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Comparing faster evolving rplB and rpsC versus SSU rRNA for improved microbial community resolution

https://doi.org/10.1101/435099
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1007s36openalex-snapshot
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
inferredcites →https://doi.org/10.1002/9780471729259.mc01e05s27openalex-snapshot
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
inferredcites →https://doi.org/10.1007/s10142-015-0433-4openalex-snapshot
Insights from 20 years of bacterial genome sequencing
inferredcites →https://doi.org/10.1007/s11084-008-9148-zopenalex-snapshot
The Most Conserved Genome Segments for Life Detection on Earth and Other Planets
inferredcites →https://doi.org/10.1016/b978-0-12-407863-5.00017-4openalex-snapshot
Assembling Full-Length rRNA Genes from Short-Read Metagenomic Sequence Datasets Using EMIRGE
inferredcites →https://doi.org/10.1016/j.soilbio.2011.03.012openalex-snapshot
The under-recognized dominance of Verrucomicrobia in soil bacterial communities
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1038/35030019openalex-snapshot
Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
inferredcites →https://doi.org/10.1038/ismej.2012.8openalex-snapshot
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
inferredcites →https://doi.org/10.1038/nmeth.2276openalex-snapshot
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1073/pnas.1015622108openalex-snapshot
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
inferredcites →https://doi.org/10.1073/pnas.1402564111openalex-snapshot
Tackling soil diversity with the assembly of large, complex metagenomes
inferredcites →https://doi.org/10.1073/pnas.1521291113openalex-snapshot
Scaling laws predict global microbial diversity
inferredcites →https://doi.org/10.1073/pnas.74.11.5088openalex-snapshot
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
inferredcites →https://doi.org/10.1073/pnas.82.20.6955openalex-snapshot
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
inferredcites →https://doi.org/10.1093/bib/bbx098openalex-snapshot
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
inferredcites →https://doi.org/10.1093/bioinformatics/btr507openalex-snapshot
FLASH: fast length adjustment of short reads to improve genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btv231openalex-snapshot
Reconstructing 16S rRNA genes in metagenomic data
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gkt1244openalex-snapshot
Ribosomal Database Project: data and tools for high throughput rRNA analysis
inferredcites →https://doi.org/10.1093/nar/gkv657openalex-snapshot
Microbial species delineation using whole genome sequences
inferredcites →https://doi.org/10.1093/nar/gkw900openalex-snapshot
ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores
inferredcites →https://doi.org/10.1093/nar/gky467openalex-snapshot
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
inferredcites →https://doi.org/10.1099/ijs.0.64483-0openalex-snapshot
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
inferredcites →https://doi.org/10.1101/gr.183012.114openalex-snapshot
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
inferredcites →https://doi.org/10.1111/1755-0998.12700openalex-snapshot
Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description
inferredcites →https://doi.org/10.1111/j.1472-765x.2007.02198.xopenalex-snapshot
Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers
inferredcites →https://doi.org/10.1111/j.1574-6941.2011.01190.xopenalex-snapshot
Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems
inferredcites →https://doi.org/10.1128/aem.00014-18openalex-snapshot
How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?
inferredcites →https://doi.org/10.1128/aem.01177-06openalex-snapshot
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies
inferredcites →https://doi.org/10.1128/aem.01282-13openalex-snapshot
Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity
inferredcites →https://doi.org/10.1128/aem.02167-10openalex-snapshot
Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
inferredcites →https://doi.org/10.1128/aem.02772-15openalex-snapshot
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes
inferredcites →https://doi.org/10.1128/msystems.00130-17openalex-snapshot
Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
inferredcites →https://doi.org/10.1142/9781848165632_0019openalex-snapshot
A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
inferredcites →https://doi.org/10.1186/2049-2618-1-22openalex-snapshot
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
inferredcites →https://doi.org/10.1186/gb-2007-8-1-r10openalex-snapshot
Prediction of effective genome size in metagenomic samples
inferredcites →https://doi.org/10.1186/gb-2008-9-10-r151openalex-snapshot
A simple, fast, and accurate method of phylogenomic inference
inferredcites →https://doi.org/10.1186/s13059-015-0611-7openalex-snapshot
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
inferredcites →https://doi.org/10.1186/s40168-015-0093-6openalex-snapshot
Xander: employing a novel method for efficient gene-targeted metagenomic assembly
inferredcites →https://doi.org/10.12688/f1000research.6924.1openalex-snapshot
The khmer software package: enabling efficient nucleotide sequence analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1001061openalex-snapshot
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
inferredcites →https://doi.org/10.1371/journal.pgen.1000255openalex-snapshot
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0039948openalex-snapshot
Reconstruction of Ribosomal RNA Genes from Metagenomic Data
inferredcites →https://doi.org/10.1371/journal.pone.0075794openalex-snapshot
A Genomic Redefinition of Pseudomonas avellanae species
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.3389/fmicb.2013.00291openalex-snapshot
FunGene: the functional gene pipeline and repository
inferredcites →https://doi.org/10.48550/arxiv.1203.4802openalex-snapshot
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41396-020-0635-1openalex-snapshot
Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
inferred← citeshttps://doi.org/10.1128/msystems.00627-24openalex-snapshot
Gut microbiome diversity within Clostridia is negatively associated with human obesity
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