<i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi
(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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | Journal of Fungi |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2309-608X/7/11/959 |
| _version_ | 1797509770520821760 |
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| author | Taiga Kawachi Yuta Inuki Yoshiyuki Ogata |
| author_facet | Taiga Kawachi Yuta Inuki Yoshiyuki Ogata |
| author_sort | Taiga Kawachi |
| collection | DOAJ |
| description | (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 <i>Gcorn fungi</i> 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: <i>Gcorn fungi</i> 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: <i>Gcorn fungi</i> is an open access database that provides a variety of information with which to understand gene function and evolution. |
| first_indexed | 2024-03-10T05:22:26Z |
| format | Article |
| id | doaj.art-31e058bc563f4bab98c361140edd6f47 |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-10T05:22:26Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-31e058bc563f4bab98c361140edd6f472023-11-22T23:56:17ZengMDPI AGJournal of Fungi2309-608X2021-11-0171195910.3390/jof7110959<i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in FungiTaiga Kawachi0Yuta Inuki1Yoshiyuki Ogata2Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, JapanGraduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, JapanGraduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan(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 <i>Gcorn fungi</i> 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: <i>Gcorn fungi</i> 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: <i>Gcorn fungi</i> is an open access database that provides a variety of information with which to understand gene function and evolution.https://www.mdpi.com/2309-608X/7/11/959databasefungievolutiongene homologynetwork analysisortholog |
| spellingShingle | Taiga Kawachi Yuta Inuki Yoshiyuki Ogata <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi Journal of Fungi database fungi evolution gene homology network analysis ortholog |
| title | <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi |
| title_full | <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi |
| title_fullStr | <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi |
| title_full_unstemmed | <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi |
| title_short | <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi |
| title_sort | i gcorn fungi i a web tool for detecting biases between gene evolution and speciation in fungi |
| topic | database fungi evolution gene homology network analysis ortholog |
| url | https://www.mdpi.com/2309-608X/7/11/959 |
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