scholarly journals Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction

2022 ◽  
Vol 10 (1) ◽  
pp. 142
Author(s):  
Hye Won Kim ◽  
Na Kyung Kim ◽  
Alex P. R. Phillips ◽  
David A. Parker ◽  
Ping Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
De Novo ◽  
Marker Gene ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Sequencing Data

Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.

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

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.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

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

2017 ◽  
Vol 5 (46) ◽  
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.

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

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.

scholarly journals Draft Genome Sequence of Methanothermobacter thermautotrophicus WHS, a Thermophilic Hydrogenotrophic Methanogen from Washburn Hot Springs in Yellowstone National Park, USA

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Luke J. McKay ◽  
Korinne B. Klingelsmith ◽  
Adam M. Deutschbauer ◽  
William P. Inskeep ◽  
Matthew W. Fields
Keyword(s):  
Carbon Dioxide ◽  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Hydrogenotrophic Methanogen ◽  
Methanothermobacter Thermautotrophicus

ABSTRACT A thermophilic methanogen was enriched in coculture from Washburn Hot Springs (Yellowstone National Park, USA), grown on carbon dioxide and hydrogen, and subsequently sequenced. The reconstructed 1.65-Mb genome sequence for Methanothermobacter thermautotrophicus WHS contributes to our understanding of hydrogenotrophic, CO2-reducing methanogenesis in geothermal ecosystems.

scholarly journals Sequencing, De Novo Assembly, and Annotation of the Complete Genome of a New Thraustochytrid Species, Strain CCAP_4062/3

2018 ◽  
Vol 6 (11) ◽  
Author(s):  
Khawla Seddiki ◽  
François Godart ◽  
Riccardo Aiese Cigliano ◽  
Walter Sanseverino ◽  
Mohamed Barakat ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
De Novo Assembly ◽  
Complete Genome ◽  
De Novo ◽  
Gc Content ◽  
Marine Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences

ABSTRACT Thraustochytrids are ecologically and biotechnologically relevant marine species. We report here the de novo assembly and annotation of the whole-genome sequence of a new thraustochytrid strain, CCAP_4062/3. The genome size was estimated at 38.7 Mb with 11,853 predicted coding sequences, and the GC content was scored at 57%.

scholarly journals Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park

2013 ◽  
Vol 79 (9) ◽  
pp. 2932-2943 ◽  
Author(s):  
Christine Romano ◽  
Seth D'Imperio ◽  
Tanja Woyke ◽  
Konstantinos Mavromatis ◽  
Roger Lasken ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Marker Gene ◽  
Genomic Analysis ◽  
Mercury Resistance ◽  
Nitrate Respiration ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Outflow Channel

ABSTRACTWe describe the complete genome sequences of four closely relatedHydrogenobaculumsp. isolates (≥99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different fromHydrogenobaculumsp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum ofHydrogenobaculumgenotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

scholarly journals Improved whole genome sequence of Phytophthora capsici generated by long-read sequencing

2021 ◽  
Author(s):  
Jinxia Shi ◽  
Wenwu Ye ◽  
Dongfang Ma ◽  
Junliang Yin ◽  
Zhichao Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
Vegetable Crops ◽  
Long Read

The soil-borne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.

scholarly journals Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense

2005 ◽  
Vol 55 (6) ◽  
pp. 2263-2268 ◽  
Author(s):  
S. Nakagawa ◽  
Z. Shtaih ◽  
A. Banta ◽  
T. J. Beveridge ◽  
Y. Sako ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Gene Sequence ◽  
Hot Springs ◽  
Carbon Sources ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Optimum Ph ◽  
Sulfur Oxidizing ◽  
The 16S Rrna Gene

A novel thermophilic, sulfur-oxidizing Gram-negative bacterium, designated strain SS-5T, was isolated from the Calcite Hot Springs in Yellowstone National Park, USA. The cells were motile rods (1·2–2·8 μm long and 0·6–0·8 μm wide). The new isolate was a facultative heterotroph capable of using elemental sulfur or thiosulfate as an electron donor and O2 (1–18 %; optimum 6 %, v/v) as an electron acceptor. Hydrogen did not support growth. The isolate grew autotrophically with CO2. In addition, strain SS-5T utilized various organic carbon sources such as yeast extract, tryptone, sugars, amino acids and organic acids. Growth was observed between 55 and 78 °C (optimum 70 °C; 3·5 h doubling time), pH 6·0 and 8·0 (optimum pH 7·5), and 0 and 0·6 % (w/v) NaCl (optimum 0 %). The G+C content of the genomic DNA was 32 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate was a member of the genus Sulfurihydrogenibium. On the basis of the physiological and molecular characteristics of the new isolate, we propose the name Sulfurihydrogenibium yellowstonense sp. nov. with SS-5T (=JCM 12773T=OCM 840T) as the type strain. In addition, emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense are proposed.

scholarly journals Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Joshua A. OHair ◽  
Hui Li ◽  
Santosh Thapa ◽  
Matthew Scholz ◽  
Suping Zhou
Keyword(s):  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Bacillus Altitudinis

ABSTRACT Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU.

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