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Thursday, August 27, 2020

Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing

Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.

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Wednesday, October 23, 2019

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system.

Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies…

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Sunday, September 22, 2019

Mesoscale variability of the summer bloom over the northern Ross Sea shelf: A tale of two banks

Multi-year satellite records indicate an asymmetric spatial pattern in the summer bloom in the Northern Ross Sea, with the largest blooms over the shallows of Pennell Bank compared to Mawson Bank. In 2010–2011, high-resolution spatiotemporal in situ sampling focused on these two banks to better understand factors contributing to this pattern. Dissolved and particulate Fe profiles suggested similar surface water depletion of dissolved Fe on both banks. The surface sediments and velocity observations indicate a more energetic water column over Mawson Bank. Consequently, the surface mixed layer over Pennell Bank was more homogeneous and shallower. Over Mawson Bank we observed…

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Sunday, September 22, 2019

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture.

Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was assembled to draft-quality. Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56.12% GC), incertae sedis Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and incertae sedis Bacteroidetes strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome consists of a single circular chromosome…

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Friday, July 19, 2019

Complete genome sequence of Vibrio campbellii strain 20130629003S01 isolated from shrimp with acute hepatopancreatic necrosis disease.

Vibrio campbellii is widely distributed in the marine environment and is an important pathogen of aquatic organisms such as shrimp, fish, and mollusks. An isolate of V. campbellii carrying the pirAB(vp) gene, causing acute hepatopancreatic necrosis disease (AHPND), has been reported. There are no previous reports about the complete genome of V. campbellii causing AHPND (VCAHPND). To extend our understanding of the pathogenesis of VCAHPND at the genomic level, the genome of V. campbellii 20130629003S01 isolated from a shrimp with AHPND was sequenced and analysed.The complete genome sequence of V. campbellii 20130629003S01 was generated using the PacBio RSII platform with…

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Sunday, July 7, 2019

Draft genome sequence of Pseudoalteromonas luteoviolacea HI1, determined using Roche 454 and PacBio single-molecule real-time hybrid sequencing.

We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain HI1 using Roche 454 and PacBio single-molecule real-time hybrid-sequencing analysis. This strain is of biological importance since it has the capacity to induce the settlement and metamorphosis of the serpulid polychaete Hydroides elegans and the coral Pocillopora damicornis. Copyright © 2015 Asahina and Hadfield.

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Sunday, July 7, 2019

Genome sequence of Polycyclovorans algicola strain TG408, an obligate polycyclic aromatic hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton.

Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with marine eukaryotic phytoplankton and exhibits the ability to utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of 63.8%. Copyright © 2015 Gutierrez et al.

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Sunday, July 7, 2019

Genome sequence of Porticoccus hydrocarbonoclasticus strain MCTG13d, an obligate polycyclic aromatic hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton.

Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is associated with marine eukaryotic phytoplankton and that almost exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source of carbon and energy. Here, we present the genome sequence of this strain, which is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%. Copyright © 2015 Gutierrez et al.

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Sunday, July 7, 2019

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.

TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements…

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Sunday, July 7, 2019

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles…

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Sunday, July 7, 2019

First complete genome sequence of Marinilactibacillus piezotolerans strain 15R, a marine lactobacillus isolated from coal-bearing sediment 2.0 kilometers below the seafloor, determined by PacBio single-molecule real-time technology.

Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic lactobacillus isolated from deep marine subsurface sediment nearly 2 km below the seafloor in the northwestern Pacific. We report here the first whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908 bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences, with no identified plasmids. Copyright © 2017 Wei et al.

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Sunday, July 7, 2019

Complete genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment 2.4 kilometers below the seafloor.

Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment down to ~2.4 km below the ocean floor in the northwestern Pacific. The strain is a Gram-positive spore-forming bacterium, closely related to Bacillus subtilis within the phylum Firmicutes This is the first complete genome sequence of a Bacillus subtilis strain from the deep biosphere. The genome sequence will provide a valuable resource for comparative studies of microorganisms from the surface and subsurface environments. Copyright © 2017 Wei et al.

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Sunday, July 7, 2019

The complete genome sequence of Exiguobacterium arabatum W-01 reveals potential probiotic functions.

Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W-01, a gram-positive and orange-pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole-genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843.98 bp and a mean GC content of 48.11%, accounting for 89.27% of the genome. Among these ORFs, 2,884 (93.5%) genes were classified into Clusters of Orthologous…

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