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Genome Research Studies on Genomic Adaptation in Peaches, SARS-CoV-2 Diversity, More

A team from China, Spain, and the US shares a map of genomic variation in peaches, profiling variants and selective sweeps that seem to influence adaptations to a range of locations and climates. Using genome sequencing and re-sequencing data for 263 peach landraces or related wild plants, the researchers looked for signs of natural selection and environmental adaptation in peaches grown in mild or more extreme environments, identifying more than 2,700 environmental variable-related loci and almost 2,100 selective sweeps with apparent ties to local climate, altitude, or other environmental factors. "Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding," they write.

Investigators at Rice University, Baylor College of Medicine, and other centers in the US and Spain consider SARS-CoV-2 sequence diversity and its potential consequences for molecular diagnostic strategies. By bringing together more than 6,900 SARS-CoV-2 consensus genomes and 129 RNA sequence sets, the team searched for single nucleotide variants and small insertions and deletions arising within and between infected hosts, including variants that turned up in parts of the SARS-CoV-2 targeted by PCR tests and amplicon sequencing strategies. "Altogether," the authors say, "our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of [intrahost single nucleotide variants] for tracking the transmission of SARS-CoV-2."

Finally, a Cleveland Clinic-led team reports on findings from a single-cell transcriptomic analysis of microglia and astrocyte brain cells in Alzheimer's disease. Reasoning that network analyses centered on disease-related microglia and astrocytes might unearth previously unappreciated treatment targets, the researchers analyzed single-cell RNA sequence and single-nucleus RNA-seq data on post-mortem superior frontal gyrus and/or entorhinal cortex brain samples from individuals with or without Alzheimer's, along with hippocampus samples from mouse models of the neurodegenerative disease. Together with available case-control data, their network analysis highlighted pathways shared by disease-related microglia and astrocytes, along with compounds that may contribute to protection against Alzheimer's pathophysiology.

The Scan

J&J Booster Support

A US Food and Drug Administration advisory panel has voted to support a booster dose of Johnson & Johnson's SARS-CoV-2 vaccine, according to the Los Angeles Times.

To Keep the Cases Moving

The president of the UK Royal College of Pathologists tells the Financial Times that more investment is needed to tackle a backlog of cases.

NAS Expels Archaeologist

Science reports Luis Jaime Castillo Butters' expulsion is the first of an international member from the US National Academy of Sciences.

PLOS Papers on Angelman Syndrome-Like Cases, Salmonella Paratyphi A, SARS-CoV-2 in Brazil

In PLOS this week: exome sequencing analysis of Angelman syndrome-like cases, genetic epidemiology of Salmonella Paratyphi A, and more.