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Monday, August 31, 2020

Colombian SMRT Grant Winners Hope HiFi Sequencing Will Help Save Critically Endangered Toads

The ‘happy toad’ (Atelopus laetissimus) comes in a variety of colors. Meet the ‘happy toad’ Atelopus laetissimus, a harlequin toad found on the slopes of the Sierra Nevada de Santa Marta mountains of Colombia. This toad is brightly colored, with an almost comical slow walk and lots of other unique attributes. But the reason it is delighting scientists and conservationists is its ability to adapt and survive while its relatives are on the brink of extinction. The 2020 Plant and Animal Sciences SMRT Grant Program co-sponsored by PacBio and the DNA Sequencing Center at Brigham Young University will enable a…

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Monday, March 16, 2020

A Menagerie of New Genomes Released by International Ensembl Project

The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP)   Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project.  The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data.    Thirteen of the new assemblies have…

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Friday, September 20, 2019

Sequencing at the Extremes: Low DNA Input Workflow Enables Study of Tiny Ice Worm with Giant Genome

It was the coolest critter Erin Bernberg (@ErinBernberg) had ever worked with – quite literally.  The senior scientist at the University of Delaware Sequencing and Genotyping Center, a PacBio certified service provider, received a shipment of tiny, live ice worms from Washington State University and immediately faced several challenges. How would she get them out of their ice cubes? How would she isolate DNA from the delicate, dark pigmented creatures? And would she be able to extract enough DNA to sequence?  Thanks to the new PacBio low DNA input protocol, the answer to the last question was yes. In fact,…

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Friday, August 30, 2019

From Parakeet to Potoo, International Consortium Releases 100 High-Quality Vertebrate Genomes

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…

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Thursday, July 11, 2019

Sanger Scientists Test Sequel II System for Tree-of-Life Projects

Today we offer the final post in our blog miniseries about early access users’ experiences with the new Sequel II System. Shane McCarthy, a scientist at the University of Cambridge who was able to use the new sequencing system at the Wellcome Sanger Institute, gave a presentation on his experience generating data for tree-of-life sequencing projects. McCarthy participates in several of these large-scale projects, such as the Vertebrate Genomes Project, the Sanger 25 Genomes Project, and the Darwin Tree of Life Project. For all of them, the goal is to produce high-quality, phased, chromosome-level assemblies with minimal gaps. Through Sanger’s…

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Monday, June 10, 2019

Catching up with Carola and the ‘Solar-Powered’ Sea Slug

Two years ago, Carola Greve and colleagues at the Zoological Research Museum Alexander Koenig in Bonn, Germany, were seeking to #SeqtheSlug as part of the 2017 Plant and Animal SMRT Grant competition, and the popular project was a close runner-up. Greve didn’t give up on her quest to sequence the ‘solar-powered’ sea slug. We caught up with her recently at the SMRT Leiden Scientific Symposium, where her update on the sea slug project earned her a Best Poster award.    Why the sea slug?   Although Mollusca represents the second largest animal phylum with around 85,000 extant species, only 23 mollusc genomes…

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Thursday, May 30, 2019

Unraveling Malaria Mysteries with Long-Read Sequencing

Plasmodium falciparum Malaria is a complicated killer, and efforts to develop effective vaccines have been hindered by gaps in our understanding of both the parasite that causes the infection, Plasmodium falciparum, and its transmitter, the mosquito. Like many virulent parasites, P. falciparum has evaded close genetic scrutiny due to its complex and changing composition. Its 23 Mb haploid genome is extremely AT rich (~80%) and contains stretches of highly repetitive sequences, especially in telomeric and subtelomeric regions. To make matters more complicated, it expands its genetic diversity during mitosis via homologous recombination, leading to the acquisition of new variants of…

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Tuesday, January 8, 2019

SMRT Grant Winner: Uncovering the Metabolic Secrets of Hibernation

What has four legs, lots of fat and fur, and will possibly help uncover novel mechanisms to combat diabetes? Photo courtesy of WSU Bear Center Grizzly bears! If humans were to undergo regular, extended cycles of weight gain and inactivity, they’d likely end up with obesity, muscle atrophy, or type 2 diabetes. But grizzly bears experience no ill effects from their annual fat gain and sedentary hibernation. Somehow they are able to switch their insulin resistance between seasons, and researchers at Washington State University are hoping to figure out how, with possible therapeutic value for humans. We’re proud to support…

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Wednesday, August 9, 2017

Iso-Seq Analysis Reveals Differential Expression in Male and Female Abalones

Photo by Toby Hudson Earlier this year, scientists from Korea reported results from a transcriptome study of Pacific abalone. In this paper, the team used SMRT Sequencing to demonstrate that alternative splicing and gene expression have sex-specific signatures in these organisms. “Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai” comes from lead authors Mi Ae Kim and Jae-Sung Rhee, senior author Young Chang Sohn, and collaborators. They focused on abalone, a marine gastropod, because of its importance to Korean aquaculture: the species they studied is estimated to represent about 10,000 metric tons of…

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Monday, August 7, 2017

SMRT Sequencing Shines at ISAG: First Sequel System Bovine Genome Presented

If you weren’t at the 36th International Society for Animal Genetics Conference in Dublin, you missed more than a chance to drink Guinness and practice an Irish brogue. The PacBio team had a great time at ISAG, learning about the latest in animal science and updating attendees on the advantages of SMRT Sequencing for generating high-quality genome assemblies and annotations. The conference drew more than 750 scientists from around the world, and we were truly impressed by the quality of research they presented in talks and posters. Long-read PacBio sequencing is already making a difference for scientists in this community,…

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