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This Week in PLOS: Dec 14, 2015

In PLOS One, Spanish researchers describe the gene expression differences they detected in apricot plants with susceptibility or resistance to a pathogen called the Plum pox virus, which can cause a disease called sharka in temperate fruit plants. The team did RNA sequencing on leaf material from apricot cultivars before and after exposure to PPV. When they compared gene expression profiles in the so-called Rojo Pasión genotype, which resists PPV infection, and in a genotype called Z506-7 that's susceptible to it, the study's authors saw gene expression differences involving more than 2,000 genes. They also identified 124 SNPs that seemed to coincide with the resistant Rojo Pasión genotype.

A Baylor College of Medicine-led team looks at structural variation at a locus in and around the NPHP1 gene, which has been implicated in an autosomal recessive condition called nephronophthisis 1. As they report in PLOS Genetics, the researchers used a combination of optical mapping and array comparative genomic hybridization to uncover three apparent NPHP1 locus haplotypes that each appear to differ somewhat structurally. In a haploid human genome, they note, such variations show promise for protecting against the type of NPHP1 deletions previously discovered in many individuals with nephronophthisis 1. Through comparisons with other primate genomes, meanwhile, the study's authors found evidence for widespread rearrangement at the NPHP1 locus over the course of primate evolution, contributing to the newly identified human haplotypes.

Finally, researchers from the University of California, San Francisco, the UCSF-Abbott Viral Diagnostics and Discovery Center, and elsewhere introduce a human pegivirus that they detected in blood samples from a subset of individuals with hepatitis C virus infection. Starting with metagenomic sequencing on hundreds of chronic liver disease patients, the team uncovered RNA sequences stemming from the virus, known as HPgV-2. From there, the group developed diagnostic strategies to screen thousands more samples, ultimately identifying and analyzing a dozen HPgV-2 strains found in the blood of individuals with HCV. GenomeWeb has more on the study, which appears in PLOS Pathogens.