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This Week in PLOS: Dec 8, 2014

In PLOS Genetics, researchers from the US Department of Agriculture Forest Service and elsewhere report on findings from their effort to characterize the genome, transcriptome, and secretome of Phlebiopsis gigantea, a white-rot fungus from the Agaricomycetes fungal class that can successfully set up shop in conifer material containing compounds that deter most other fungal species. Using a combination of sequencing and mass spectrometry, the team took a look at the fungus' genome sequence, expressed transcripts, and secreted compounds, comparing them to related species and considering the effects of pine extract on the pathogen's gene expression patterns.

A PLOS Neglected Tropical Disease study outlines improvements and upgrades to the original draft genome assemblies for Paracoccidioides, dimorphic fungal pathogen species that cause a South American tropical disease known as paracoccidioidomycosis. A team from Colombia and the US did deep Illumina genome re-sequencing on three strains of Paracoccidioides fungus, representing two different species. By incorporating this data into existing Sanger assemblies, the researchers were able to re-annotate the genomes and establish improved predictions about the pathogens' genes and transcripts, including those suspected of contributing to virulence.

Genetic patterns in a population of non-migratory humpback whales found in the Arabian Sea suggests the animals have low genetic diversity and high levels of isolation from other humpback whales. As they say in PLOS One, researchers from the US, Portugal, Oman, and elsewhere profiled microsatellite and mitochondrial sequences in tissue samples from 67 humpback whales in the Arabian Sea. Through comparisons with existing data on humpback whales in the Southern Hemisphere and North Pacific, the team estimates that the Arabian Sea population shares ancestry with humpback whales in the Southern Ocean, though it appears to have been isolated for up to 70,000 years. Based on the low levels of genetic diversity, limited population size, and potential environmental threats, the study's authors argue in favor of classifying the population as critically endangered rather than endangered (its current designation on the International Union for Conservation of Nature Red List).

The Scan

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

Science writes that a paper reporting that SARS-CoV-2 can occasionally integrate into the host genome is drawing criticism.

Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.