In this CSHL Biology of Genomes 2021 virtual workshop, Michelle Vierra from PacBio discusses examples of how advances in highly accurate long-read (HiFi) sequencing have enabled exciting developments in plant…
In this talk, Aaron Wenger from PacBio uses industry examples to describe how using highly accurate long-reads, or HiFi reads, provides the most comprehensive result, giving you greater than 99.9%…
In this video, Dave Miller from PacBio and Alvaro Hernandez PhD from the University of Illinois Urbana- Champaign discuss how to create Core Lab demand using PacBio highly accurate long-read,…
PacBio Sequencing and software enable the generation of highly accurate (>99.9%) long reads. HiFi reads are accurate, essential, affordable, and can be used across a range of applications, including detection…
Brett Hannigan, Computational Biology Project Leader at DNAnexus, demonstrates a fast, accurate, and cost-efficient solution for diploid-aware de novo genome assembly utilizing FALCON on the DNAnexus platform.
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…
In this PAG 2017 presentation, Ben Matthews describes a new genome assembly for Aedes aegypti, the mosquito responsible for spreading Zika virus, yellow fever, and other infectious diseases. By using…
Rebecca Johnson, director of the Australian Museum Research Institute presents finding from de novo sequencing of the koala genome. Using PacBio sequencing the Koala Genome Consortium obtained an assembly with…
At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing…
At AGBT 2017, the Broad Institute’s Daniel Neafsey reported a large collaborative effort to sequence the mosquito that carries Zika virus. The team is using long-read PacBio sequencing to produce…
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…
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…
In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the…
We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
Background Assemblies of diploid genomes are generally unphased, pseudo-haploid representations that do not correctly reconstruct the two parental haplotypes present in the individual sequenced. Instead, the assembly alternates between parental haplotypes and may contain duplications in regions where the parental haplotypes are sufficiently different. Trio binning is an approach to genome assembly that uses short reads from both parents to classify long reads from the offspring according to maternal or paternal haplotype origin, and is thus helped rather than impeded by heterozygosity. Using this approach, it is possible to derive two assemblies from an individual, accurately representing both parental contributions in their entirety with higher continuity and accuracy than is possible with other methods.Results We used trio binning to assemble reference genomes for two species from a single individual using an interspecies cross of yak (Bos grunniens) and cattle (Bos taurus). The high heterozygosity inherent to interspecies hybrids allowed us to confidently assign >99% of long reads from the F1 offspring to parental bins using unique k-mers from parental short reads. Both the maternal (yak) and paternal (cattle) assemblies contain over one third of the acrocentric chromosomes, including the two largest chromosomes, in single haplotigs.Conclusions These haplotigs are the first vertebrate chromosome arms to be assembled gap-free and fully phased, and the first time assemblies for two species have been created from a single individual. Both assemblies are the most continuous currently available for non-model vertebrates.MbmegabaseskbkilobasesMYAmillions of years agoMHCmajor histocompatibility complexSMRTsingle molecule real time
If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.