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Nature Papers Include Analysis of Rapeseed Genome, Target Enrichment Method for Metagenomics

A genomic analysis of rapeseed (Brassica napus) is presented in Nature Plants this week, providing insights that may help in the genetic improvement of this economically important oilseed crop plant. Scientists from Huazhong Agricultural University report the sequencing, de novo assembly, and annotation of eight B. napus accessions, which they analyzed to identify millions of small variations and 77.2 to 149.6  megabase presence and absence variations (PAV). Other findings include variations liked to silique length, seed weight, and flowering time. 

A method for titrating gene expression in human cells using CRISPR single-guide RNAs (sgRNAs) is presented in Nature Biotechnology this week. A University of California, San Francisco, team used large-scale measurements across multiple cell models to characterize activities of sgRNAs containing mismatches to their target sites and derived rules governing mismatched sgRNA activity using deep learning. With the rules, they built a compact sgRNA library to titrate the expression of roughly 2,400 genes essential for robust cell growth, as well as to construct an in silico sgRNA library spanning the human genome. They demonstrate the utility of their approach by mapping gene expression levels to phenotypes with single-cell resolution, enabling the identification of gene-specific viability thresholds and expression level-dependent cell fates. The work, the authors write, "provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression."

A universal target enrichment method for metagenomic sequencing for viral detection and genomic surveillance is reported in Nature Microbiology this week. Called metagenomic sequencing with spiked primer enrichment, or MSSPE, the technique enriches targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens, according to its developers at the University of California, San Francisco, and elsewhere. The investigators tested MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47 percent increase in the breadth of genome coverage over metagenomic next-generation sequencing alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels, meantime, was comparable in sensitivity to specific PCR, demonstrating 95 percent accuracy for the detection of Zika, Ebola, dengue, chikungunya, and yellow fever viruses in plasma samples from infected patients. Notably, MSSPE is low-cost, fast, and deployable on benchtop and portable nanopore sequencers, making it directly applicable for diagnostic laboratory and field use, the researchers write.