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Thursday, November 12, 2020

Case Study: Mining complex metagenomes for protein discovery with long-read sequencing

The bacteria living on and within us can impact health, disease, and even our behavior, but there is still much to learn about the breadth of their effects. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and the public alike. Scientists at Second Genome are hoping to apply these insights to improve human health, leveraging their bioinformatics expertise to mine bacterial communities for potential therapeutics. Recently they teamed up with scientists at PacBio to explore how long-read sequencing might supplement their short-read-based pipeline for gene discovery, using an environmental sample as a test…

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Thursday, November 12, 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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Sunday, October 25, 2020

AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria

In this AGBT 2017 poster, the University of Helsinki’s Petri Auevinen reports on efforts to understand bacteria that grow on, and subsequently spoil, food. This analysis monitored DNA modifications and transcriptomic changes in three species of lactic acid bacteria. Scientists discovered that the organisms’ metabolic profiles change substantially when grown together compared to those cultured individually, and are now studying how Cas protein activity changes under these conditions too.

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Sunday, October 25, 2020

AGBT Presentation: Feed the World – Developing genomic resources for insects as food

In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.

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Sunday, October 25, 2020

Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing

Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…

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Sunday, October 25, 2020

PAG Conference: Endless forms: Genomes from the Darwin Tree of Life Project

Mark Blaxter, project lead of the Sanger Institute’s Darwin Tree of Life, shared an update of the ambitious effort to sequence all 60,000 species believed to be on the British Isles over the next 12 years in this presentation at the PAG 2020 Conference. The Sanger team has already generated data for 94 species, including 44 new moth and butterfly (Lepidoptera) PacBio assemblies, which Blaxter describes in this presentation.

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Sunday, October 25, 2020

Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information

In this webinar, Kristin Mars, Sequencing Specialist, PacBio, presents an introduction to PacBio’s technology and its applications followed by a panel discussion among sequencing experts. The panel discussion addresses such things as what long reads are and how are they useful, what differentiates PacBio long-read sequencing from other technologies, and the applications PacBio offers and how they can benefit scientific research.

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Sunday, October 25, 2020

Webinar: Bioinformatics lunch & learn – Command line analysis with Cromwell in PacBio SMRT Link v8.0

In this webinar, Matthew Seetin a PacBio Bioinformatics Field Application Scientist, presents one of the biggest engineering changes in SMRT Link v8.0 – the migration from pbsmrtpipe to Cromwell. With this change, a number of new features particularly suited for pipeline engineers and production facilities are now available for use. Learn from our BFX FAS to see how you can best take advantage of this new, versatile and scalable platform. Topics covered include: What is Cromwell and how does it help you? New features including data caching and job restart, and guidance for building custom workflows combining PacBio & 3rd…

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Tuesday, April 21, 2020

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of…

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Tuesday, April 21, 2020

Complete Genome Sequence of a Chlorobenzene Degrader, Pandoraea pnomenusa MCB032.

Chlorobenzenes are ubiquitously distributed, highly persistent, and toxic environmental contaminants. Pandoraea pnomenusa MCB032 was isolated as a new dominant chlorobenzene-utilizing strain from a functionally stable bioreactor during the treatment of chlorobenzenes when strain Burkholderia sp. JS150 disappeared. In study, we report the complete genome sequence of strain MCB032 which consists of a circular chromosome and three plasmids, which are?~?6 Mb in length with 5450 open reading frames-12 encoding rRNAs and 77 encoding tRNAs. We further identified 17 putative genes encoding the enzymes involved in the methyl-accepting chemotaxis proteins in sensing chemical gradients during chemotaxis. The annotated complete genome sequence of this…

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Tuesday, April 21, 2020

De novo assembly of a wild pear (Pyrus betuleafolia) genome.

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism,…

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Tuesday, April 21, 2020

Evolution of a 72-kb cointegrant, conjugative multiresistance plasmid from early community-associated methicillin-resistant Staphylococcus aureus isolates.

Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline and penicillin-resistance genes on plasmid pWBG753 (~30 kb). WA-5 and pWBG753 appeared only briefly in WA, however, fusidic-acid-resistance plasmids related to pWBG753 were also present in the first European CA-MRSA at the time. Here we characterized a 72-kb conjugative plasmid pWBG731 present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a…

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Tuesday, April 21, 2020

Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal.

We tested extended-spectrum ß-lactamase producing bacteria from wild gulls (Larus spp.) sampled in 2009 for the presence of mcr-1. We report the detection of mcr-1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin-resistant bacteria in European wildlife.Published 2019. This article is a U.S. Government work and is in the public domain in the USA.

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