Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

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Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

10.21203/rs.2.24663/v1 ◽

2020 ◽

Author(s):

Xueping LI ◽

Jianhong Li ◽

Yonghong Qi ◽

Yonggang Liu ◽

Minquan Li

Keyword(s):

Molecular Mechanisms ◽

Gc Content ◽

Whole Genome Sequence ◽

Effective Control ◽

Sequence Length ◽

Comparative Genomic ◽

Whole Genome ◽

Illumina Hiseq ◽

Fusarium Equiseti ◽

Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

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Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Bioscience Reports ◽

10.1042/bsr20192252 ◽

2020 ◽

Vol 40 (2) ◽

Author(s):

Sheng-yong Xu ◽

Na Song ◽

Shi-jun Xiao ◽

Tian-xiang Gao

Keyword(s):

Microsatellite Markers ◽

Gc Content ◽

The Philippines ◽

Whole Genome Sequence ◽

Northwestern Pacific ◽

Whole Genome ◽

Survey Analysis ◽

Genome Survey ◽

Sebastiscus Marmoratus ◽

Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

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Whole-Genome Sequence of a Unique Elioraea Species Strain Isolated from a Yellowstone National Park Hot Spring

Microbiology Resource Announcements ◽

10.1128/mra.00907-19 ◽

2019 ◽

Vol 8 (44) ◽

Author(s):

Sydney Robertson ◽

Robert F. Ramaley ◽

Terry Meyer ◽

John A. Kyndt

Keyword(s):

New Species ◽

Genome Sequence ◽

Yellowstone National Park ◽

National Park ◽

Photosynthetic Bacteria ◽

Hot Spring ◽

Whole Genome Sequence ◽

Whole Genome ◽

Anoxygenic Photosynthetic Bacteria

The genus Elioraea has only one species characterized microbiologically and two genomes sequenced. We have sequenced the genome of a unique Elioraea strain isolated from Yellowstone National Park and found it to be a distinct new species. Elioraea is suggested to be a member of the aerobic anoxygenic photosynthetic bacteria.

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The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab246 ◽

2021 ◽

Author(s):

Endang Rahmat ◽

Inkyu Park ◽

Youngmin Kang

Keyword(s):

Gc Content ◽

Whole Genome Sequence ◽

Diospyros Kaki ◽

Whole Genome ◽

The Novel ◽

Data Set ◽

Draft Assembly ◽

Future Possibility ◽

Complete Set ◽

New Yeast

Abstract The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high quality whole-genome assembly of M. persimmonesis produced by PacBio RSII sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

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Whole-Genome Sequence of Fish-Pathogenic Enterococcus faecalis Strain BFFF11

Microbiology Resource Announcements ◽

10.1128/mra.01447-19 ◽

2020 ◽

Vol 9 (7) ◽

Cited By ~ 1

Author(s):

Tasmina Akter ◽

M. Mahbubur Rahman ◽

Alfred Chin Yen Tay ◽

Rakib Ehsan ◽

M. Tofazzal Islam

Keyword(s):

Enterococcus Faecalis ◽

Genome Sequence ◽

Gc Content ◽

Fish Farm ◽

Pathogenic Bacterium ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type

A fish-pathogenic bacterium, Enterococcus faecalis strain BFFF11, was isolated from a tilapia suffering from streptococcosis in a fish farm in the Gazipur district of Bangladesh. The whole genome of this strain, BFFF11, was 3,067,042 bp, with a GC content of 37.4%.

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Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora

Genome Announcements ◽

10.1128/genomea.01285-17 ◽

2017 ◽

Vol 5 (46) ◽

Cited By ~ 1

Author(s):

Pushpa Lata ◽

Subramaniam S. Govindarajan ◽

Feng Qi ◽

Jian-Liang Li ◽

Santosh K. Maurya ◽

...

Keyword(s):

Genome Sequence ◽

De Novo ◽

Gc Content ◽

Whole Genome Sequence ◽

Whole Genome ◽

Coding Sequences ◽

Central Florida ◽

Magnolia Grandiflora ◽

Extended Spectrum

ABSTRACT Pantoea americana strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from Magnolia grandiflora in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.

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Amphiplicatus metriothermophilus gen. nov., sp. nov., a thermotolerant alphaproteobacterium isolated from a hot spring

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.062471-0 ◽

2014 ◽

Vol 64 (Pt_8) ◽

pp. 2805-2811 ◽

Cited By ~ 15

Author(s):

Zhang Zhen-Li ◽

Zhang Xin-Qi ◽

Wu Nan ◽

Zhang Wen-Wu ◽

Zhu Xu-Fen ◽

...

