Tag: Fungal research

New Fungal Alignments Available in the Comparative Genome Viewer (CGV)

Recognizing Fungal Disease Awareness Week

Fungal pathogens are a growing threat to global public health. To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as Fungal Disease Awareness Week.

In honor of this week, we’re highlighting whole genome alignments for fungal pathogens that are now available in the Comparative Genome Viewer (CGV) – NCBI’s latest genome visualization tool.  Alignment displays in CGV help you identify rearrangements and differences in genomic structure such as deletions, inversions, and translocations. These differences can be important for understanding genome plasticity, genetic diversity within species (PMC8640552) and the response to environmental stresses such as exposure to anti-fungal drugs (PMC5555451).    Continue reading “New Fungal Alignments Available in the Comparative Genome Viewer (CGV)” →

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 Colletotrichum species are challenging to identify accurately, and public sequences may contain out of date taxonomic information.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

Continue reading “Fungal species identification using DNA: an NCBI and USDA-APHIS collaboration with a focus on Colletotrichum” →

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences

This post is geared toward fungi researchers as well as RefSeq and BLAST users.

Fungi have unique characteristics that can make it difficult to identify and classify species based on morphology. To address these issues, Conrad Schoch, NCBI’s fungi taxonomist, and Barbara Robbertse, NCBI’s fungi RefSeq curator, in collaboration with outside mycology experts, are curating a set of fungal sequences from internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA genes. This set of standard DNA sequences for fungal taxa not only addresses these difficulties in identifying and classifying fungal species by morphology, but is also essential for analyzing environmental (metagenomics) sequencing studies. The curated ITS sequences, described in a recent article in Database (PMC Free Article), all have associated specimen data and, when possible, are taken from sequences from type materials, ensuring correct species identification and tracking of name changes. This article will show you how to access these ITS sequences and search them using the specialized Targeted Loci BLAST service.

The fungal ITS sequences are a RefSeq Targeted Loci BioProject (PRJNA177353). As you may know, a BioProject is a collection of biological data related to a single initiative; in this case, the goal is to collect and curate fungal sequences from targeted loci – specific molecular markers such as protein coding or ribosomal RNA genes used for phylogenetic analysis.

Continue reading “Accessing the Hidden Kingdom: Fungal ITS Reference Sequences” →