Scientists are utilizing long-read PacBio sequencing to provide uniquely comprehensive views of complex plant and animal genomes. These efforts are uncovering novel biological mechanisms, enabling progress in crop development, and much more. To date, scientists have published over 1000 papers with Single Molecule, Real-Time (SMRT) Sequencing, many covering breakthroughs in the plant and animal sciences. In this case study, we look at examples in model organisms Drosophila and C. elegans and non-model organisms coffee, Oropeitum, danshen, and sugarbeet, where SMRT Sequencing has contributed to a more accurate understanding of biology. These efforts underscore the broad applicability of long-read sequencing in…
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.
The Sequel System, powered by Single Molecule, Real Time (SMRT) Technology, delivers long reads, high consensus accuracy, uniform coverage and epigenetic characterization.
To bring personalized medicine to all patients, cancer researchers need more reliable and comprehensive views of somatic variants of all sizes that drive cancer biology.
The Sequel II System, powered by Single Molecule, Real Time (SMRT) Technology, delivers highly accurate long reads for a comprehensive view of genomes, transcriptomes and epigenomes.
Learn how Single Molecule, Real-Time (SMRT) Sequencing and the Sequel II System and will accelerate your research by delivering highly accurate long reads to provide the most comprehensive view of genomes, transcriptomes and epigenomes.
Richard Kuo’s research at the Roslin Institute exploring non-coding RNA of avian species requires high accuracy. SMRT Sequencing on the PacBio Sequel II System and the Iso-Seq method have given him confidence in annotations across entire genomes and transcriptomes.
The Earlham Institute was one of the first labs to adopt the PacBio Sequel II System. Karim Gharbi, Head of Genomics Pipelines, discusses how SMRT Sequencing and HiFi reads have increased throughput and reduced costs for genome, transcriptome, and metagenomics projects.
Jeremy Schmutz discusses the increased throughput and reduced project costs using HiFi reads from the PacBio Sequel II System in his work sequencing, assembling, and analyzing a variety of genomes at the HudsonAlpha Institute for Biotechnology.
Highly accurate long reads, known as HiFi reads, are a new tool in scientists’ sequencing toolbox. Hear PacBio users share how they are using HiFi reads to explore the genomes, transcriptomes, metagenomes and the benefits HiFi reads provide for their addressing critical life science questions.
Accurate sequencing data is key for University of Florida scientist Ana Conesa. She is using PacBio HiFi reads from the Sequel II System to identity alternative isoforms and determine the functional impact of different isoform expression in her transcriptome research.
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…
Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline and penicillin-resistance genes on plasmid pWBG753 (~30 kb). WA-5 and pWBG753 appeared only briefly in WA, however, fusidic-acid-resistance plasmids related to pWBG753 were also present in the first European CA-MRSA at the time. Here we characterized a 72-kb conjugative plasmid pWBG731 present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a…