Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation

Степанов, В. П.; Tirumalai, Madhan R.; Montazari, Saied; Checinska, Aleksandra; Venkateswaran, Kasthuri; Fox, George E.

doi:10.1371/journal.pone.0157331

Cited by 26 publications

(21 citation statements)

References 39 publications

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“…The accumulation of numerous draft genomes creates massive databases; unfortunately, the quality of the genomes is decreased since it is based on incomplete and/or incorrect genomic data [ 41 , 42 ]. Indeed, draft genome assemblies are not sufficient for studying large-scale genome architecture [ 43 ], can result in incomplete or incorrectly annotated genes (e.g., partitioned annotation of ORFs), and may hinder evolutionary studies [ 44 , 45 ] by leaving significant portions of the genome unclear or inaccurate [ 17 ]. Furthermore, some studies have demonstrated the limitations and difficulties associated with using drafts for studies involving HGT analysis, phylogenomics, the evolution of genome synteny, genome structural analysis, and pangenomic approaches [ 34 , 42 , 46 , 47 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains

et al. 2018

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BackgroundWithout knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation.ResultsWe showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains.ConclusionsIn this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4429-4) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains

et al. 2018

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“…This comparison identified several genes and a mobile genetic element in SAFR-032 that may be associated with the elevated resistance [40]. Since this previous study was completed, minor corrections to the SAFR-032 gene order were made and the annotation was updated [1]. In addition, a draft genome of MERTA was reported [41].…”

Section: Introductionmentioning

confidence: 99%

Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

Tirumalai

Степанов

Wünsche

et al. 2018

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BackgroundBacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.ResultsThe FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061T. The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all safensis/pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061T, and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. pumilus while the other houses all the B. safensis strains.ConclusionsIt is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. pumilus actually belong to the B. safensis group.

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“…This process proceeds iteratively until 35 the organism can produce no new compounds. The state of the organism's network 36 when expansion ceases is referred to as the organism's scope-and it contains all of the 37 compounds which can be synthesized by an organism, plus the compounds provided by 38 the environment (the seed set). 39 While there are other methods which can be used to computationally assess 40 organismal viability, relying on some combination of integer linear programming, kinetic 41 modeling using differential equations, elementary mode analysis, and flux balance 42 analysis (FBA), they require catalytic rates which are difficult to acquire and sparsely 43 catalogued, or a curated list of stoichiometrically balanced reactions [27].…”

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“…We could analyze the metabolisms of ecosystems, through 254 metagenomic data, in addition to simple genomes. If we were specifically focused on the 255 question of planetary contamination, we might also rerun these analyses on organisms 256 which are known to exist in spacecraft sterilized clean rooms, like Bacillus pumilus 257 SAFR-032 [36]. Further network expansion analyses could even be used to guide 258 development of the composition of spacecraft materials to avoid metals which, if in 259 contact with certain environments, could provide rich sources of cofactors or other 260 compounds.…”

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Assessing the viability of biochemical networks across planets

Smith

Drew

Walker

2019

Preprint

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The concept of the origin of life implies that initially, life emerged from a non-living medium. If this medium was Earth's geochemistry, then that would make life, by definition, a geochemical process. The extent to which life on Earth today could subsist outside of the geochemistry from which it is embedded is poorly quantified. By leveraging large biochemical datasets in conjunction with planetary observations and computational tools, this research provides a methodological foundation for the quantitative assessment of our biology's viability in the context of other geospheres. Investigating a case study of alkaline prokaryotes in the context of Enceladus, we find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a map for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent.It is probable that the geochemical process known as life had already commenced when 2 today's oldest minerals began to crystallize. While there is widely accepted evidence 3 that the process of life has been present on Earth continuously for the past 3.4Gy [1], 4 the lack of evidence prior to this date has more to do with the paucity of 5 fossil-preserving rocks than concrete evidence of life's absence [14,32]. Despite the 6 biosphere's apparent interminable coexistence with the geosphere, there remain many 7 open questions on the matter of life persisting in Earth's absence [3,35], not to mention 8 the questions of Earth persisting in life's absence [21,23,24]. For example, Visionaries 9 dream of terraforming planets while program officers fret over "contaminating" 10 them [25,31,34]. While the terraformers tend to believe that seeding another planet 11 1/16 would require careful human or robotic (and usually Earth-assisted) cultivation, 12 planetary protection officers take the more conservative stance that a small, 13 semi-sterilized spacecraft of Earth origin could cause life to spill onto a planet in the 14 same way that a small perturbation to a super cooled liquid would cause the entire 15 volume to quickly crystallize. In both cases, there is the predominately implicit 16 assumption that Earth-life would be viable outside of the Earth. 17When life is viewed as a geologic process, this is a somewhat surprising assumption. 18 In the words of Morowitz et al., "the metabolic character of life is a planetary 19 phenomenon, no less than the atmosphere, hydrosphere, or geosphere" [30]. If this 20 "metabolic character of life" is truly a planetary phenomenon, does that imply that life 21 is inextricable from the planet through which it emerged? Or is it possible that an 22 97We ran the network expansion algorithm on the subs...

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Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation

Cited by 26 publications

References 39 publications

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains

Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

Assessing the viability of biochemical networks across planets

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