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Friday, February 5, 2021

PAG PacBio Workshop: SMRT Sequencing for complete genomes

PacBio CSO Jonas Korlach kicks off the PAG 2017 SMRT Sequencing workshop with acknowledgement of the remarkable work scientists have done with long-read sequencing technology, culminating in more than 2,000 papers so far. Also: Sequel System data, new chemistry and software release, longer libraries, and more.

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Friday, February 5, 2021

ASHG Virtual Poster: Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads

PacBio bioinformatician Aaron Wenger presents this ASHG 2016 poster demonstrating human structural variation detection at varying coverage levels with SMRT Sequencing on the Sequel System. Results were compared to truth sets for well-characterized genomes. Results indicate that even low coverage of SMRT Sequencing makes it possible to detect hundreds of SVs that are missed in high-coverage short-read sequencing data.

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Friday, February 5, 2021

PAG PacBio Workshop: Introducing 5 new high-quality PacBio genome assemblies for rice to help solve the 10-billion people question

At PAG 2017, Rod Wing presented five new, high-quality rice genome assemblies developed with SMRT Sequencing, including one that has eight complete chromosomes including centromeres. He also offered an early look at data generated with the Sequel System for a new assembly underway. This work is done with the goal of developing rice varieties that will be better suited to feeding a rapidly growing global population.

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Friday, February 5, 2021

PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti

In this PAG 2017 presentation, Ben Matthews describes a new genome assembly for Aedes aegypti, the mosquito responsible for spreading Zika virus, yellow fever, and other infectious diseases. By using PacBio long-read sequencing, scientists produced an assembly that is much more complete and contiguous than a previous assembly; 7,500 transcripts map to the new contigs but not to the old assembly. The genome is important for designing guide RNAs for CRISPR, understanding resistance to mosquito repellants, and much more.

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Friday, February 5, 2021

PAG PacBio Workshop: Comparative analyses of next generation technologies for generating chromosome-level reference genome assemblies

At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing and scaffolding technologies. Analyses include gene content, error rate, chromosome metrics, and more. Plus: a long-read look at four genes associated with vocal learning.

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Friday, February 5, 2021

AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples

At AGBT 2017, Mike Schatz from Johns Hopkins University and Cold Spring Harbor Laboratory presented data from sequencing, assembling, and analyzing personalized, phased diploid genomes with either Illumina, 10x Genomics, and PacBio SMRT Sequencing. Compared to the short-read-based methods, PacBio data assembled in large, complete contigs and contained the broadest range of structural variants with the best resolution. Plus: unexpected translocation findings with SMRT Sequencing, validated in follow-up studies.

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Friday, February 5, 2021

Video: Get ready for super coffee strains. Scientists just sequenced the plant’s DNA

Genes are the future of coffee. Not nitro cold brewing or beans pooped out by civets, but genes. And coffee’s gene-fueled future just drew nearer, now that scientists have sequenced the genome of the Coffea arabica coffee plant—the species that makes up the vast majority of global production—and made the data public. That means the world is in for a coffee renaissance, as breeders use the information to develop new plant varieties—think new flavors and better resistance to cold and disease. That means more coffee grown in more places, a big deal as global warming throws local climates into chaos.

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Friday, February 5, 2021

PAG PacBio Workshop: De novo sequencing of the koala genome

Rebecca Johnson, director of the Australian Museum Research Institute presents finding from de novo sequencing of the koala genome. Using PacBio sequencing the Koala Genome Consortium obtained an assembly with an N50 of 11.5 Mbp and have undertaken functional genomic analysis highlighting the unique genes associated with lactation and immune function of koalas. Johnson goes on to describe efforts to obtain a chromosome level assembly and current work using ‘super scaffolding’ to compare shared synteny across diverse lineages to generate chromosome scaffold maps.

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Friday, February 5, 2021

PAG Conference: Domestication: through the canines of a dingo

In this PAG 2018 presentation, Bill Ballard of University of New South Wales, presents research into the origins and potential domestication of the Australian dingo, winner of the 2017 SMRT Grant Program. Ballard used PacBio long-read whole genome sequencing to sequence and assemble the dingo genome. Ongoing work focuses on identifying common and unique genomic regions with a domestic dog genome to better understand shared ancestry and ultimately to aid in dingo conservation efforts.

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Tuesday, April 21, 2020

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads.

The sequence and assembly of human genomes using long-read sequencing technologies has revolutionized our understanding of structural variation and genome organization. We compared the accuracy, continuity, and gene annotation of genome assemblies generated from either high-fidelity (HiFi) or continuous long-read (CLR) datasets from the same complete hydatidiform mole human genome. We find that the HiFi sequence data assemble an additional 10% of duplicated regions and more accurately represent the structure of tandem repeats, as validated with orthogonal analyses. As a result, an additional 5 Mbp of pericentromeric sequences are recovered in the HiFi assembly, resulting in a 2.5-fold increase in…

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Tuesday, April 21, 2020

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens…

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Tuesday, April 21, 2020

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.

Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important. Here we present a high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate. In two artificial communities of known composition, our method recovered the full complement of full-length 16S sequence variants from expected community members…

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Tuesday, April 21, 2020

SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection.

Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a…

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Tuesday, April 21, 2020

Recipients receiving better HLA-matched hematopoietic cell transplantation grafts, uncovered by a novel HLA typing method, have superior survival: A retrospective study

HLA matching at an allelic-level resolution for volunteer unrelated donor (VUD) hematopoietic cell transplanta- tion (HCT) results in improved survival and fewer post-transplant complications. Limitations in typing technolo- gies used for the hyperpolymorphic HLA genes have meant that variations outside of the antigen recognition domain (ARD) have not been previously characterized in HCT. Our aim was to explore the extent of diversity out- side of the ARD and determine the impact of this diversity on transplant outcome. Eight hundred ninety-one VUD-HCT donors and their recipients transplanted for a hematologic malignancy in the United Kingdom were ret- rospectively HLA typed at…

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PacBio Grants Equity Incentive Award to New Employee

Friday, November 19, 2021

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