Tag: Representative genome

Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”

NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets.

A genome is labeled reference if it is deemed to be the best available genome for the species based on assembly, annotation metrics (when available), and, in a small number of cases, curatorial review. The set of eukaryotic reference assemblies is updated continuously as new assemblies are submitted to GenBank. The set of prokaryotic references are recalculated three times a year.

Important Note: Classification of “reference genome” is separate from inclusion in RefSeq – while genomes in RefSeq are preferentially used to pick the reference genome, a reference genome can also be chosen for species not included in RefSeq. Continue reading “Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”” →

Updated prokaryotic representative genomes collection includes 685 new species!

We are happy to announce an updated bacterial and archaeal representative genomes collection. The current collection contains a total of 15,507 assemblies selected from 236,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by five percent since August 2021. A total of 685 species are represented for the first time. In addition, 370 species are represented by a better assembly, and 84 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.

Prokaryotic representative genomes update–over 900 new species!

We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

Continue reading “Prokaryotic representative genomes update–over 900 new species!” →

Prokaryotic representative genomes updated — now over 13 thousand assemblies!

We have updated the bacterial and archaeal representative genome collection! The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020. We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and have removed 65 species because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We have also updated the Representative Genomes Database on the Microbial Nucleotide BLAST page as well as the RefSeq Representative Genome Database on basic nucleotide BLAST, to reflect these changes. Continue reading “Prokaryotic representative genomes updated — now over 13 thousand assemblies!” →

RefSeq Release 202 is public

RefSeq release 202 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of September 8, 2020, and contains 255,571,455 records, including 186,755,483 proteins, 33,077,068 RNAs, and sequences from 104,969 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Updated human genome Annotation Release 109.20200815
Updated Annotation Release 109.2020815 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here.

The annotation products are available in the sequence databases and on the FTP site.

This update includes around 15,000 updated RefSeq transcripts revised to use CAGE and polyA data to define 5′ and 3′ ends, and match the reference GRCh38 sequence.

Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements
The RefSeq Functional Elements project at NCBI has prioritized curation of experimentally validated regulatory elements for human host genes associated with SARS-CoV-2 entry into cells. The annotations include several enhancers, promoters, cis-regulatory elements and protein binding sites, among other feature types. We annotated 236 regulatory features for 27 distinct biological regions, including regulatory elements for the ABO, ACE2, ANPEP, CD209, CLEC4G, CLEC4M, CTSL, DPP4, and TMPRSS2 genes. More information can be found here.

New eukaryotic genome annotations
This release includes new annotations generated by NCBI’s eukaryotic genome annotation pipeline for 27 species, including:

maize annotation release 103, based on the new assembly Zm-B73-REFERENCE-NAM-5.0 (GCF_902167145.1)
marmoset annotation release 105, based on the new assembly Callithrix_jacchus_cj1700_1.1 (GCF_009663435.1)
Chinese hamster annotation release 104, based on the assembly CriGri_1.0 (GCF_000223135.1) and the new assembly CriGri-PICRH-1.0 (GCF_003668045.3)
Asian giant hornet annotation release 100, based on the new assembly V.mandarinia_Nanaimo_p1.0 (GCF_014083535.2)
Florida lancelet annotation release 100, based on the new assembly Bfl_VNyyK (GCF_000003815.2)
Anopheles stephensi annotation release 100, based on the new assembly UCI_ANSTEP_V1.0 (GCF_013141755.1)

Updated and improved collection of RefSeq representative genome assemblies now available
The collection of representative genome assemblies for Bacteria and Archaea contains 11,727 prokaryotic assemblies to represent their respective species. More information can be found here.

Updated protein family models used by PGAP available for download
Release 3.0 of the NCBI protein family models used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available.

This release contains 17,350 models: 12,864 HMMs built at NCBI (111 more than in release 2.0) and 4,486 TIGRFAM HMMs. In addition, since release 2.0, we have assigned product names to over 2,000 Pfam HMMs, bringing the total to 6,698 Pfam HMMs with names that can be transferred by PGAP to the annotated proteins they hit. More information can be found here.

Future change: Mouse Reference Assembly Update
RefSeq annotation of the new mouse GRCm39 assembly is in progress, and is expected to be included in the next release.

Updated and improved collection of RefSeq representative genome assemblies now available

We have updated the collection of representative genome assemblies for Bacteria and Archaea. As announced in April, this set is now recalculated three times a year. We selected a total of 11,727 prokaryotic assemblies to represent their respective species among the 192,000 assemblies in RefSeq. Six hundred and thirty-five species were included in the collection for the first time, while 395 organisms from undefined species (such as Bacillus bacterium) were removed. We were able to choose a higher-quality representative than in the previous set for 18% of Bacterial and Archaeal species due to improvements in the logic of the selection that is now based on the assembly length, number of pseudo CDSs called in the PGAP annotation, number of scaffolds, whether Gene IDs are available in the Gene database for the assembly that is currently representative, and type strain status. You can see the exact criteria in order of importance on the Prokaryotic RefSeq Genomes page. Now that the new selection process is in place, we expect future updates to have fewer changes. We will replace a representative only if the assembly has changed RefSeq status or if a substantially better assembly becomes available.

We have updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative Genome Database, to reflect these changes.

You can download the reference and representative set from the Assembly resource. If you are interested in the annotation on these genomes, you can limit searches to proteins annotated on representative genomes by adding “refseq_select[filter]” to any query in the Protein database. For example, you can find all proteins annotated on representative genomes in the genus Klebsiella by using the query: “Klebsiella[organism] AND refseq_select[filter]“. A BLAST database of proteins annotated on representative genomes will be coming soon. Stay tuned!

Recalculation of prokaryotic reference and representative genome assemblies

We have updated the collection of representative and reference assemblies for Bacteria and Archaea to better reflect the taxonomic breadth of the prokaryotes in RefSeq. We chose the 11,478 representative assemblies in the new collection from the 180,000+ prokaryotic assemblies in RefSeq today. We have selected one representative or reference assembly for every species based on several criteria including contiguity, completeness and whether the assembly is from type material. We have also updated the reference and representative microbial Blast database to reflect these changes. This reference and representative set will be updated three times a year to reflect changes in RefSeq. In addition, as we announced on Feb 14, we have reduced the number of reference genome assemblies — the subset of representative assemblies with annotation provided by outside experts — to 15. See the list in our previous post . We have re-annotated the 104 assemblies that are no longer reference with or Prokaryotic Genome Annotations Pipel (PGAP).