Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
Reads0
Chats0
TLDR
The specI (species identification tool) as mentioned in this paper ) is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes, applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters.Abstract:
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.read more
Citations
More filters
Journal ArticleDOI
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simão,Robert M. Waterhouse,Panagiotis Ioannidis,Evgenia V. Kriventseva,Evgeny M. Zdobnov +4 more
TL;DR: Zdobnov et al. as discussed by the authors proposed a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, and implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs.
Journal ArticleDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs
TL;DR: This work proposes a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, implemented in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.
Journal ArticleDOI
NCBI prokaryotic genome annotation pipeline
Tatiana Tatusova,Michael DiCuccio,Azat Badretdin,Vyacheslav Chetvernin,Eric P. Nawrocki,Leonid Zaslavsky,Alexandre Lomsadze,Kim D. Pruitt,Mark Borodovsky,James Ostell +9 more
TL;DR: The new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies less on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence.
Journal ArticleDOI
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
TL;DR: The overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla was investigated, finding an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI.
References
More filters
Journal ArticleDOI
The species concept for prokaryotes.
Ramon Rosselló-Móra,Rudolf Amann +1 more
TL;DR: The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines as discussed by the authors, and it has been widely accepted as useful, pragmatic and universally applicable within the prokaryotic world.
Journal ArticleDOI
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
Francesca D. Ciccarelli,Tobias Doerks,Christian von Mering,Christopher J. Creevey,Berend Snel,Peer Bork +5 more
TL;DR: An automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains is developed, revealing interdomain discrepancies in taxonomic classification and suggesting a thermophilic last universal common ancestor.
Journal ArticleDOI
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Ivica Letunic,Peer Bork +1 more
TL;DR: Current version of iTOL introduces numerous new features and greatly expands the number of supported data set types.
Journal ArticleDOI
A novel free-living prochlorophyte abundant in the oceanic euphotic zone
Sallie W. Chisholm,Robert J. Olson,Erik R. Zettler,Ralf Goericke,John B. Waterbury,Nicholas A. Welschmeyer +5 more
TL;DR: In this paper, a new group of photosynthetic picoplankters was identified, which are extremely abundant, and barely visible using traditional microscopic techniques, reaching concentrations greater than 105 cells ml−1 in the deep euphotic zone.
Journal ArticleDOI
Towards a Genome-Based Taxonomy for Prokaryotes
TL;DR: The AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes, and could contribute significantly to a genome-based taxonomy for all microbial organisms.
Related Papers (5)
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin,Ruiqiang Li,Jeroen Raes,Manimozhiyan Arumugam,Kristoffer Sølvsten Burgdorf,Chaysavanh Manichanh,Trine Nielsen,Nicolas Pons,Florence Levenez,Takuji Yamada,Daniel R. Mende,Junhua Li,Junming Xu,Shaochuan Li,Dongfang Li,Jianjun Cao,Bo Wang,Huiqing Liang,Huisong Zheng,Yinlong Xie,Julien Tap,Patricia Lepage,Marcelo Bertalan,Jean-Michel Batto,Torben Hansen,Denis Le Paslier,Allan Linneberg,H. Bjørn Nielsen,Eric Pelletier,Pierre Renault,Thomas Sicheritz-Pontén,Keith Turner,Hongmei Zhu,Chang Yu,Shengting Li,Min Jian,Yan Zhou,Yingrui Li,Xiuqing Zhang,Songgang Li,Nan Qin,Huanming Yang,Jian Wang,Søren Brunak,Joël Doré,Francisco Guarner,Karsten Kristiansen,Oluf Pedersen,Julian Parkhill,Jean Weissenbach,Peer Bork,S. Dusko Ehrlich,Jun Wang +52 more