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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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Wednesday, August 26, 2020

Pangenome of Soybean Generated to Capture Genomic Diversity

A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…

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Wednesday, August 19, 2020

A TAL Tale: PacBio Sequencing Helps Unravel Mechanisms of Plant Infection

How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment.  For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing.  Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…

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Monday, August 17, 2020

In Alabama, Scientists Use HiFi Data to Uncover the Genetic Cause of Rare Neurodevelopmental Disorders

UPDATE: This paper has now been published in HGG Advances from Cell Press   In an exciting new preprint, scientists from the HudsonAlpha Institute for Biotechnology and the University of Alabama at Birmingham describe the use of PacBio highly accurate long-read sequencing to identify pathogenic variants responsible for previously undiagnosable, rare neurodevelopmental disorders. Lead author Susan Hiatt (@suzieqhiatt), senior author Gregory Cooper, and collaborators conducted genomic analyses of several family trios in an attempt to find causal genetic variants that had been missed with earlier studies. “Large fractions of [neurodevelopmental disorders] cannot be attributed to currently detectable genetic variation,” they…

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Tuesday, August 11, 2020

In precisionFDA Challenge, PacBio HiFi Reads Outperform Both Short Reads and Noisy Long Reads

In the recent precisionFDA Truth Challenge V2, which evaluated methods for variant calling in human genomes, approaches that use PacBio HiFi reads delivered the highest precision and recall in all categories: genome-wide, specifically in difficult-to-map regions, and in the major histocompatibility complex (Figure 1).  The challenge had 64 total entries: 17 using PacBio HiFi reads, 24 using Illumina reads, 3 using Oxford Nanopore reads, and 20 using multiple technologies. Twenty-five of the 26 overall most accurate callsets used PacBio HiFi reads (12 PacBio-only, 13 multi-technology), including all of the top 12 (3 PacBio-only, 9 multi-technology). A submission from Google DeepVariant…

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Thursday, August 6, 2020

“Murder Hornet” Genome Rapidly Assembled by USDA as Part of Real-Time Invasive Species Response Initiative

With a nickname like “murder hornet,” it’s no wonder the two-inch long Asian giant hornet (Vespa mandarinia) has caused a stir amongst those terrified of insect invasions.  Various species of paper wasp (left) compared to the Asian giant hornet (right) Photo by Hanna Royals, USDA. The wasps — which are actually more dangerous to bees than humans — have made another recent appearance in Washington state, and Agricultural Research Service (ARS) scientists are hoping a new rapidly-generated genome sequence of one of the insects will help in their quest to quash an invasion. Released August 6, the first high-quality genome…

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Friday, December 3, 2021

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