Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon; Ovchinnikova, Galina; Verezemska, Olena; Isbandi, Michelle; Thomas, Alex D.; Ali, Rida; Sharma, Kaushal Kishore; Kyrpides, Nikos C.; Reddy, T. B. K.

doi:10.1093/nar/gkw992

Cited by 147 publications

(109 citation statements)

References 51 publications

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“…Traditionally, most isolate sequencing projects are chosen based on the clinical or biotechnological relevance of the target organisms or their physiology 1 . In 2015, 43% of sequenced bacterial genomes comprised just ten human pathogenic species.…”

Section: R E S O U R C Ementioning

confidence: 99%

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

et al. 2017

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We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

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Section: R E S O U R C Ementioning

confidence: 99%

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

et al. 2017

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“…The third generation appeared between 2011 and 2014 with sequencing technologies that produce reads of unprecedented length (average~2-10 Kb). Currently, long reads can be obtained with two methods, "single-molecule real-time" sequencing (SMRT-seq; i.e., (Mukherjee et al, 2017).…”

Section: Ge Nome Sequencing Techn Iquesmentioning

confidence: 99%

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

2017

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Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.

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“…(i) Thermotogae and Aquificae abound in hyperthermophilic species, wherein structurally disordered regions are generally heavily shortened and affected by adaptive sequence composition changes (Pancsa et al, 2019b). To assess if this could be the reason for their low predicted LLPS propensity, we identified hyperthermophilic species (optimum growth temperature ≥ 75°C based on the Genomes Online (Mukherjee et al, 2017) and/or BacDive databases (Reimer et al, 2019)) in the whole dataset (respective SSBs highlighted in red). (ii) We also identified SSB sequences that appeared to be fragments based on the absence of the CTP motif (and often the IDL too) but could not be excluded due to the lack of orthologs (highlighted in blue).…”

Section: Author Contributionsmentioning

confidence: 99%

Phase separation by ssDNA binding protein controlledviaprotein-protein and protein-DNA interactions

Harami

Kovács

Pancsa

et al. 2019

Preprint

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Bacterial single stranded (ss) DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL) and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein-protein interactions with DNA-metabolizing proteins. Here we show that the E. coli SSB protein forms liquid-liquid phase separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA and SSBinteracting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage. RESULTS SSB forms dynamic LLPS condensates in physiologically relevant conditions in vitroDue to the fact that SSB shares several features with hitherto described LLPS drivers, we sought to determine if LLPS could be a yet undiscovered capability of SSB facilitating its multifaceted roles in genome maintenance. We performed a bioinformatics analysis that revealed that E. coli SSB, in particular its IDL region, shows high propensity for LLPS, according to multiple dedicated sequencebased prediction methods (Bolognesi et al., 2016;Lancaster et al., 2014;Vernon et al., 2018) (Fig. 1B-D). This feature of SSB is universally conserved among bacteria, as the majority of analyzed SSBs (72.1 %) harbored by representative bacterial species from 15 large phylogenetic groups show similar LLPS propensities (Tables S1-2; Fig. 1E).In line with its predicted LLPS propensity, purified E. coli SSB (30 µM; SSB concentrations are expressed as those of tetramer molecules throughout the paper) forms an opaque, turbid solution at low NaCl concentration (50 mM) in vitro at room temperature and also at the native temperature of E. coli cells (37°C) ( Fig. 2A-B). The process is reversible as elevation of NaCl concentration to 200 mM leads to immediate loss of turbidity. The Clconcentration in E. coli cells depends on their environment (Schultz et al., 1962); however, while the exact value is not known, it can be assumed to be in a similar range (5-100 mM) as that measured for the cells of mammalian E. coli hosts, whereas the major metabolic anion in bacterial cells is glutamate (Glu; 100 mM) (Bennett et al., 2009). Strikingly, SSB forms a turbid solution even in 200 mM NaGlu ( Fig. 2A-B). (It must be noted that experiments using NaGlu always contained a fixed amount of 20 mM NaCl, for technical reasons.) Investigation of the protein solution by differential interference contrast (DIC) microscopy after diluting SSB into low-salt buffer revealed the formation of regular spherical drop...

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Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Cited by 147 publications

References 51 publications

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Phase separation by ssDNA binding protein controlledviaprotein-protein and protein-DNA interactions

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