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This Week in Nature: Nov 4, 2010

In this week's Nature, Craig Venter and his colleagues at the J. Craig Venter Institute report the "sequencing of 137 diverse marine isolates collected from around the world," which they analyzed along with previously published genomes for marine isolates and metagenomic data in order to "gain insights into the ecology of the surface ocean prokaryotic picoplankton." According to their data, Venter et al. suggest that the sequenced genomes can be categorized into two microbial groups: the first is distinctly "composed of only a few taxa that are nearly always abundant in picoplanktonic communities," and the "genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments," the team writes.

Over at Nature Genetics, a team led by researchers at the Boyce Thompson Institute for Plant Research in Ithaca, N.Y., reports in a paper published online in advance "the developmental dynamics of the maize leaf transcriptome," which the authors suggest "will serve as the foundation for a systems biology approach to the understanding of photosynthetic development." After mapping more than 120 million reads relevant to gene structure and alternative splicing, the team "found that 64 percent and 21 percent of genes were differentially expressed along the developmental gradient and between bundle sheath and mesophyll cells, respectively."

In another paper published online in Nature Genetics this week, an international research team reports their comparison of 17 whole genome sequences for Yersinia pestis isolates acquired across the globe. By screening each isolate for 933 SNPs, the team was able to make phylogenetic predictions based on parsimony, and suggest that "Y. pestis evolved in or near China and spread through multiple radiations … leading to country-specific lineages that can be traced by lineage-specific SNPs."

And in the current issue of Nature Genetics, researchers at Riken report their analysis of the genome sequence of a Japanese individual, which they obtained via high-throughput sequencing at up to 40-fold coverage. The authors write they found 3,132,608 SNVs and, when compared to six published human genomes, "an excess of singleton nonsense and non-synonymous SNVs, as well as singleton SNVs in conserved non-coding regions," adding their suggestion that "considerable variation remains undiscovered in the human genome."

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.