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Friday, February 5, 2021

Podcast: The 9 billion people problem – Rod Wing on plant genomics

By 2050, there will be 9 billion people on the planet. What will they eat? This is the question that led Rod Wing, Director of the Arizona Genomics Institute, into the field of plant genomics. What has been accomplished so far in the mission to come up with some super green crops? And how does Rod see anti-GMO sentiment and the recent trend toward gluten free diets factoring in? After answering these questions, he dives into a discussion on which sequencing instruments he has used for plant work. Unsurprisingly, Rod prefers the PacBio long reads even though the cost is…

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Friday, February 5, 2021

PAG 2016 Highlights: Customer interviews

See what PacBio users had to say about SMRT Sequencing at the Plant and Animal Genome (PAG) Conference in San Diego. This brief video captures highlights from posters, presentations, and the exhibit hall. See how SMRT Sequencing benefits plant and animal scientists in their genomic investigations. [Engligh, some Mandarin]

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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: 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

Tutorial: HGAP4 de novo assembly application [SMRT Link v5.0.0]

This tutorial provides an overview of the Hierarchical Genome Assembly Process (HGAP4) de novo assembly analysis application. HGAP4 generates accurate de novo assemblies using only PacBio data. HGAP4 is suitable for assembling a wide range of genome sizes and complexity. HGAP4 now includes some support for diploid-aware assembly. This tutorial covers features of SMRT Link v5.0.0.

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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

Webinar: Understanding, curating, and analyzing your diploid genome assembly

The goal of this session is to help users complete their PacBio genome assembly and generate the best resource for their research. Kingan begins with a brief review of the diploid assembly process used by FALCON and FALCON-Unzip, highlighting the enhanced phasing of the Unzip module, and concluding with recommendations for genome polishing. Next, she explores how heterozygosity can influence the assembly process and how read coverage depth along the assembly can reveal important characteristics of assembly structure. Kingan then recommends approaches, including specific tools, that can be used to quality filter and curate the assembly, including annotation-, coverage-, and…

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Friday, February 5, 2021

Webinar: An introduction to PacBio’s long-read sequencing & how it has been used to make important scientific discoveries

In this Webinar, we will give an introduction to Pacific Biosciences’ single molecule, real-time (SMRT) sequencing. After showing how the system works, we will discuss the main features of the technology with an emphasis on the difference between systematic error and random error and how SMRT sequencing produces better consensus accuracy than other systems. Following this, we will discuss several ground-breaking discoveries in medical science that were made possible by the longs reads and high accuracy of SMRT Sequencing.

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Friday, February 5, 2021

Webinar: SMRT Sequencing applications in plant and animal sciences: an overview

In this webinar, Emily Hatas of PacBio shares information about the applications and benefits of SMRT Sequencing in plant and animal biology, agriculture, and industrial research fields. This session contains an overview of several applications: whole-genome sequencing for de novo assembly; transcript isoform sequencing (Iso-Seq) method for genome annotation; targeted sequencing solutions; and metagenomics and microbial interactions. High-level workflows and best practices are discussed for key applications.

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Friday, February 5, 2021

PAG Conference: Long-read sequencing reveals complex genomic architecture in independent carnivorous plant lineages

In this PAG 2018 presentation, Tanya Renner of Pennsylvania State University shares research using PacBio SMRT Sequencing to understand the genomes and transcriptomes of carnivorous plants. She describes the humped bladderwort, Utricularia gibba, as having an extreme genome due to its small size (100 Mbp) despite containing numerous tandem gene duplications and having undergone two whole genome duplications. Renner shares ongoing research into two Drosera species, commonly known as sundews, which through whole genome sequencing are illuminating carnivorous plant genome structural evolution including the transition from monocentric to holocentric chromosomes.

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Friday, February 5, 2021

Educational Video: Step 1 – from sample to sequencing data for de novo assembly

This video provides an overview of the techniques and steps of preparing samples, DNA, and libraries for PacBio Single Molecule, Real-Time (SMRT) Sequencing to be used in de novo assembly projects. In this video, a PacBio scientist covers how to assess DNA quantity and purity, size-selection of DNA libraries, and provides and introduction to SMRT Sequencing, including the benefits of long-reads when generating high-quality genome assemblies.

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Friday, February 5, 2021

Educational Video: Step 2 – de novo assembly of a genome

This video provides an overview of the techniques and steps of generating a de novo genome assembly with long-read sequencing data generated using PacBio Single Molecule, Real-Time (SMRT) Sequencing. In this video, a PacBio scientist covers the benefits of long reads when generating high-quality genome assemblies, the latest tools for creating assemblies, including HGAP, FALCON and FALCON-Unzip, how to polish and assess the quality of a genome assembly, and how to submit an assembly to NCBI.

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Friday, February 5, 2021

Webinar: Smoking out structural variants in the cannabis genome

In this webinar, Sarah Kingan, Staff Scientist, PacBio, and Kevin McKernan, Founder and Chief Science Officer, Medicinal Genomics, describe their work assembling the most comprehensive and complete cannabis genome of a Type II (THCA and CBDA producing) plant. They also share the latest advances in cannabis genomics, including how PacBio long-read sequencing enables high-quality genomics research in plants, annotation of the cannabis reference genome using full-length transcript sequencing, and new insights into cannabinoid synthesis across different types of cannabis plants.

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Friday, November 19, 2021

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