Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Cindy J. Castelle,Kelly C. Wrighton,Brian C. Thomas,Laura A. Hug,Christopher T. Brown,Michael J. Wilkins,Kyle R. Frischkorn,Susannah G. Tringe,Andrea Singh,Lye Meng Markillie,Ronald C. Taylor,Kenneth H. Williams,Jillian F. Banfield +12 more
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TLDR
This study sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River and reconstructed the first complete genomes for Archaea using cultivation-independent methods, which dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum.About:
This article is published in Current Biology.The article was published on 2015-03-16 and is currently open access. It has received 463 citations till now. The article focuses on the topics: Nanohaloarchaea & Phylum.read more
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Lists of names of prokaryotic Candidatus taxa.
TL;DR: The authors present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidate taxa was first established, and the end of 2018, where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryote and its Orthography appendix.
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A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column.
TL;DR: This study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages, including two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs.
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The Modern Synthesis in the Light of Microbial Genomics.
TL;DR: The theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis are reviewed and a piecemeal toolkit approach to evolutionary biology is advocated, in lieu of any grand unified theory updated to include microbial genomics.
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Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean.
TL;DR: HMT is a group of putatively heterotrophic marine thaumarchaeota with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia.
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Microbial community structure and diversity within hypersaline Keke Salt Lake environments
TL;DR: The microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes, expanding the understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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