Tag: Assembly

Fungal species identification using DNA: an NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

Fungal species identification using DNA: an NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

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 Colletotrichum species are challenging to identify accurately, and public sequences may contain out of date taxonomic information.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.

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Come see NCBI at the ASM Microbe Conference 2022

Come see NCBI at the ASM Microbe Conference 2022

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”

NCBI’s Genome Data viewer now displays both NCBI RefSeq and submitted assemblies

NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms.

Figure 1 shows a GenBank apple assembly (GCA_004115385) displayed in GDV.

Figure 1. Submitter-annotated Malus domestica (apple) assembly displayed in GDV. GDV provides submitter-provided gene annotation, as well as some additional tracks including interspersed repeats identified by RepeatMasker and six-frame translations (not shown). Red boxes indicate useful tools and panels including a search box, an exon navigator, and interfaces to add user data and conduct NCBI BLAST searches. 

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A new service to evaluate the quality of your assembled genome!

A new service to evaluate the quality of your assembled genome!

Are you wondering about the quality of a human, mouse or rat genome that you have assembled?

We offer a new service for evaluating the completeness, correctness, and base accuracy of your human, mouse or rat genome assembly compared to a reference assembly. You simply provide NCBI with one or more assemblies in FASTA format and we will do an annotation-based evaluation of the genome(s) using the expert-curated, high-confidence RefSeq transcripts for the species.

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Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI

Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI

This post is in support of the CDC’s Fungal Disease Awareness Week — September 20-24, 2021.

The impact of fungal diseases on human health has often been neglected, but increased association of fungal infections with severe illness and death during the COVID-19 pandemic has brought fungal diseases into the spotlight.

According to the CDC, the most common fungal co-infections in patients with COVID-19 include aspergillosis or invasive candidiasis including healthcare-associated infection from Candida auris.  Other reported diseases are mucormycosis, coccidioidomycosis and cryptococcosis. Aspergillosis is commonly caused by Aspergillus fumigatus, mucormycosis by Rhizopus species, coccidioidomycosis by Coccidioides immitis and C. posadasii and cryptococcosis by Cryptococcus neoformans.

This post explores several NCBI resources that have relevant information about the fungal pathogens implicated in these COVID-19 related illnesses.

Assembled genomes

Correctly identified and annotated genome assemblies are available for the fungal taxa implicated as co-infections in COVID-19 patients are summarized in table below.  These and  many other fungi are also available as curated RefSeq genome assemblies.

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Introducing the new NCBI Datasets Genomes page

The updated NCBI Datasets Genomes page now has genome data for all domains of life, including bacterial and viral genomes.

The genomes table (Figure 1) now offers filters for:

  • Reference genomes — switch it on to only show reference or representative genomes
  • Annotated — switch it on to only show annotated genomes
  • Assembly level — use the assembly level slider to select higher-quality genomes
  • Year released — use the slider to limit your results to recent genomes

In addition, the new Actions column connects you to NCBI’s Genome Data Viewer, BLAST, and Assembly. The Text filter box lets you search by the name of the assembly, species/infraspecies, or submitter.Figure 1. The new Datasets Genomes page with primate assemblies showing the STATUS switches (reference genomes, annotated); expanded filters section with ASSEMBLY LEVEL and YEAR RELEASED sliding selectors; and the Actions column menu with access to Assembly details, BLAST, the Genome Data Viewer, and Download options. Continue reading “Introducing the new NCBI Datasets Genomes page”

Vertebrate Genome Project genome assemblies annotated by NCBI

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.  See the VGP press release  for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank  and the European Nucleotide Archive.  NCBI has annotated 94 of the VGP assemblies from 85 species using the NCBI Eukaryotic Genome Annotation Pipeline.

These sequence and annotation data are available through NCBI web resources including Gene, Assembly, Nucleotide, Protein, and Datasets and are included in the GenBank and RefSeq releases. You can browse the assemblies in the Genome Data Viewer  and  download metadata, sequence, and annotation data for the latest assemblies in the VGP BioProject using the NCBI Datasets command-line tools  as shown below. Continue reading “Vertebrate Genome Project genome assemblies annotated by NCBI”

Assembly database passes 1 million genome assemblies!

The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species.

Assembly crossed the 1 million genome assemblies milestone on Sunday, April 18, 2021 (Figure 1).

Figure 1. Assembly status and growth. More than 1 million assemblies are now searchable through the NCBI web site (top panel). The number of genome assemblies at NCBI has accelerated rapidly in the past decade.

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Improvements to NCBI Assembly

NCBI’s genome Assembly has a number of significant improvements!

Assembly records now have a link to Primer-BLAST making it easy to design primers in the context of a specific eukaryote genome assembly.  Figure 1 shows the Assembly page for the Genome Reference Consortium Mouse Build 39 (GRCm39) with the link to Primer-BLAST.

Figure 1. The Assembly page for the mouse reference genome (GCF_000001635.27). Showing the new Run Primer-BLAST link, which loads the assembly as a database in the Primer-BLAST search (bottom) and the new expandable note sections, Genome-Annotation-Data in this case. 
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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!”