Skip to main content
Premium Trial:

Request an Annual Quote

This Week in PLOS: Aug 15, 2016

In PLOS Genetics, researchers from Canada and the Netherlands describe a gene discovery strategy that couples mutation strain sequencing with a Sequence Kernel Association Test (SKAT) statistical method for prioritizing candidate genes. The researchers applied this approach to whole-genome sequence data generated for 480 random multi-mutation Caenorhabditis elegans strains from the Million Mutation Project to search for gene involved in a phenotype of interest — an alteration in sensory neuron cilia with potential implications for understanding cilia disruptions in human disease. The search led to three candidate genes not implicated in ciliated sensory neuron functions in the past, the study's author report, noting that "our novel approach is useful for any organism with a small genome that can be quickly sequenced and where many mutant strains can be easily isolated and phenotyped."

Whole-genome sequencing can successfully distinguish persistent drug-resistant infections with Mycobacterium tuberculosis from new drug-resistant TB infections, according to a PLOS One study. A team from Thailand and Singapore did whole-genome sequencing on seven M. tuberculosis isolates collected sequentially from two individuals with multi-drug resistant TB (MDR-TB) and one individual with extensively drug-resistant TB (XDR-TB). In contrast to re-infection cases, which involved differences at dozens of SNPs in samples taken two years apart, the analysis uncovered just two SNP differences in isolates taken two months to nine months apart in persistently infected patients. From these and other findings, the study's authors argue that "[whole-genome sequencing] provided comprehensive results regarding molecular epidemiology, distinguishing between persistent infection and reinfection in M/XDR-TB and potentially can be used for detection of novel mutations associated with drug resistance."

Chinese researchers report on findings from a genome sequencing study of the apple chorotic leaf spot virus for another paper in PLOS One. Using genetic material from three ACLSVs collected from as many hawthorn plant accessions at the Shenyang Agricultural University, the team did high-throughput sequencing and together genome assemblies for ACLSV ranging from 7,543 nucleotides to 7,561 nucleotides apiece with between almost 83 percent and more than 92 percent sequence identity to one another. Compared to sequences from other ACLSV isolates in the National Center for Biotechnology Information database, the hawthorn isolates were most similar to an accessions previously reported on pear plants from China and least like an accession found in peach plants in the US.