The manuscript written by Li et al entitled "3000 rice genomes" was well written and is suitable for publication in GigaScience. This reviewer is very much thankful for a chance to read this kind of announcement paper before publication. The followings are several minor revision comments to improve this manuscript.

1. Abstract
   Line 5: This paper briefly reports -> Here, we briefly reports.
2. Background section
   Line 1: To date, few studies -> To date, a few studies. Legend of Additional Table 1A should read like “Additional Table 1A. Information of the 2,466 rice accessions from the International Rice Genebank Collection (IRGC) at International Rice Research Institute”
3. Sequencing section
   “Purified 500 bp DNA fragments from 24 accessions were separately” is ambiguous. I understand that each of sets of 24 accessions was handled separately. Is it right?
4. Data generation and analyses
   The clean reads were mapped to the temperate japonica Nipponbare reference genome, unified-build release Os-Nipponbare-Reference-IRGSP-7.0 (IRGSP-7.0) [10]. -> Reference number should be ‘9’. Please check all the rest of reference numbering after this sentence.
5. Potential implications
   “Such analyses are expected to uncover within O. sativa diversity and the population genomic structure in great detail” does not read well. Is it meaning ‘within-species diversity and genome-level population structure of O. sativa in great detail’?
6. Availability of supporting data
   “Supporting data will be available after the first scientific paper on the population genomic structure of the 3k rice genomes is published later this year” -> This may have to be rewritten. I understand that SNP position data will not be released with this paper. I also understand that this paper is intended to announce release of raw sequence data. Anyway, I am not comfortable with the term ‘supporting data’.

Level of interest: An exceptional article

Quality of written English: Needs some language corrections before being published

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.