Legacy pages will be redirected effective June 2023
In June 2023, NCBI’s Assembly and Genome record pages will be redirected to new Datasets pages as part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.
We will update the following pages:
The NCBI Assembly pages will be redirected to the new DatasetsGenome pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.
The NCBIGenome pages will be redirected to the DatasetsTaxonomy pages that provide a taxonomy-focused portal to genes, genomes and additional NCBI resources.
During this transition, you will have the option to return to the legacy Genome and Assembly pages.
We recognize that the traditional influenza virus names like ‘Influenza A virus’ and ‘Influenza B virus’ are broadly used in public health, educational institutions, and research. To minimize the impact of this change to those who use NCBI resources, the taxonomy schema will keep the former names in the lineages for each species; however, they will be moved below the (new) species taxa in the hierarchy. See example below.
An updated bacterial and archaeal reference genome collection is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.
A total of 497 species are included in this collection for the first time. In addition, comparing to the October 2022 set, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the documentation for details.
You will still see the previous names on records and can search using them, but they will not be displayed as prominently as before. The organism names on Entrez records will not change (e.g., Bacillus subtilis). However, we will update the phylum names on the displayed lineages for ~276 million records (see an example in Figure 1 below). Continue reading “Prokaryotic phylum name changes coming soon!”→
As reported in the journal Plant Disease, a recent collaboration between National Library of Medicine’s NCBI and the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS) analyzed public sequence records for the fungal genus Colletotrichum, an important group of fungal plant pathogens that are a significant threat to food production. Colletotrichum species are challenging to identify accurately, and public sequences may contain out of date taxonomic information. The study improved the accuracy of species names assigned to Colletotrichum database sequences, verified a comprehensive set of reliable reference markers for the genus, and produced a multi-marker tree as well as the genome based interactive tree shown in Figure 1.
Figure 1. Views from genome assembly derived multi-protein distance tree that shows the analysis of publicly available Colletotrichum genomes. The interactive tree is available online. You can browse, search, download, and export the tree. As an example search, you can demonstrate that assembly GCA_002901105.1 was incorrectly labeled as Colletotrichum gloeosporioides. Searching the tree for the name “Colletotrichum gloeosporioides” highlights two clades. Clicking the node for the Truncatum species complex and clicking “Show descendants” expands the clade and shows that assembly GCA_002901105.1, which was labelled as gloeosporioides, clusters with the Truncatum species complex. You can find more details on the tree building process in the supplementary material for the publication and on GitHub.
NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks!
Reflections from a few of our NCBI experts
“It was a great honor for me to receive the ASM Elizabeth O. King Lecturer Award. Thank you to my colleagues, without whom so much of my work would not have been possible, and to all of those who attended my presentation on Making Genomics Accessible to Aid Public Health and Research.”
An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.
The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C.
NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth (#1128) to address your questions. Drop by to see what’s new and provide your feedback. We hope to see you there! Check out NCBI’s schedule of activities: Continue reading “Come see NCBI at the ASM Microbe Conference 2022”→