line 15. Item 2. nr database vs “nr” database Item 3. First reference to IGB is page 11, line 1, but an acronym is given page 11, line 25.

Item 4. Figure 6B lower left half is a mirror of upper right half. I would recommend eliminating one or the other.

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 Review of: RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening biosynthesis of bioactive compounds and stage-specific alternative splicing Item 1. The manuscript should be carefully edited for typo errors. E,g. Page 25, line 15. Item 2. nr database vs “nr” database Item 3. First reference to IGB is page 11, line 1, but an acronym is given page 11, line 25.

Item 4. Figure 6B lower left half is a mirror of upper right half. I would recommend eliminating one or the other. Review of: RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening biosynthesis of bioactive compounds and stage-specific alternative splicing Item 1. The manuscript should be carefully edited for typo errors. E,g. Page 25, line 15. Item 2. nr database vs “nr” database Item 3. First reference to IGB is page 11, line 1, but an acronym is given page 11, line 25.

Item 4. Figure 6B lower left half is a mirror of upper right half. I would recommend eliminating one or the other.

Competing interests I declare that I have no competing interests