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. 2015 Jan;43(Database issue):D599-605.
doi: 10.1093/nar/gku1062. Epub 2014 Dec 15.

Update on RefSeq microbial genomes resources

Tatiana Tatusova  1 , Stacy Ciufo  2 , Scott Federhen  2 , Boris Fedorov  2 , Richard McVeigh  2 , Kathleen O'Neill  2 , Igor Tolstoy  2 , Leonid Zaslavsky  2
Affiliations

Update on RefSeq microbial genomes resources

Tatiana Tatusova et al. Nucleic Acids Res. 2015 Jan.

Abstract

NCBI RefSeq genome collection http://www.ncbi.nlm.nih.gov/genome represents all three major domains of life: Eukarya, Bacteria and Archaea as well as Viruses. Prokaryotic genome sequences are the most rapidly growing part of the collection. During the year of 2014 more than 10,000 microbial genome assemblies have been publicly released bringing the total number of prokaryotic genomes close to 30,000. We continue to improve the quality and usability of the microbial genome resources by providing easy access to the data and the results of the pre-computed analysis, and improving analysis and visualization tools. A number of improvements have been incorporated into the Prokaryotic Genome Annotation Pipeline. Several new features have been added to RefSeq prokaryotic genomes data processing pipeline including the calculation of genome groups (clades) and the optimization of protein clusters generation using pan-genome approach.

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Figures

Figure 1.
Figure 1.
Growth of genomes, species and genera: rapid growth of the number of isolates with relatively slow growth of new genera. Note that the data does not include assemblies from environmental studies where the number of novel species is growing much faster.
Figure 2.
Figure 2.
Shigella–Escherichia coli pan-genome: core and mobile components.
Figure 3.
Figure 3.
Escherichia coli genomes grouped by BLAST similarity distance; each green box represents a short proximity genome group.
Figure 4.
Figure 4.
RefSeq prokaryotic genome processing: pan-genome and genome close proximity groups.
None
See this image and copyright information in PMC

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