Korean service provider DNA Link has established strong expertise with the PacBio sequencing platform in response to high global demand for the technology.
From crop improvement to breeding healthier livestock to modeling human disease, scientists are using PacBio Sequencing to advance understanding of plant and animal genomes. In this article, we look at four examples of plant and animal genome references improved or made possible with SMRT Sequencing, including an early example of transcriptome sequencing of a chicken for improved annotation. These examples highlight insights gained with SMRT Sequencing that are missed with short-read data, such as complex regions or novel genes.
Scientists from WashU, Macrogen, and Mount Sinai are using long-read sequencing with single-molecule, next-generation genome mapping to create gold-quality de novo assemblies of human genomes. Unbiased de novo assembled genomes also highlight the substantial amount of structural variation unique to individuals and populations, which cannot be accessed by short-read technologies that use a reference-based re-sequencing approach.
At the University of Arizona, a leading genomics research facility benefits from decades of BAC- based sequencing expertise, original studies of crop genomes, and a unique emphasis on high molecular weight DNA.
Scientists at the USDA and Cold Spring Harbor Laboratory know that better breeding of maize to feed a growing population will depend on an accurate reference assembly. They tackled the previously intractable crop with a combination of PacBio Sequencing and BioNano Genomics® genome maps, leading to the first-ever high-quality reference assembly.
Single Molecule, Real-Time (SMRT) Sequencing directly detects DNA modifications by measuring variation in the polymerase kinetics of DNA base incorporation during sequencing. With high throughput, long reads, and the sensitivity to detect epigenetic modification without amplification or chemical conversions, the PacBio Systems offer scalable solutions for assessing DNA modifications in bacterial and eukaryotic genomes.
Scientists in Brazil paired PacBio long-read sequencing with Dovetail Genomics chromatin proximity ligation to generate a highly contiguous genome assembly for the cashew tree. With this resource, they are on their way to improving breeding programs to protect the plant from disease and boost yield.
At the National Center for Genome Resources in Santa Fe, New Mexico, scientists run a world- renowned sequencing service facility that’s heavy on long reads and bioinformatics expertise. It also supports a wide range of microbial, plant, and animal projects.
It is now easier and more affordable than ever to do a genome project with PacBio Single Molecule, Real-Time (SMRT) Sequencing—the gold standard for generating contiguous, highly accurate reference genomes. Assembly is no longer a challenge with the wealth of bioinformatics tools developed and optimized for SMRT Sequencing data, enabling you to generate high-quality genome assemblies on any budget.
Explore how highly accurate long-read sequencing enabled sequencing the large and highly complex California redwood genome.
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.
In this LabRoots webinar, Jonas Korlach the CSO of PacBio provides an introduction to PacBio HiFi sequence reads, which are both long (up to 25 kb currently) and accurate (>99%) at the individual single-molecule sequence read level andhave allowed for advances in de novo genome assemblies. Korlach reviews the characteristics of HiFi read data obtained with the Sequel II System, followed by examples of high-quality genome assemblies for human, plant and animal genomes including the different aspects of evaluating genome assemblies (contiguity, accuracy, completeness and allelic phasing) and illustrates their high quality by examples of resolving centromeres, telomeres, segmental duplications…
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and…
Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513?Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated…
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated at the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light-HL versus low light -LL) enabled…