Abstract
(1) Background: Fungi contain several millions of species, and the diversification of fungal genes has been achieved by speciation, gene duplication, and horizontal gene transfer. Although several databases provide information on orthologous and paralogous events, these databases show no information on biases between gene mutation and speciation. Here, we designed the Gcorn fungi database to better understand such biases. (2) Methods: Amino acid sequences of fungal genes in 249 species, which contain 2,345,743 sequences, were used for this database. Homologous genes were grouped at various thresholds of the homology index, which was based on the percentages of gene mutations. By grouping genes that showed highly similar homology indices to each other, we showed functional and evolutionary traits in the phylogenetic tree depicted for the gene of interest. (3) Results: Gcorn fungi provides well-summarized information on the evolution of a gene lineage and on the biases between gene evolution and speciation, which are quantitatively identified by the Robinson–Foulds metric. The database helps users visualize these traits using various depictions. (4) Conclusions: Gcorn fungi is an open access database that provides a variety of information with which to understand gene function and evolution.
Highlights
Fungi are one of the most diverse groups of organisms, are essential to ecosystems, and are closely related to the soil carbon cycle, plant nutrition, and pathology [1]
(4) Conclusions: Gcorn fungi is an open access database that provides a variety of information with which to understand gene function and evolution
The Gcorn fungi database provides information on relatively new homologous events related to a gene of interest, and well-summarized information on the evolution of a gene lineage, which is depicted by classifying homologous gene groups, and on the bias between gene evolution and speciation, which is quantitatively identified by the RF metric [18], which shows the distance between a pair of phylogenetic trees
Summary
Fungi are one of the most diverse groups of organisms, are essential to ecosystems, and are closely related to the soil carbon cycle, plant nutrition, and pathology [1]. The estimated number of fungal species on the earth ranges from 1.5 million to 10 million [2]. It is difficult to know the exact number of fungal species, there is no doubt that they represent a high degree of eukaryote diversity. The diversification of genes is, in general, due to speciation, gene duplication, and horizontal gene transfer. There are various types of speciation (e.g., allopatric and sympatric) [3]. Speciation is driven by natural selection over a long period of time
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