Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

Abstract The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or ge...

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Autores principales:	Sandra Regina Maruyama, Luana Aparecida Rogerio, Patricia Domingues Freitas, Marta Maria Geraldes Teixeira, José Marcos Chaves Ribeiro
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/621c8bd43681428cae759433ffcfeb0f
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spelling	oai:doaj.org-article:621c8bd43681428cae759433ffcfeb0f2021-12-02T14:21:53ZTotal Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes10.1038/s41598-021-81926-w2045-2322https://doaj.org/article/621c8bd43681428cae759433ffcfeb0f2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81926-whttps://doaj.org/toc/2045-2322Abstract The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.Sandra Regina MaruyamaLuana Aparecida RogerioPatricia Domingues FreitasMarta Maria Geraldes TeixeiraJosé Marcos Chaves RibeiroNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sandra Regina Maruyama Luana Aparecida Rogerio Patricia Domingues Freitas Marta Maria Geraldes Teixeira José Marcos Chaves Ribeiro Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
description	Abstract The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.
format	article
author	Sandra Regina Maruyama Luana Aparecida Rogerio Patricia Domingues Freitas Marta Maria Geraldes Teixeira José Marcos Chaves Ribeiro
author_facet	Sandra Regina Maruyama Luana Aparecida Rogerio Patricia Domingues Freitas Marta Maria Geraldes Teixeira José Marcos Chaves Ribeiro
author_sort	Sandra Regina Maruyama
title	Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
title_short	Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
title_full	Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
title_fullStr	Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
title_full_unstemmed	Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
title_sort	total ortholog median matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/621c8bd43681428cae759433ffcfeb0f
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_version_	1718391490171895808

Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

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