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Eight new genomes of organohalide-respiring Dehalococcoides mccartyi reveal evolutionary trends in reductive dehalogenase enzymes

https://doi.org/10.1101/345173
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome reduction as the dominant mode of evolution
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DNA Rearrangement of the Shufflon Determines Recipient Specificity in Liquid Mating of IncI1 Plasmid R64
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Contaminated Soils, Sediments and Water
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Bioaugmentation for Groundwater Remediation
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Site-specific recombination following conjugation in Escherichia coli K-12
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Mutation rate and genome reduction in endosymbiotic and free-living bacteria
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Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene
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Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria
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Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride
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Deletional bias and the evolution of bacterial genomes
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Field Demonstration of Successful Bioaugmentation To Achieve Dechlorination of Tetrachloroethene To Ethene
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Carbon and Sulfur Cycling by Microbial Communities in a Gypsum-Treated Oil Sands Tailings Pond
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Experimental factors affecting PCR-based estimates of microbial species richness and evenness
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Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species
inferredcites →https://doi.org/10.1038/ismej.2017.127openalex-snapshot
Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes
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Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium
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Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation
inferredcites →https://doi.org/10.1038/nbt1131openalex-snapshot
Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrmicro2312openalex-snapshot
Call of the wild: antibiotic resistance genes in natural environments
inferredcites →https://doi.org/10.1038/s41396-018-0254-2openalex-snapshot
Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes
inferredcites →https://doi.org/10.1038/srep15204openalex-snapshot
A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a
inferredcites →https://doi.org/10.1073/pnas.0903507106openalex-snapshot
The genomic basis of trophic strategy in marine bacteria
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
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Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls
inferredcites →https://doi.org/10.1080/10889860601021399openalex-snapshot
Characterization of a Microbial Consortium Capable of Rapid and Simultaneous Dechlorination of 1,1,2,2-Tetrachloroethane and Chlorinated Ethane and Ethene Intermediates
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Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
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DaliLite workbench for protein structure comparison
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btq683openalex-snapshot
Scaffolding pre-assembled contigs using SSPACE
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/femsec/fiw235openalex-snapshot
Genomic characterization of Dehalococcoides mccartyi strain 11a5 reveals a circular extrachromosomal genetic element and a new tetrachloroethene reductive dehalogenase gene
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gki593openalex-snapshot
BASys: a web server for automated bacterial genome annotation
inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
inferredcites →https://doi.org/10.1093/nar/gkw569openalex-snapshot
NCBI prokaryotic genome annotation pipeline
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004050openalex-snapshot
Evolution of Microbial Genomes: Sequence Acquisition and Loss
inferredcites →https://doi.org/10.1098/rstb.2012.0317openalex-snapshot
Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi
inferredcites →https://doi.org/10.1098/rstb.2012.0320openalex-snapshot
Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity
inferredcites →https://doi.org/10.1098/rstb.2012.0322openalex-snapshot
Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
inferredcites →https://doi.org/10.1099/ijs.0.005884-0openalex-snapshot
Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba
inferredcites →https://doi.org/10.1099/ijs.0.034926-0openalex-snapshot
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the…
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.200901openalex-snapshot
The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study
inferredcites →https://doi.org/10.1111/1574-6968.12160openalex-snapshot
Genome sequences of two dehalogenation specialists- Dehalococcoides mccartyistrains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region
inferredcites →https://doi.org/10.1111/j.1574-6941.2006.00243.xopenalex-snapshot
Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides
inferredcites →https://doi.org/10.1126/science.1102226openalex-snapshot
Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes
inferredcites →https://doi.org/10.1126/science.1258118openalex-snapshot
Structural basis for organohalide respiration
inferredcites →https://doi.org/10.1126/science.276.5318.1568openalex-snapshot
Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.00215-07openalex-snapshot
Expression of Reductive Dehalogenase Genes in Dehalococcoides ethenogenes Strain 195 Growing on Tetrachloroethene, Trichloroethene, or 2,3-Dichlorophenol
inferredcites →https://doi.org/10.1128/aem.00536-15openalex-snapshot
Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes
inferredcites →https://doi.org/10.1128/aem.00767-09openalex-snapshot
Isolation and Characterization of “ Dehalococcoides ” sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans -1,2-Dichloroethene
inferredcites →https://doi.org/10.1128/aem.01649-07openalex-snapshot
Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1
inferredcites →https://doi.org/10.1128/aem.01873-12openalex-snapshot
Functional Characterization of Reductive Dehalogenases by Using Blue Native Polyacrylamide Gel Electrophoresis
inferredcites →https://doi.org/10.1128/aem.01886-09openalex-snapshot
