Database resources of the National Center for Biotechnology Information

Sayers, Eric W; Barrett, Tanya; Benson, D. A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Mike; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J.; Madden, Thomas; Maglott, Donna; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexander; Starchenko, Grigory; Tatusova, Tatiana; Wagner, Lukas; Yaschenko, Eugene; Ye, J.

doi:10.1093/nar/gkn741

Cited by 902 publications

(870 citation statements)

References 45 publications

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“…Nitrospirae (23) Nitrospinae (5) Acidobacteria (35) Aminicenantes (10) Chlorobi Bacteroidetes (1,513) Ignavibacteriae (29) Calditrichaeota (5) Marinimicrobia (46), UBP11 (1) Fibrobacteres (17), Gemmatimonadetes (39) Zixibacteria, UBP14 (1), TA06, UBP1 (3), UBP2 (6) Cloacimonetes (31), Hyd24-12 (5), WOR-3 (10) Lentisphaerae (12), Chlamydiae, UBP17 (1) Verrucomicrobia (178) Planctomycetes (61) Hydrogenedentes (2) Poribacteria Elusimicrobia (23) Aerophobetes, UBP5 (2) Omnitrophica (14), UBP3 (4), UBP4 (2) Firmicutes (1,666) Armatimonadetes (24) UBP13 (1) Actinobacteria (336) Deinococcus-thermus (6) Chloroflexi (182) UBP9/SHA-109 (8) UBP12 (1) Cyanobacteria (48) Thermotogae (11) Acetothermia (10) Dictyoglomi Coprothermo. Caldiserica (5) Synergistetes (47) Atribacteria (5) UBP16 (1) UBP15 (1) Epsilonproteobacteria (52) Calescamantes Spirochaetes (135) UBP8 (5) UBP7 (2) Patescibacteria (245) 'Candidate phyla radiation' UBP6 (4) Aquificae (1) Deferribacteres (5) Fusobacteria (8) Dependentiae (1) Latescibacteria …”

Section: Articlesmentioning

confidence: 99%

“…Genome trees were annotated using taxonomic information from the NCBI Taxonomy Database 39 . Only the canonical seven taxonomic ranks (species to domain) were considered for each genome, and this information was used to annotate internal lineages using tax2tree 63 .…”

Section: Nature Microbiologymentioning

confidence: 99%

“…Taxonomic diversity and the percentage of lineages of equal evolutionary distance unique to the UBA genomes were determined using the mean branch length to extant taxa criterion 30 . Lineages of equal evolutionary distance were related to the distribution of NCBI taxa 39 as defined on 19 May 2016 and used to construct the phylum-level lineage view ( Supplementary Fig. 7) by evaluating the number of groups formed at mean branch length values of 0.5 to 1.1 with a step size of 0.025.…”

Section: Nature Microbiologymentioning

confidence: 99%

“…2) and archaeal (11 of 18, Fig. 3) phyla, as defined in the NCBI taxonomy 39 . In addition, they comprise the first genomic representatives of 17 bacterial and 3 archaeal phyla (see section 'UBA genomes are the first representatives of several phyla').…”

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confidence: 99%

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

et al. 2017

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Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from > 1,500 public metagenomes. All genomes are estimated to be ≥ 50% complete and nearly half are ≥ 90% complete with ≤ 5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by > 30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter. Articles NATuRe MiCRobiologyform the UBA data set as they met our filtering criteria of having an estimated quality ≥ 50 (defined as the estimated completeness of a genome minus five times its estimated contamination) and consisting of ≤ 500 scaffolds with an N50 ≥ 10 kb ( Fig. 1 and Supplementary Table 2). Over 93% of the 7,903 UBA genomes have an average coverage of ≥ 10× (5th percentile, 9.2× , 95th percentile, 268× ) and 95.8% have > 5× coverage over 90% of bases, providing assurance of high-quality base-calling across the genomes 3,36 . Among the UBA genomes is a subset of 3,438 near-complete genomes (3,225 bacterial and 213 archaeal) estimated to be ≥ 90% complete with ≤ 5% contamination (Fig. 1a). These genomes consist of ≤ 100 scaffolds in 70.2% of cases (≤ 200 scaffolds in 92.0% genomes) and have an average N50 of 136 kb. Comparison of near-complete UBA genomes that are conspecific strains of complete isolate genomes also suggest that the recovered MAGs have no systematic loss of genomic content, with the exception of extrachromosomal elements such as plasmids (Supplementary Note 1).The UBA data set was also assessed relative to the criteria used by the Human Microbiome Project (HMP) for defining high-quality draft genomes 3,37 . Of the 3,438 UBA genomes we have defined as near complete, 3,201 (93.1%) pass all of the HMP criteria, with the only substantial exception being 4.8% of the genomes having scaffolds with an N50 of < 20 kb (Supplementary Table 3). Nearly half of the remaining 4,465 UBA genomes also pass the HMP criteria for being high quality except that they are estimated to be < 90% complete.The presence of tRNAs for the standard 20 amino acids was examined as a secondary measure of genome quality (Fig. 1c). The 3,438 near-complete UBA genomes have tRNAs that encode for an average of 17.3 ± 2.2 of the 20 amino acids and ≥ 15 amino acids in 90.3% of the genomes. The correlation between estimated genome completeness and identified tRN...

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Section: Articlesmentioning

confidence: 99%

Section: Nature Microbiologymentioning

confidence: 99%

Section: Nature Microbiologymentioning

confidence: 99%

mentioning

confidence: 99%

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

et al. 2017

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“…Table 3 (Appendix) lists the considered species, together with their abbreviations, and Figure 5 (Appendix) describes the size distribution of the gene trees. The corresponding reference species tree, denoted by S 0 , is depicted in Appendix (Figure 4) and corresponds to the NCBI taxonomy tree [19], except that three nodes of the tree were considered as multifurcations due to different phylogenetic hypothesis regarding the corresponding clades (see [11,17]). …”

Section: Resultsmentioning

confidence: 99%

Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees

Doyon

Chauve²

2011

Advances in Experimental Medicine and Biology

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Abstract. We describe a Branch-and-Bound algorithm for computing a parsimonious species tree given a set of gene family trees. Our algorithm can compute a parsimonious species tree for three cost measures: number of gene duplications, number of gene losses, and both combined. Moreover, to cope with intrinsic limitations of Branch-and-Bound algorithms for species trees inference regarding the number of taxa that can be considered, our algorithm can naturally take into account predefined relationships between sets of taxa. We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa.

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Resources for Small Regulatory RNAs

Bell

Lewitter

2009

CP Molecular Biology

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In the past fifteen years, new classes of regulatory RNAs have been discovered, previously hidden in the transcriptome mostly due to their small size. These small regulatory RNAs include small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). Numerous databases have been developed to store information about these small regulatory RNAs, and many tools have been developed to work with the data. This overview introduces the reader to the many resources available for working with small regulatory RNAs.

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Database resources of the National Center for Biotechnology Information

Cited by 902 publications

References 45 publications

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees

Resources for Small Regulatory RNAs

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