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Auto Tag: Hierarchical Genome Assembly

July 7, 2019

Characterization and genome analysis of a phthalate esters-degrading strain Sphingobium yanoikuyae SHJ.

A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as Sphingobium yanoikuyae SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101.4 hours, respectively. The optimum degradation rate of DBP by SHJ was observed at 30°C and weak alkaline (pH 7.5). Genome sequence of the strain SHJ showed a circular chromosome and additional two circular plasmids with whole genome size of 5,669,383 bp and GC content of 64.23%. Functional annotation of SHJ revealed a total of 5,402 genes, with 5,183 protein-encoding genes, 143 pseudogenes, and 76 noncoding RNA genes. Based on genome annotation, 44 genes were identified to be involved in PAEs hydrolysis potentially. Besides, a region with size of about 6.9 kb comprised of seven ORFs, which is located on the smaller plasmid pSES189, was presumed to be responsible for the biodegradation of phthalate. These results provide insights into the genetic basis of DBP biodegradation in this strain.

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July 7, 2019

Complete genome sequence of Bacillus sp. HBCD-sjtu, an efficient HBCD-degrading bacterium.

Environmental pollution caused by the release of industrial chemicals is currently one of the most important environmental harms. Manufacturing chemicals can be biodegraded, and valuable intermediates can be used as pharmacophores in drug targeting and have several other useful purposes. Hexabromocyclododecane (HBCD), a non-aromatic brominated flame retardant, is a toxic compound that consists of a cycloaliphatic ring of 12 carbon atoms to which six bromine atoms are attached. It is formed by bromination of cis-trans-trans-1,5,9-cyclododecatriene, but its use is now restricted in several countries, because it is an environmental pollutant. Little is known about whether bacteria can degrade HBCD. A bacterial strain that degrades HBCD was recently isolated using enrichment culture techniques. Based on morphological, biochemical and phylogenetic analysis this isolate was categorized as Bacillus cereus and named strain HBCD-sjtu. Maximum growth and HBCD-degrading activity were observed when this strain was grown at 30 °C, pH 7.0 and 200 RPM in mineral salt medium containing 0.5 mm HBCD. The genome of strain HBCD-sjtu, which consists of only one circular chromosome, was sequenced. This whole genome sequence will be crucial for illuminating the molecular mechanisms of HBCD degradation.

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July 7, 2019

Genomic characterization of methylotrophy of Oharaeibacter diazotrophicus strain SM30T.

Oharaeibacter diazotrophicus strain SM30T, isolated from rice rhizosphere, is an aerobic, facultative lanthanide (Ln3+)-utilizing methylotroph and diazotroph that belongs to the Methylocystaceae family. In this research, the complete genome sequence of strain SM30T was determined, and its methylotrophy modules were characterized. The genome consists of one chromosome and two plasmids, comprising a total of 5,004,097 bp, and the GC content was 71.6 mol%. A total of 4497 CDSs, 67 tRNA, and 9 rRNA were encoded. Typical alpha-proteobacterial methylotrophy genes were found: pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) (mxaF and xoxF1-4), methylotrophy regulatory proteins (mxbDM and mxcQE), PQQ synthesis, H4F pathway, H4MPT pathway, formate oxidation, serine cycle, and ethylmalonyl-CoA pathway. SDS-PAGE and subsequent LC-MS analysis, and qPCR analysis revealed that MxaF and XoxF1 were the dominant MDH in the absence or presence of lanthanum (La3+), respectively. The growth of MDH gene-deletion mutants on alcohols and qPCR results indicated that mxaF and xoxF1 are also involved in ethanol and propanol oxidation, xoxF2 participates in methanol oxidation in the presence of La3+, while xoxF3 was associated with methanol and ethanol oxidation in the absence of La3+, implying that XoxF3 is a calcium (Ca2+)-binding XoxF. Four Ln3+ such as La3+, cerium (Ce3+), praseodymium (Pr3+), and neodymium (Nd3+) served as cofactors for XoxF1 by supporting ?mxaF growth on methanol. Some heavier lanthanides inhibited growth of SM30 on methanol. This study contributes to the understanding of the function of various XoxF-type MDHs and their roles in methylotrophs. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Clostridium kluyveri JZZ applied in Chinese strong-flavor liquor production.

Chinese strong-flavor liquor (CSFL), accounting for more than 70% of both Chinese liquor production and sales, was produced by complex fermentation with pit mud. Clostridium kluyveri, an important species coexisted with other microorganisms in fermentation pit mud (FPM), could produce caproic acid, which was subsequently converted to the key CSFL flavor substance ethyl caproate. In this study, we present the first complete genome sequence of C. kluyveri isolated from FPM. Clostridium kluyveri JZZ contains one circular chromosome and one circular plasmid with length of 4,454,353 and 58,581 bp, respectively. 4158 protein-coding genes were predicted and 2792 genes could be assigned with COG categories. It possesses the pathway predicted for biosynthesis of caproic acid with ethanol. Compared to other two C. kluyveri genomes, JZZ consists of longer chromosome with multiple gene rearrangements, and contains more genes involved in defense mechanisms, as well as DNA replication, recombination, and repair. Meanwhile, JZZ contains fewer genes involved in secondary metabolites biosynthesis, transport, and catabolism, including genes encoding Polyketide Synthases/Non-ribosomal Peptide Synthetases. Additionally, JZZ possesses 960 unique genes with relatively aggregating in defense mechanisms and transcription. Our study will be available for further research about C. kluyveri isolated from FPM, and will also facilitate the genetic engineering to increase biofuel production and improve fragrance flavor of CSFL.

