Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy

Abstract In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along t...

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Autores principales:	Marcos Parras-Moltó, Daniel Aguirre de Cárcer
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/456548fc12ca4f06ab7de12dbb9aab7a
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spelling	oai:doaj.org-article:456548fc12ca4f06ab7de12dbb9aab7a2021-12-02T18:02:48ZAssessment of phylo-functional coherence along the bacterial phylogeny and taxonomy10.1038/s41598-021-87909-12045-2322https://doaj.org/article/456548fc12ca4f06ab7de12dbb9aab7a2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87909-1https://doaj.org/toc/2045-2322Abstract In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data ( https://git.io/Jec5U ).Marcos Parras-MoltóDaniel Aguirre de CárcerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-6 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marcos Parras-Moltó Daniel Aguirre de Cárcer Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
description	Abstract In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data ( https://git.io/Jec5U ).
format	article
author	Marcos Parras-Moltó Daniel Aguirre de Cárcer
author_facet	Marcos Parras-Moltó Daniel Aguirre de Cárcer
author_sort	Marcos Parras-Moltó
title	Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
title_short	Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
title_full	Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
title_fullStr	Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
title_full_unstemmed	Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
title_sort	assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/456548fc12ca4f06ab7de12dbb9aab7a
work_keys_str_mv	AT marcosparrasmolto assessmentofphylofunctionalcoherencealongthebacterialphylogenyandtaxonomy AT danielaguirredecarcer assessmentofphylofunctionalcoherencealongthebacterialphylogenyandtaxonomy
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Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy

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