Publications

Detailed Information

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi

Cited 6 time in Web of Science Cited 7 time in Scopus
Authors

Kim, Dongwook; Gilchrist, Cameron L. M.; Chun, JongsikSteinegger, Martin

Issue Date
2023-01
Publisher
Oxford University Press
Citation
Nucleic Acids Research, Vol.51 No.D1, pp.D777-D784
Abstract
In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in singlecopy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic Glade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.
ISSN
0305-1048
URI
https://hdl.handle.net/10371/189398
DOI
https://doi.org/10.1093/nar/gkac894
Files in This Item:
There are no files associated with this item.
Appears in Collections:

Related Researcher

  • College of Natural Sciences
  • School of Biological Sciences
Research Area Development of algorithms to search, cluster and assemble sequence data, Metagenomic analysis, Pathogen detection in sequencing data

Altmetrics

Item View & Download Count

  • mendeley

Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.

Share