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Auto Tag: Genome assembly

July 7, 2019  |  

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.

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July 7, 2019  |  

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.

Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both on strains and on food matrix. Several B. thermosphacta genome sequences have been reported, all issued from meat isolates. Here, we report four genome sequences, one complete and three as drafts. The four B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated from different ecological niches (seafood or meat products either spoiled or not and bovine slaughterhouse). These strains known as phenotypically and genetically different were selected to represent intraspecies diversity. CD 337 genome is 2,594,337 bp long, complete and circular, containing 2593 protein coding sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding sequences, respectively. These genomes were compared with two other B. thermosphacta complete genome sequences. The main genome content differences between strains are phages, plasmids, restriction/modification systems, and cell surface functions, suggesting a similar metabolic potential but a different niche adaptation capacity.

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July 7, 2019  |  

PacBio genome sequences of Escherichia coli serotype O157:H7, diffusely adherent E. coli, and Salmonella enterica strains, all carrying plasmids with an mcr-1 resistance gene.

We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2 strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene on an IncI2 or IncX4 plasmid. We also determined that pMCR-1-CTSe is identical to a previously published plasmid, pMCR-1-CT.

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July 7, 2019  |  

Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements.

Recent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae.The L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade.Our results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.

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July 7, 2019  |  

Genomic insights into date palm origins.

With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.

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July 7, 2019  |  

Complete genome sequence of Bordetella sp. HZ20 sheds light on the ecological role of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment

Bordetella sp. HZ20 was isolated from the surface of brown seaweed (Laminaria japonica) and absence of the abilities to decompose the brown seaweed. The genome of Bordetella sp. HZ20 was sequenced and comprised of one circular chromosome with the size of 4,227,194?bp and DNA G?+?C content of 55.5%. Genomic annotation showed that, Bordetella sp. HZ20 may have chitin degradation related enzymes, heparin-sulfate lyase-like protein and enzymes related to the synthase and utilization of polyhydroxyalkanoate for carbon utilization, nitrate and nitrite reductase, glutamate dehydrogenase, glutamate synthase and glutamine synthetase for nitrogen cycle, polyphosphate kinases (pkk1 and pkk2), the high-affinity phosphate-specific transport (Pst) system and the low-affinity inorganic phosphate transporter (pitA) for phosphorus cycle, cysteine synthase and type III acyl coenzyme A transferase (dddD) for sulfur cycle. These features indicated the metabolic patterns of Bordetella sp. HZ20 in C, N, P and S cycles. In addition, the predicted Pst system and cysteine synthase were also related to biofilm formation which showed the potential pathogenicity of Bordetella sp. HZ20 to the cells of animals or plants. This study provides evidences about the metabolic patterns of Bordetella sp. HZ20 and broadens our understandings about ecological roles of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment.

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July 7, 2019  |  

Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization.

Water kefir is a traditional fermented beverage made from sucrose, water, kefir granules, dried or fresh fruits. In our water kefir granules, Lactobacillus (L.) hordei is one of the predominant lactic acid bacteria (LAB) species of this presumed symbiotic consortium. It faces abundant sucrose versus limitation of amino- and fatty acids in an acidic environment. Sequencing of the genome of L. hordei TMW 1.1822 revealed one chromosome plus three plasmids. The size of the chromosome was 2.42?Mbp with a GC content of 35% GC and 2461 predicted coding sequences. Furthermore, we identified 1474 proteins upon growth on water kefir medium. Metabolic prediction revealed all enzymes required for the glycolytic Embden-Meyerhof (EMP) and phosphoketolase (PKP) pathways. Genes encoding all enzymes involved in citrate, pyruvate and mannitol metabolism are present. Moreover, it was confirmed that L. hordei is prototrophic for 11 amino acids and auxotrophic for 6 amino acids when combining putative biosynthesis pathways for amino acids with physiological characterization. Still, for glycine, serine and methionine no sure auxotype could be determined. The OppABCDF peptide transport system is complete, and 13 genes encoding peptidases are present. The arginine deiminase system, was predicted to be complete except for carbamate kinase, thus enabling neutralization reactions via ammonium formation but no additional energy generation. Taken together our findings enable prediction of the L. hordei lifestyle in water kefir: Abundant sucrose is consumed directly via parallel EMP and PK pathways and is also extracellularly converted to dextran and fructose by a glucansucrase, leaving fructose as additional carbon source. Essential amino acids (in the form of peptides) and citrate are acquired from fruits. In the lack of FabB unsaturated fatty acids are synthesized by predicted alternative enzymes. Formation of acetoin and diacetyl as well as arginine conversion reactions enable acidification limitation. Other members of the water kefir consortium (yeasts, acetic acid bacteria) likely facilitate or support growth of L. hordei by delivering gluconate, mannitol, amino- and fatty acids and vitamins. Copyright © 2018 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

Draft genome sequence of the xanthocidin-producing strain Streptomyces sp. AcE210, isolated from a root nodule of Alnus glutinosa (L.).

Streptomyces sp. strain AcE210 exhibited antibacterial activity toward Gram-positive microorganisms and turned out to be a rare producer of the special- ized metabolite xanthocidin. The 10.6-Mb draft genome sequence gives insight into the complete specialized metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster of xanthocidin.

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July 7, 2019  |  

Genome analysis of Rhodococcus Sp. DSSKP-R-001: A highly effective ß-estradiol-degrading bacterium.

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4?Mbp with G?+?C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.

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July 7, 2019  |  

Complete genome sequence of the endophytic bacterium Chryseobacterium indologenes PgBE177, isolated from Panax quinquefolius.

Chryseobacterium indologenes PgBE177, isolated from the root tissue of a 4-year-old Panax quinquefolius plant, showed antagonistic activity against Pseu- domonas syringae pv. tomato DC3000, a bacterial pathogen. Here, we report the whole-genome sequence of C. indologenes PgBE177. The bacterium contains bacteri- ocin gene clusters and has the potential to stimulate plant growth.

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July 7, 2019  |  

Complete genome sequence of lanthionine-producing Lactobacillus brevis strain 100D8, generated by PacBio sequencing.

Lactobacillus brevis strain 100D8 was isolated from rye silage and showed rapid acidification ability in vitro and antifungal activity against mycotoxin- producing fungi. We report here the complete genome sequence of L. brevis strain 100D8, which has a circular chromosome (2,351,988 bp, 2,304 coding sequences [CDSs]) and three plasmids (45,061 bp, 57 CDSs; 40,740 bp, 40 CDSs; and 39,943 bp, 57 CDSs).

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July 7, 2019  |  

Genome analysis of Vallitalea guaymasensis strain L81 isolated from a deep-sea hydrothermal vent system.

Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.

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