An updated bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies here.
The prokaryote genomes collection has grown by 4% since May 2022. A total of 610 species are represented for the first time. In addition, 204 species are represented by a better assembly (including 120 which are more complete), and 36 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.
We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). Find more information here.