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July 7, 2019

Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities.

Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, ß-glucosidase, and ß-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.

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July 7, 2019

BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species.

Bacterial meningitis is a life-threatening infection that remains a public health concern. Bacterial meningitis is commonly caused by the following species: Neisseria meningitidis, Streptococcus pneumoniae, Listeria monocytogenes, Haemophilus influenzae and Escherichia coli. Here, we describe BMScan (Bacterial Meningitis Scan), a whole-genome analysis tool for the species identification of bacterial meningitis-causing and closely-related pathogens, an essential step for case management and disease surveillance. BMScan relies on a reference collection that contains genomes for 17 focal species to scan against to identify a given species. We established this reference collection by supplementing publically available genomes from RefSeq with genomes from the isolate collections of the Centers for Disease Control Bacterial Meningitis Laboratory and the Minnesota Department of Health Public Health Laboratory, and then filtered them down to a representative set of genomes which capture the diversity for each species. Using this reference collection, we evaluated two genomic comparison algorithms, Mash and Average Nucleotide Identity, for their ability to accurately and rapidly identify our focal species.We found that the results of Mash were strongly correlated with the results of ANI for species identification, while providing a significant reduction in run-time. This drastic difference in run-time enabled the rapid scanning of large reference genome collections, which, when combined with species-specific threshold values, facilitated the development of BMScan. Using a validation set of 15,503 genomes of our species of interest, BMScan accurately identified 99.97% of the species within 16 min 47 s.Identification of the bacterial meningitis pathogenic species is a critical step for case confirmation and further strain characterization. BMScan employs species-specific thresholds for previously-validated, genome-wide similarity statistics compiled from a curated reference genome collection to rapidly and accurately identify the species of uncharacterized bacterial meningitis pathogens and closely related pathogens. BMScan will facilitate the transition in public health laboratories from traditional phenotypic detection methods to whole genome sequencing based methods for species identification.

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July 7, 2019

Draft genome sequence of Deinococcus koreensis SJW1-2T, a gamma radiation-resistant bacterium isolated from river water.

Deinococcus koreensis SJW1-2Twas isolated from river water and was observed to be highly resistant to gamma radiation. In this study, we report a draft genome sequence which revealed that SJW1-2Tpossesses genes involved in nucleo- tide excision repair. The primary genomic information will aid in elucidating the DNA repair mechanism during ionizing radiation.

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July 7, 2019

Complete genome sequence of Rhizobium sp. strain 11515TR, isolated from tomato rhizosphere in the Philippines.

Rhizobium sp. strain 11515TR was isolated from the rhizosphere of to- mato in Laguna, Philippines. The 7.07-Mb complete genome comprises three repli- cons, one chromosome, and two plasmids, with a G?C content of 59.4% and 6,720 protein-coding genes. The genome encodes gene clusters supporting rhizosphere processes, plant symbiosis, and secondary bioactive metabolites.

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July 7, 2019

Near- complete genome sequences of Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.

Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines, are active against Bacillus subtilis subsp. subtilis KCTC 3135T. The near-complete genome sequences reported here represent a possible source of ribosomally synthesized, posttranslationally mod- ified peptides, such as lantipeptides, bacteriocins, linaridin, and a lasso peptide.

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July 7, 2019

DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection

Genes prot6E and sefA are used as targets for detection of Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella ser. Enteritidis). We investigated variations in these genes across 64 different Salmonella ser. Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. Isolates were sequenced using Illumina technologies. Based on the resulting phylogenetic tree, our isolates clustered in 2 distinct clades. All isolates carried prot6E and sefA. Comparative genomic analyses indicated two non-synonymous mutations (Glycine ? Serine and Valine ? Isoleucine) of prot6E in 11 isolates (9 egg samples, 2 chicken samples). However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. We identified one non-synonymous mutation (Valine ? Glutamic Acid) in the sefA gene in 4 isolates from egg samples. The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. Enteritidis isolates revealed prot6E gene was located on the tail of the plasmid. Based on the biosynthesis of amino acids – Reference pathway in the KEGG pathway Database, the transition of amino acid from sefA Var. was a transversion from essential amino acid to non-essential amino acid, while that of prot6E Var.1 happened between the conditionally non-essential amino acid, and prot6E Var. 2 occurred between essential amino acids. Properties of these mutated amino acids, such as side-chain polarity or charge, may contribute to the occurrence and rate of mutations in prot6E and sefA. These insights can be used to improve detection methods for Salmonella ser. Enteritidis.

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July 7, 2019

Complete genome sequence of an efficient vitamin D3-hydroxylating bacterium, Pseudonocardia autotrophica NBRC 12743.

Pseudonocardia autotrophica NBRC 12743 contains a cytochrome P450 vitamin D3hydroxylase, and it is used as a biocatalyst for the commercial produc- tion of hydroxyvitamin D3, a valuable compound for medication. Here, we report the complete genome sequence of P. autotrophica NBRC 12743, which could be useful for improving the productivity of hydroxyvitamin D3.

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July 7, 2019

Near-complete genome sequence of Ralstonia solanacearum T523, a phylotype I tomato phytopathogen isolated from the Philippines.

Ralstonia solanacearum strain T523 is the major phytopathogen causing tomato bacterial wilt in the Philippines. Here, we report the complete chromosome and draft megaplasmid genomes with predicted gene inventories supporting rhizo- sphere processes, extensive plant virulence effectors, and the production of bioac- tive signaling metabolites, such as ralstonin, micacocidin, and homoserine lactone.

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