Nearly gapless, reference-quality chromosome-level assemblies — in less than a day? Yes, it’s possible, thanks to the high accuracy and low computational needs of PacBio HiFi reads. Kevin Fengler, computational genomics lead at Corteva Agriscience, welcomed watchers to the brave new world of the pangenome during the recent webinar, “Beyond a Single Reference Genome – The Advantages of Sequencing Multiple Individuals.” We are now living in an era where you can generate a reference genome assembly that’s specific for each application or trait of interest, Fengler said. Graphic alignment of dozens of genomes in a pangenome collection allows researchers to…
It’s been more than a year since we introduced HiFi sequencing to generate highly accurate long reads. In that time, we’ve seen many PacBio users make HiFi sequencing their go-to setting because it’s simple, reliable, and cost-effective. For scientists who have yet to generate their own HiFi data, we thought it might be helpful to publish a few data sets for exploration and analysis. In a new preprint, we have released HiFi data sets for five samples: mouse, frog, maize, strawberry, and a mock metagenome community. We like to think there’s a data set for everyone here, whatever your research…
California redwoods: Not only are they giants in height and age (up to 379 feet high, 29 feet round, and thousands of years old), but the famous towering trees are also derived from a massive 27 Gb genome. Seeking a sequencing challenge for the Sequel II System, we picked the California redwood, or Sequoia sempervirens as it’s known to scientists. There also happened to be several fine specimens at nearby Stanford University. A small crew of PacBio scientists — Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), and Michelle Vierra (@the_mvierra) — headed to campus to acquire samples equipped with ice, scissors,…
Assembling the genomes of the tetraploid rose has been challenging, but PacBio HiFi reads are helping Dutch researchers overcome the hurdles. The genome of the rose is almost as complicated as its connotations when given as a gift on Valentine’s Day or other special occasions. Although relatively small in size, at 400-750 Mb, with seven chromosomes, the cells of roses have multiple sets of chromosomes beyond the basic set. And these can vary widely between the commercial varieties. Some are diploids, with two homologous copies of each chromosome (like humans, with one from the mother and one from the father),…
The team from AgriGenome and MedGenome helped assemble the genome and transcriptome of the lethal Indian Cobra (Naja naja) using PacBio long-read sequencing Snake milking, horse blood harvesting and brewing — antivenom production is still more medieval art than modern science. But a new high-quality snake genome may finally pull it into the 21st century. As recently reported in Nature Genetics, a team of scientists led by Somasekar Seshagiri, a former staff scientist at Genentech and now president of the nonprofit SciGenom Research Foundation (@SGRF_Science) in India, assembled the genome and transcriptome of the lethal Indian Cobra (Naja naja) using…
100 high-quality assemblies released by the Vertebrate Genome Project include the genome of the critically endangered vaquita porpoise UPDATE (October 2020): A preprint of the vaquita reference genome has been published. With her distinctive dark eyeshadow, grey lipstick-like markings and delicate disposition, she was a natural film star. And her life certainly provided enough drama for any Hollywood blockbuster, complete with high-speed boat chases in pursuit of black market “cocaine of the sea” cartels. Unfortunately, her ending was not a happy one. But efforts by an international consortium of conservation geneticists are making sure her legacy isn’t lost. The DNA…
Crucial assembly sites and mitosis mediators, centromeres are central to every cell, but missing from even the most complete genome assemblies. Until now. In a PLOS Biology paper, Amanda Larracuente and colleagues at the University of Rochester and Barbara G. Mellone of the University of Connecticut, described how they sequenced the repetitive regions of the fruit fly genome, including its centromeres, using SMRT Sequencing. Embedded in blocks of highly repetitive satellite DNA, centromeres have eluded efforts at assembly. Only recently, long-read single molecule sequencing technologies have made it possible to obtain assemblies of highly repetitive parts of multicellular genomes such…