UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

Na, Seong-In; Kim, Yeong Ouk; Yoon, Seok-Hwan; Ha, Seung Min; Baek, Inwoo; Chun, Jongsik

doi:10.1007/s12275-018-8014-6

Cited by 1,085 publications

(899 citation statements)

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“…For genome‐based phylogenetic analyses, we used the up‐to‐date bacterial core gene set and pipeline for phylogenomic tree reconstruction (UBCG; Na et al ., ) to identify and extract 92 universal bacterial core genes in 32 Nitrospira and two Leptospirillum genomes. As all included genomes were lacking a gene for the phenylalanine‐tRNA ligase, beta subunit ( pheT ), all downstream analyses were performed using the 91 remaining core genes identified by Na and colleagues.…”

Section: Methodsmentioning

confidence: 99%

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Poghosyan

Koch

Lavy

et al. 2019

Environmental Microbiology

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Summary The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high‐quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome‐assembled genomes were compared with other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clades A and B respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I–V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clades A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated.

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Section: Methodsmentioning

confidence: 99%

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Poghosyan

Koch

Lavy

et al. 2019

Environmental Microbiology

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“…1Phylogenetic analysis of the genus Nitrospira based on 91 core genes. The UBCG pipeline was used to identify the core gene set consisting of single-copy genes found in most bacterial genomes and for the concatenation of the nucleotide sequence alignments (Na et al 2018). The tree was reconstructed using RaxML (Stamatakis 2014) on the CIPRES Science Gateway (Miller et al 2010), using the GTR substitution and GAMMA rate heterogeneity models and 100 bootstrap iterations.…”

Section: Environmental Distribution Of Comammox Nitrospira Compared Tmentioning

confidence: 99%

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Koch

Kessel

Lücker

2018

Appl Microbiol Biotechnol

261

148

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Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.Electronic supplementary materialThe online version of this article (10.1007/s00253-018-9486-3) contains supplementary material, which is available to authorized users.

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“…With the new assignation for these five, the 261 universal genes encode eight proteins: aspartate-tRNA ligase, phenylalanine-tRNA ligase alpha subunit, valine-tRNA ligase, isoleucine-tRNA ligase, elongation factor G (name according to bacteria, corresponding to the archaeal and eukaryotic elongation factor 2), elongation factor Tu (name according to bacteria, corresponding to the archaeal and eukaryotic elongation factor 1), DNA-directed RNA polymerase subunit beta, and Obg-like ATPase 1 (Table 3 and S7 Table). Five of these eight belong to the Up-to-date bacterial core gene set (the two elongation factors and valine-tRNA ligase do not) (16).…”

Section: Resultsmentioning

confidence: 99%

The Absence of Universally-Conserved Protein-coding Genes

Tan

2019

Preprint

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2Public access to thousands of completely sequenced and annotated genomes provides a great 3 opportunity to address the relationships of different organisms, at the molecular level and on a 4 genome-wide scale. Via comparing the phylogenetic profiles of all protein-coding genes in 317 5 model species described in the OrthoInspector3.0 database, we found that approximately 6 29.8% of the total protein-coding genes were orphan genes (genes unique to a specific species) 7 while < 0.01% were universal genes (genes with homologs in each of the 317 species 8 analyzed). When weighted by potential birth event, the orphan genes comprised 82% of the 9 total, while the universal genes accounted for less than 0.00008%. Strikingly, as the analyzed 10 genomes increased, the sum total of universal and nearly-universal genes plateaued while that 11 of orphan and nearly-orphan genes grew continuously. When the compared species increased 12 to the inclusion of 3863 bacteria, 711 eukaryotes, and 179 archaea, not one of the universal 13 genes remained. The results speak to a previously unappreciated degree of genetic biodiversity, 14which we propose to quantify using the birth-event-weighted gene count method. 15

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UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

Cited by 1,085 publications

References 27 publications

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

The Absence of Universally-Conserved Protein-coding Genes

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