<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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Taiga Kawachi, Yuta Inuki, Yoshiyuki Ogata
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	database fungi evolution gene homology network analysis ortholog Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/31e058bc563f4bab98c361140edd6f47
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:31e058bc563f4bab98c361140edd6f47
record_format	dspace
spelling	oai:doaj.org-article:31e058bc563f4bab98c361140edd6f472021-11-25T18:06:12Z<i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi10.3390/jof71109592309-608Xhttps://doaj.org/article/31e058bc563f4bab98c361140edd6f472021-11-01T00:00:00Zhttps://www.mdpi.com/2309-608X/7/11/959https://doaj.org/toc/2309-608X(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.Taiga KawachiYuta InukiYoshiyuki OgataMDPI AGarticledatabasefungievolutiongene homologynetwork analysisorthologBiology (General)QH301-705.5ENJournal of Fungi, Vol 7, Iss 959, p 959 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	database fungi evolution gene homology network analysis ortholog Biology (General) QH301-705.5
spellingShingle	database fungi evolution gene homology network analysis ortholog Biology (General) QH301-705.5 Taiga Kawachi Yuta Inuki Yoshiyuki Ogata <i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi
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.
format	article
author	Taiga Kawachi Yuta Inuki Yoshiyuki Ogata
author_facet	Taiga Kawachi Yuta Inuki Yoshiyuki Ogata
author_sort	Taiga Kawachi
title	<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_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_sort	<i>gcorn fungi</i>: a web tool for detecting biases between gene evolution and speciation in fungi
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/31e058bc563f4bab98c361140edd6f47
work_keys_str_mv	AT taigakawachi igcornfungiiawebtoolfordetectingbiasesbetweengeneevolutionandspeciationinfungi AT yutainuki igcornfungiiawebtoolfordetectingbiasesbetweengeneevolutionandspeciationinfungi AT yoshiyukiogata igcornfungiiawebtoolfordetectingbiasesbetweengeneevolutionandspeciationinfungi
_version_	1718411609180733440

<i>Gcorn fungi</i>: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi

Ejemplares similares