Evidence for Nitrogen Fixation by “ Dehalococcoides ethenogenes ” Strain 195
inferredcites →https://doi.org/10.1128/aem.02017-15openalex-snapshot
Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans -Dichloroethene Reductive Dehalogenase, TdrA
inferredcites →https://doi.org/10.1128/aem.02037-08openalex-snapshot
Characterization of a Dehalobacter Coculture That Dechlorinates 1,2-Dichloroethane to Ethene and Identification of the Putative Reductive Dehalogenase Gene
inferredcites →https://doi.org/10.1128/aem.02129-06openalex-snapshot
Comparative Proteomics of Dehalococcoides spp. Reveals Strain-Specific Peptides Associated with Activity
inferredcites →https://doi.org/10.1128/aem.02130-14openalex-snapshot
Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit
inferredcites →https://doi.org/10.1128/aem.02208-07openalex-snapshot
Temporal Transcriptomic Microarray Analysis of “Dehalococcoides ethenogenes” Strain 195 during the Transition into Stationary Phase
inferredcites →https://doi.org/10.1128/aem.02411-13openalex-snapshot
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
inferredcites →https://doi.org/10.1128/aem.02927-13openalex-snapshot
Identification and Environmental Distribution ofdcpA, Which Encodes the Reductive Dehalogenase Catalyzing the Dichloroelimination of 1,2-Dichloropropane to Propene in Organohalide-Respiring Chloroflexi
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1128/aem.06416-11openalex-snapshot
Transcriptional Analysis of a Dehalococcoides-Containing Microbial Consortium Reveals Prophage Activation
inferredcites →https://doi.org/10.1128/aem.06510-11openalex-snapshot
Natural Niche for Organohalide-Respiring Chloroflexi
inferredcites →https://doi.org/10.1128/aem.66.12.5141-5147.2000openalex-snapshot
Trichloroethene Reductive Dehalogenase from Dehalococcoides ethenogenes : Sequence of tceA and Substrate Range Characterization
inferredcites →https://doi.org/10.1128/aem.68.2.485-495.2002openalex-snapshot
Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe
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Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution
inferredcites →https://doi.org/10.1128/aem.70.9.5290-5297.2004openalex-snapshot
Multiple Nonidentical Reductive-Dehalogenase-Homologous Genes Are Common in Dehalococcoides
inferredcites →https://doi.org/10.1128/aem.70.9.5538-5545.2004openalex-snapshot
Characterization of a Highly Enriched Dehalococcoides -Containing Culture That Grows on Vinyl Chloride and Trichloroethene
inferredcites →https://doi.org/10.1128/aem.71.12.8257-8264.2005openalex-snapshot
Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides- Containing Cultures
inferredcites →https://doi.org/10.1128/aem.72.3.1980-1987.2006openalex-snapshot
Quantitative PCR Confirms Purity of Strain GT, a Novel Trichloroethene-to-Ethene-Respiring Dehalococcoides Isolate
inferredcites →https://doi.org/10.1128/aem.72.4.2765-2774.2006openalex-snapshot
Quantitative PCR Targeting 16S rRNA and Reductive Dehalogenase Genes Simultaneously Monitors MultipleDehalococcoidesStrains
inferredcites →https://doi.org/10.1128/genomea.01375-16openalex-snapshot
Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride
inferredcites →https://doi.org/10.1128/jb.00419-16openalex-snapshot
The MarR-Type Regulator Rdh2R Regulates rdh Gene Transcription in Dehalococcoides mccartyi Strain CBDB1
inferredcites →https://doi.org/10.1128/microbiolspec.mdna3-0047-2014openalex-snapshot
Site-specific DNA Inversion by Serine Recombinases
inferredcites →https://doi.org/10.1146/annurev.biochem.73.011303.073908openalex-snapshot
Mechanisms of Site-Specific Recombination
inferredcites →https://doi.org/10.1186/1471-2164-12-287openalex-snapshot
Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides
inferredcites →https://doi.org/10.1186/1471-2164-13-327openalex-snapshot
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community
inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot
The RAST Server: Rapid Annotations using Subsystems Technology
inferredcites →https://doi.org/10.1186/gb-2005-6-2-r14openalex-snapshot
Accelerated evolution associated with genome reduction in a free-living prokaryote
inferredcites →https://doi.org/10.1371/journal.pgen.1000714openalex-snapshot
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
inferredcites →https://doi.org/10.1371/journal.pone.0011147openalex-snapshot
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
inferredcites →https://doi.org/10.1371/journal.pone.0052038openalex-snapshot
Semi-Automatic In Silico Gap Closure Enabled De Novo Assembly of Two Dehalobacter Genomes from Metagenomic Data
inferredcites →https://doi.org/10.1371/journal.pone.0094808openalex-snapshot
New Insights into Dehalococcoides mccartyi Metabolism from a Reconstructed Metabolic Network-Based Systems-Level Analysis of D. mccartyi Transcriptomes
inferredcites →https://doi.org/10.3133/sir20075165openalex-snapshot
Microbial consortia development and microcosm and column experiments for enhanced bioremediation of chlorinated volatile organic compounds, West Branch Canal Creek wetland area, Aberdeen Proving Ground, Maryland
inferredcites →https://doi.org/10.3389/fmicb.2014.00742openalex-snapshot
Evolution of small prokaryotic genomes
inferredcites →https://doi.org/10.3389/fmicb.2018.00812openalex-snapshot
Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi (D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments
inferredcites →https://doi.org/10.48550/arxiv.1203.4802openalex-snapshot
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s11356-019-05571-7openalex-snapshot
Growth of Dehalococcoides spp. and increased abundance of reductive dehalogenase genes in anaerobic PCB-contaminated sediment microcosms
inferred← citeshttps://doi.org/10.1016/j.chemosphere.2019.124449openalex-snapshot
Application of γ-PGA as the primary carbon source to bioremediate a TCE-polluted aquifer: A pilot-scale study
inferred← citeshttps://doi.org/10.1021/acs.est.9b02339openalex-snapshot
Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides -Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH
inferred← citeshttps://doi.org/10.1021/acsestengg.5c00240openalex-snapshot
Microbial Response Following a Carboxymethyl Cellulose-Stabilized Sulfidated Nano Zero-Valent Iron Injection: A Long-Term Field Study
inferred← citeshttps://doi.org/10.1038/s41396-018-0254-2openalex-snapshot
Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes
inferred← citeshttps://doi.org/10.1039/c9em00605bopenalex-snapshot
Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification
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