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Sunday, October 25, 2020

Movie: The new biology part IV – food & conclusion

Part IV of The New Biology documentary. This documentary film features the wave of cutting-edge technologies that now provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself. The potential impact for humanity is immense: from fighting complex diseases such as cancer, enabling proactive surveillance of virulent pathogens, and increasing food crop production.

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Sunday, October 25, 2020

PAG PacBio Workshop: Using PacBio reads and pbjelly software to improve genomes – a cost-effective approach to finishing

Kim Worley from Baylor’s Human Genome Sequencing Center describes the improvement of the sooty mangabey primate genome. Sooty mangabey is a model organism for HIV research, since this particular primate can be infected with the immunodeficiency virus and never develop any symptoms. Worley and her team used PacBio long reads in conjunction with their own assembly tool, PBJelly, closing 64% and improving another 19% of the gaps.

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Sunday, October 25, 2020

AGBT Virtual Poster: Mind the gap – upgrading reference genomes with Pacific Biosciences RS long read sequencing technology

Adam English, lead bioinformatics programmer at Baylor College of Medicine, discusses challenges with resolving gaps in high-quality draft genome assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. For more facile assembly and automated finishing of draft genomes, he presents an automated approach to finishing using long reads from the PacBio System. The tool PBJelly automates the finishing process using long sequence reads in a reference-guided assembly process. Using PBJelly and SMRT Sequencing, they upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version…

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Sunday, October 25, 2020

PAG PacBio Workshop: Sequencing the Potentilla micrantha genome to study the evolution of fruiting in strawberry

Judson Ward, principal scientists at Driscoll’s Strawberries in California, introduces a genome assembly for Potentilla micrantha, which is closely related to strawberry but lacks fleshy ‘fruits’ or berries. Comparative genomics between P. micrantha and strawberry will yield significant information regarding the genetic mechanisms controlling fruit development. Using SMRT Sequencing Driscoll’s sequenced the 240 Mb P. micaranthagenome and produced a draft genome assembly, spanning the majority of the predicted sequence length. A comparison of sequence data produced using the Illumina HiSeq2000 and the PacBio RS platform demonstrated that PacBio sequencing produced a significantly longer N50 contig size and permitted a more complete genome…

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Sunday, October 25, 2020

PAG PacBio Workshop: Resolving the complexity of genomic and epigenomic variations in arabidopsis

Chongyuan Luo from the Salk Institute for Biological Studies describes sequencing three strains of Arabidopsis thaliana using PacBio technology. The goal: uncover structural variants that have been missed by short-read and other sequencers. Luo notes that PacBio sequencing provides highly accurate SNP detection and also extends the mappability of reads beyond what is possible with short-read data, producing better and more accurate assemblies.

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Sunday, October 25, 2020

PAG PacBio Workshop: De novo assembly of a complex panicoid grass genome using ultra-long PacBio reads with P6-C4 chemistry

Robert VanBuren of the Danforth Plant Science Center and winner of the 2014 SMRT Grant Program presents a de novo assembly of the Oro grass genome (Oropetium thomaeum). The reference genome will aid scientist studying drought tolerance in common crop species, especially cereals, though comparative genomics to understand potential key genetic underpinnings for this “resurrection” trait. Initial comparative results to Brachypodium and maize are presented, as well as secondary analysis to identify key metabolic traits.

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Sunday, October 25, 2020

ASHG PacBio Workshop: Resolving complexity of the human genome

Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discusses his use of the PacBio system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a number of rapidly evolving hot spots in the human genome that are associated with disease. These regions are quite long and have extremely repetitive DNA sequence, making them difficult to elucidate with short-read sequencing and very expensive to interrogate with Sanger sequencing. Eichler’s goal is to fill in the missing regions of the human genome reference, many of which contain segmental duplications.

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Sunday, October 25, 2020

AGBT Virtual Poster: Observing heterozygotic DNA methylation patterns in diploid genomes using kinetics data from the PacBio RS

Yuta Suzuki from the University of Tokyo presents his AGBT poster on heterozygotic DNA methylation patterns. He used kinetic data from SMRT Sequencing to generate epigenetic information on samples ranging from human to medaka fish and was able to analyze haplotype-specific methylation data. He also shows that long reads are better able to capture data about CpG islands than short-read sequences.

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Sunday, October 25, 2020

PAG Conference: Sequencing and assembly of the rice variety N22 (aus group) – A new reference genome to study comparative, evolutionary and functional genomics of rice

David Kudrna, Rod Wing, and the Arizona Genomics Institute (AGI) plan to fully sequence and annotate the genomes and transcriptomes of 3-4 accessions from each of the estimated 9-15 subpopulation of rice. These subpopulation-specific references will be used to map resequencing data of 3,000 individuals for variation discovery, GWAS, and genomic selection studies to address important traits such as biotic and abiotic stress tolerances, yield, and grain quality. Here Dr. Kudrna presents the first high-quality genome sequence of the rice variety Nagina22. AGI produced and assembled 65-fold coverage of SMRT Sequencing data, resulting in an assembly of 373 Mb with…

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Sunday, October 25, 2020

PAG Conference: Wild rice genome sequences explain the evolution and domestication of Japonica and Indica rice

Robert Henry, Professor of Innovation in Agriculture and Director of the Queensland Alliance for Agriculture and Food Innovation at the University of Queensland, Australia, discusses how whole genome analysis of Australian wild rice is being used to better understand rice domestication, with the goal of making a diverse genetic resource available for increased rice food security worldwide. The wild “A genome” species represent an effective gene pool for rice. SMRT Sequencing and assembly of two taxon of wild Australian rice has allowed analysis of the relationships with this group. Domesticated rice (Oryza sativa ssp. japonica) nuclear genome shows close relationship…

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Sunday, October 25, 2020

PAG Conference: An extreme metabolism: Iso-Seq analysis of the ruby-throated hummingbird transcriptome

Winston Timp from Johns Hopkins University studies the metabolism of hummingbirds, which sustain the highest metabolic rates among all vertebrates. Notably, hummingbirds can switch rapidly between a fuel of lipids to newly ingested sugars. This remarkable metabolism is supported by enzymes which operate at the extreme limit of catalytic efficiency. Understanding the molecular basis of enzymatic action will provide a foundation enabling rational engineering of metabolic circuits in other systems. To do this, Dr. Timp and his team generated a de novo transcriptome of the hummingbird liver using the Iso-Seq method. Characterization of the resulting protein coding sequences provides clues…

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