The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing using a full-length transcript approach become clearer.
Interested to learn about pangenomes? Explore this guide to learn how they provide a more complete picture of the core genes of a given species and how that can provide better biological understanding.
At DuPont Pioneer, DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in commercial crops such as maize, soybean, sorghum, sunflower, alfalfa, canola, wheat, rice, and others. They cannot afford to wait the years it has historically taken for high-quality reference genomes to be produced. Nor can they rely on a single reference to represent the genetic diversity in its germplasm.
Single Molecule, Real-Time (SMRT) Sequencing uses the natural process of DNA replication to sequence long fragments of native DNA. As such, starting with high-quality, high molecular weight (HMW) genomic DNA (gDNA) will result in better sequencing performance across difficult to sequence regions of the genome. To obtain the highest quality, long DNA it is important to start with sample types compatible with HMW DNA extraction methods. This technical note is intended to give general guidance on sample collection, preparation, and storage across a range of commonly encountered sample types used for SMRT Sequencing whole genome projects. It is important to…
Dr. Olga Vinnere Pettersson, Uppsala Genome Center (Uppsala University), presents best practices for qualifying genomic DNA from a variety of sources to be suitable for Single Molecule, Real-Time Sequencing. Factors that affect single molecule sequencing and recommendations for extracting high-quality genomic DNA will be described. (requires file download to view)
Hélène Berges, managing director of the Plant Genomic Center at the Institut National de la Recherche Agronomique (INRA) in Toulouse, France, discusses how obtaining accurate and reliable sequence data is still challenging when targeting specific genomic regions. These issues are even more noticeable for complex plant genomes. To overcome these issues, Dr. Berges and her team have developed a strategy to reduce the genome complexity by using the large insert BAC libraries combined with next-generation sequencing technologies. She compares different technologies to sequence pools of BAC clones from several species (maize, wheat, strawberry, barley, sugarcane, and sunflower) known to be…
Valerie Schneider of the National Center for Biotechnology Information discuss how the Genome Reference Consortium (GRC) is bringing more ethnic diversity to the latest human reference assembly (GRCh38) by adding patches and alternate loci scaffolds. Scientists working with population graphs are among the early adopters of these new alternate loci scaffolds. She also discusses work underway at the McDonnell Genome Institute at Washington University to generate a set of high-quality, de novo whole genomes from a wide variety of populations. The new ethnic genomes “are also intended to stand on their own as complements to the reference so users can…
In this podcast, Gibbs shares his perspective on the complementary roles genomics and genetics plays in driving our understanding of human biology. Richard says that the Human genome project was actually a departure from had been typical in the field of human genetics. He notes, “there really was this departure between human genetics and genomics for a decade and a half or more, really because of the demands of doing the genome project there was too much to do to stop and think about some of these more fundamental problems in genetics.” Gibbs observes that we have now entered a…
In this podcast Sarah Tishkoff discusses what led her to study African genetics, and why she believes there is a need for more diversity in our genomic databases, with a particular emphasis on structural variation.
This tutorial provides an overview of the PacBio Demultiplex Barcodes analysis application in SMRT Link, followed by de novo assembly of the demultiplexed samples using HGAP4 for the Multiplexed Microbial Assembly analysis application. This tutorial covers features of SMRT Link v5.1.0.
In this presentation Fritz Sedlazeck describes his latest work to obtain comprehensive genomes leveraging long-read sequencing and linked reads.
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.
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.
In this PacBio User Group Meeting presentation, Jonas Korlach and Roberto Lleras share the latest updates to the structural variation application and analysis tools.
In this PacBio User Group Meeting presentation, Tim Smith of the USDA’s Agricultural Research Service describes efforts to generate reference-grade genome assemblies for various bovine species and analyze them to understand factors such as how selective breeding has affected certain breeds. Genome assemblies he presents span cattle, water buffalo, and gaur. Smith shows data for each assembly, noting that as data production shifted to the Sequel System, long-read PacBio data became even better at producing highly contiguous assemblies.