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Wednesday, November 25, 2020

Better Apple Pies: HiFi Reads are a Perfect Recipe for High-Quality Apple Genome and Pangenome Assemblies 

Zhangjun Fei inspects a Mutsu apple at Indian Creek Farm in Ithaca, NY. Image credit: Boyce Thompson Institute Scientists at the Boyce Thompson Institute, Cornell University and the USDA Agricultural Research Service have reported significant progress in understanding the genomic features of domestic and wild apples. They used HiFi reads, highly accurate long reads, generated by the Sequel II System to build phased, diploid genome assemblies, as well as apple pangenomes to represent more of the remarkable genetic diversity in this lineage and better characterize its historic domestication.  The paper, published in Nature Genetics, comes from lead authors Xuepeng Sun (@XuepengBio), Chen Jiao, and Heidi Schwaninger; senior author Zhangjun Fei (@fei_lab), and collaborators.  We asked Fei about the highlights of…

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Tuesday, November 17, 2020

Scientists Pinpoint Pathogenic Inversion in Intellectual Disability Case Using HiFi Sequencing

Scientists at Yokohama City University Graduate School of Medicine and Osaka Women’s and Children’s Hospital have discovered a novel pathogenic variant associated with intellectual disability. They made the discovery using HiFi sequencing after previous short-read investigations failed to produce an answer. In the journal Genomics, the team reports the case of 12-year-old monozygotic twin girls who exhibited developmental delays, severely drooping eyelids, and seizures since the age of 5 months. Clinical symptoms matched Dravet syndrome, but no molecular evidence was available to confirm that diagnosis. Their case had previously been analyzed with short-read exome sequencing, but no pathogenic variants were…

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Tuesday, November 10, 2020

Secrets to Longevity Explored in de novo Genome of 115-Year-Old Woman

Hendrikje van Andel-Schipper, at age 108 A new publication from scientists in The Netherlands and Belgium offers tantalizing insights that may shed light on age-related neurodegenerative disorders. The team used SMRT Sequencing to produce a de novo diploid assembly of the genome of a Dutch woman named Hendrikje van Andel-Schipper, who died at the age of 115 with no signs of cognitive decline, and then performed a detailed analysis of variants detected. The data are publicly available to the scientific community. The paper, released in Translational Psychiatry, comes from lead author Jasper Linthorst and senior author Henne Holstege (@HolstegeHenne) at…

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