Keyword(s):

Hot Spring ◽

Sequence Similarity ◽

Rrna Gene ◽

Strictly Aerobic ◽

Aerobic Bacterium ◽

Respiratory Quinone ◽

Content Type ◽

North West ◽

Link Type ◽

Major Respiratory Quinone

A thermotolerant, Gram-strain-negative, non-spore-forming and strictly aerobic bacterium, designated GU51T, was isolated from Guhai hot spring in Jimsar county, Xinjiang province, north-west China. Each cell of strain GU51T consisted of an oval body and two symmetrical long (3–6 µm) prosthecae. The strain moved by polar flagellum. Oxidase and catalase were produced. Strain GU51T grew within the ranges of 37–65 °C (optimum 48–50 °C), 0.5–7.5 % (w/v) NaCl (optimum 2–3 %) and pH 6.0–9.0 (optimum pH 7.5). The major respiratory quinone detected was ubiquinone 10 (U-10) and the genomic DNA G+C content was 66.7±0.4 mol%. Major fatty acids (>5 %) were C16 : 0, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipids consisted of diphosphatidylglycerol, five glycolipids, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis showed the closest relatives of strain GU51T were members of the genus Parvularcula with 92.3 % 16S rRNA gene sequence similarity. On the basis of this polyphasic taxonomic characterization, it is suggested that strain GU51T represents a novel species of a new genus in the family ‘ Parvularculaceae ’, for which the name Amphiplicatus metriothermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is GU51T ( = CGMCC 1.12710T = JCM 19779T).

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Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

10.21203/rs.3.rs-1176760/v1 ◽

2021 ◽

Author(s):

Tofazzal Islam ◽

Nadia Afroz ◽

ChuShin Koh ◽

M. Nazmul Haque ◽

Md. Jillur Rahman ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Genome Sequence ◽

De Novo ◽

Agricultural Research ◽

Gc Content ◽

Whole Genome Sequence ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

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Whole Genome Sequence Analysis of Brucella melitensis Phylogeny and Virulence Factors

Microbiology Research ◽

10.3390/microbiolres12030050 ◽

2021 ◽

Vol 12 (3) ◽

pp. 698-710

Author(s):

Peter Rabinowitz ◽

Bar Zilberman ◽

Yair Motro ◽

Marilyn C. Roberts ◽

Alex Greninger ◽

...

Keyword(s):

Virulence Factors ◽

Pathogenic Bacteria ◽

Virulence Genes ◽

Brucella Melitensis ◽

Geographic Region ◽

Clinical Severity ◽

Whole Genome Sequence ◽

Whole Genome ◽

Pan Genome ◽

Wide Range

Brucellosis has a wide range of clinical severity in humans that remains poorly understood. Whole genome sequencing (WGS) analysis may be able to detect variation in virulence genes. We used Brucella melitensis sequences in the NCBI Sequence Read Archive (SRA) database to assemble 248 whole genomes, and additionally, assembled 27 B. melitensis genomes from samples of human patients in Southern Israel. We searched the 275 assembled genomes for the 43 B. melitensis virulence genes in the Virulence Factors of Pathogenic Bacteria Database (VFDB) and 10 other published putative virulence genes. We explored pan-genome variation across the genomes and in a pilot analysis, explored single nucleotide polymorphism (SNP) variation among the ten putative virulence genes. More than 99% of the genomes had sequences for all Brucella melitensis virulence genes included in the VFDB. The 10 other virulence genes of interest were present across all the genomes, but three of these genes had SNP variation associated with particular Brucella melitensis genotypes. SNP variation was also seen within the Israeli genomes obtained from a small geographic region. While the Brucella genome is highly conserved, this novel and large whole genome study of Brucella demonstrates the ability of whole genome and pan-genome analysis to screen multiple genomes and identify SNP variation in both known and novel virulence genes that could be associated with differential disease virulence. Further development of whole genome techniques and linkage with clinical metadata on disease outcomes could shed light on whether such variation in the Brucella genome plays a role in pathogenesis.

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Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum ‘Bacteroidetes’ and the proposal of Schleiferiaceae fam. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.028852-0 ◽

2011 ◽

Vol 61 (10) ◽

pp. 2450-2455 ◽

Cited By ~ 28

Author(s):

Luciana Albuquerque ◽

Fred A. Rainey ◽

M. Fernanda Nobre ◽

Milton S. da Costa

Keyword(s):

Hot Spring ◽

Thermophilic Bacterium ◽

Rrna Gene ◽

Strictly Aerobic ◽

The Novel ◽

Respiratory Quinone ◽

Optimum Growth Temperature ◽

Physiological And Biochemical Characteristics ◽

Gene Sequence Analysis ◽

Major Respiratory Quinone

A bacterial isolate, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.5, was recovered from a hot spring in the Furnas area of the Island of São Miguel in the Azores. The novel isolate is orange-pigmented, forms non-motile, rod-shaped cells that stain Gram-negative, is strictly aerobic, oxidase-positive and catalase-negative. The major fatty acids of strain TU-20T are 16 : 1ω6c, 17 : 0 iso 3-OH and 15 : 0 iso. Menaquinone 6 is the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain TU-20T ( = DSM 21410T = LMG 24594T) for which we propose the name Schleiferia thermophila gen nov., sp. nov. We also propose the family Schleiferiaceae fam. nov. to accommodate this new genus.

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