ArticleBMC bioinformatics2008
FUNYBASE: a FUNgal phYlogenomic dataBASE.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 65 citations in OpenAlex.
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- Fast and reliable molecular methods to detect fungal pathogens in woody plants.Applied microbiology and biotechnology · 2020Review
- Genomic biosurveillance of forest invasive alien enemies: A story written in code.Evolutionary applications · 2020Review
- Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera.PloS one · 2020Article
- FGMP: assessing fungal genome completeness.BMC bioinformatics · 2019Article
- A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni.Genome biology and evolution · 2018Article
- Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.PLoS genetics · 2018Article
- Several steps of lateral gene transfer followed by events of 'birth-and-death' evolution shaped a fungal sorbicillinoid biosynthetic gene cluster.BMC evolutionary biology · 2016Article
- Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire.Scientific reports · 2016Article
- The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis.Genome biology and evolution · 2015Article
- Basidioascus undulatus: genome, origins, and sexuality.IMA fungus · 2015Article
- Draft Genome of Cladophialophora immunda, a Black Yeast and Efficient Degrader of Polyaromatic Hydrocarbons.Genome announcements · 2015Article
- Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer.BMC genomics · 2015Article
- Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses.Scientific reports · 2014Article
- Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection.Frontiers in plant science · 2014Article
- Gray mold populations in german strawberry fields are resistant to multiple fungicides and dominated by a novel clade closely related to Botrytis cinerea.Applied and environmental microbiology · 2013Article
- Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets.BioMed research international · 2013Article
- Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.PLoS pathogens · 2013Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi. DESCRIPTION: FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented.
conclusionFUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.