Genome Project Standards in a New Era of Sequencing

Chain, Patrick; Grafham, Darren; Fulton, Robert S.; FitzGerald, Michael G.; Hostetler, Jessica B.; Muzny, Donna M.; Ali, Johar; Birren, Bruce W.; Bruce, David; Buhay, Christian; Cole, James R.; Ding, Yan; Dugan, Shannon; Field, Dawn; Gibbs, Richard A.; Graves, Tina; Han, Cliff; Harrison, Scott H.; Highlander, Sarah K.; Hugenholtz, Philip; Khouri, Hoda; Kodira, C. D.; Kolker, Eugene; Kyrpides, Nikos C.; Lang, Dorothy; Lapidus, Alla; Malfatti, Stephanie; Markowitz, Victor; Metha, T.; Nelson, Karen E.; Parkhill, Julian; Pitluck, Sam; Qin, Xiang; Read, Timothy D.; Schmutz, Jeremy; Sozhamannan, Shanmuga; Sterk, Peter J.; Strausberg, Robert L.; Sutton, Granger; Thomson, Nicholas R.; Tiedje, J. M.; Weinstock, George M.; Wollam, Aye; Detter, John C.

doi:10.1126/science.1180614

Cited by 373 publications

(328 citation statements)

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“…2 and 3). The 7,903 genomes reported in this study range in quality from 50% complete to meeting the HMP criteria for high-quality draft genomes 3,37 (Fig. 1).…”

Section: Discussionmentioning

confidence: 94%

“…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).…”

Section: Articlesmentioning

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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“…2 and 3). The 7,903 genomes reported in this study range in quality from 50% complete to meeting the HMP criteria for high-quality draft genomes 3,37 (Fig. 1).…”

Section: Discussionmentioning

confidence: 94%

Section: Articlesmentioning

confidence: 99%

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

et al. 2017

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“…Currently, T49 T is the only complete Armatimonadetes genome that is publically available, and it has undergone extensive automated and manual improvement to remove gaps and resolve problematic regions in order to conform to the definition of 'improved highquality draft' (Chain et al, 2009). The prospect of additional Armatimonadetes genomic data (in particular the two known characterised species, A. rosea YO-36 T (Tamaki et al, 2011) and F. ginsengisoli GSoil348 T ), provides an exciting opportunity to further understand common genomic features and evolution of this newly described phylum.…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

et al. 2014

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Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49 T and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49 T to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49 T relies on the relatively abundant r-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49 T to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.

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“…The two rRNA operons assembled into a single contigs, which were manually corrected, as were contig boundaries where possible. Manual insertion of capillary‐sequenced hctB and tarp gene sequences was followed by self‐mapping with all the sequence reads to confirm the assembled sequence and resulted in an improved high‐quality draft sequence (Chain et al ., 2009). After this process, the assembly of strain F/SWFP− comprised three contigs.…”

Section: Methodsmentioning

confidence: 99%

Plasmid deficiency in urogenital isolates ofChlamydia trachomatisreduces infectivity and virulence in a mouse model

et al. 2013

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We hypothesized that the plasmid of urogenital isolates of Chlamydia trachomatis would modulate infectivity and virulence in a mouse model. To test this hypothesis, we infected female mice in the respiratory or urogenital tract with graded doses of a human urogenital isolate of C. trachomatis, serovar F, possessing the cognate plasmid. For comparison, we inoculated mice with a plasmid‐free serovar F isolate. Following urogenital inoculation, the plasmid‐free isolate displayed significantly reduced infectivity compared with the wild‐type strain with the latter yielding a 17‐fold lower infectious dose to yield 50% infection. When inoculated via the respiratory tract, the plasmid‐free isolate exhibited reduced infectivity and virulence (as measured by weight change) when compared to the wild‐type isolate. Further, differences in infectivity, but not in virulence were observed in a C. trachomatis, serovar E isolate with a deletion within the plasmid coding sequence 1 when compared to a serovar E isolate with no mutations in the plasmid. We conclude that plasmid loss reduces virulence and infectivity in this mouse model. These findings further support a role for the chlamydial plasmid in infectivity and virulence in vivo.

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Genome Project Standards in a New Era of Sequencing

Abstract: More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.

Cited by 373 publications

References 4 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

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

Plasmid deficiency in urogenital isolates ofChlamydia trachomatisreduces infectivity and virulence in a mouse model

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