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This Week in Genome Biology: Mar 30, 2011

In a paper published online in Genome Biology this week, investigators at the Laboratoire de Microbiologie et Génétique Moléculaire in France present ISsaga, a Web application that "provides computational tools and methods for high-quality IS [insertion sequence] annotation." Using established insertion sequence annotation standards, ISsaga "permits rapid processing of single or multiple prokaryote genomes," and provides both a genomic context for single insertion sequences and a "graphical overview of IS distribution around the genome of interest," the authors write.

A team led by investigators at France's Université d'Evry reports its assembly of the stramenopile Blastocystis subtype 7 isolate genome, which at 18.8 Mb makes this anaerobic human pathogen "the smallest stramenopile genome sequenced to date." When compared with other stramenopile genomes, the authors write, the Blastocystis subtype 7 isolate genome encodes "effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer." Among other things, the team suggests that its study could help power future projects that aim to assess Blastocystis-host interactions.

A trio of researchers at Penn State University applied both principal components and canonical correlation multivariate analyses to primate and rodent genomic alignments and enabling them to "investigate the structure of rate co-variation for four mutation types and simultaneously explore the associations with multiple genomic features at different genomic scales and phylogenetic distances." Overall, the researchers report in a recent Genome Biology paper, they observed "a consistent, largely linear co-variation among rates of nucleotide substitutions, small insertions and small deletions, with some non-linear associations detected among these rates on chromosome X and near autosomal telomeres." The team suggests that its analyses might enable future progress in deducing the roles of "replication, recombination and repair and local chromatin environment in mutagenesis."

Investigators at the Georgia Institute of Technology and the Massachusetts Institute of Technology reports their integration of metagenomic and metratranscriptomic data sets obtained via "shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments and from forest soil." Across samples, the Georgia Tech-MIT team found that "expressed genes with transcripts in the RNA sample were significantly more conserved than non-expressed gene sets," and also that "highly expressed genes were significantly more likely to fall within an orthologous gene set shared between closely related taxa," consistent with the idea of "core genes." The researchers report online in Genome Biology that their observations "support the hypothesis … that gene expression level is a primary correlate of evolutionary rate across diverse microbial taxa from natural environments."

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.