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.
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.
The utility of new highly accurate long reads, or HiFi reads, was first demonstrated for calling all variant types in human genomes. It has since been shown that HiFi reads can be used to generate contiguous, complete, and accurate human genomes, even in repeat structures such as centromeres and telomeres. In this virtual workshop scientists from PacBio as well as Tina Graves-Lindsay from the McDonnell Genome Institute at Washington University share the many improvements we’ve made to HiFi sequencing in the past year, tools that take advantage of HiFi data for variant detection and assembly, and examples in numerous genomics…
In this presentation at PAG 2020, Bart Nijland of Genetwister Technologies explains how his team set out to make a haplotype-aware assembly of the highly complex tetraploid Rosa x hybrida L. genome in order to capture its full range of genetic variation. HiFi reads generated from PacBio’s Sequel II System have made it possible to parse out critical information from many of the plant’s parental genes.
Fritz Sedlazeck, a postdoc at Johns Hopkins University, describes his structural variant detection tool Sniffles in this poster from AGBT 2016. Included: examples of structural variants that could not be detected with other algorithms.
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…
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.
In a poster presented at AGBT 2017, Fritz Sedlazeck from Johns Hopkins University describes the comparison of genome assemblies produced using long-read PacBio sequencing and short-read sequencing with 10x Genomics scaffolding. An alignment reveals regions missed by the short-read assembly, including repeats, exons, and even whole genes.
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.
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.
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.
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…
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.
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.