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Literature Lineup

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Orangutan Genome
Locke DP, Hillier LW, Warren WC, et al. (2011). Comparative and demographic analysis of orang-utan genomes. Nature. Epub: doi 10.1038/nature09687.

In this paper, Devin Locke and his colleagues at Washington University in St. Louis report a draft genome assembly based upon short read sequence data obtained from five Sumatran and five Bornean orangutans. The authors suggest that their -findings provide a resource that may offer new insights into evolutionary genomics, hominoid biology, and future conservation efforts. Their analyses reveal that the orangutan genome contains several unique features compared with other primate genomes, as well as a polymorphic neocentromere that emphasizes the slow evolution of the orangutan genome structure.

Optimized Pooling
Lee JS, Choi M, Yan X, et al. (2011). On optimal pooling designs to identify rare variants through massive resequencing. Genetic Epidemiology. Epub: doi 10.1002/gepi.20561.

Joon Sang Lee et al. examine DNA pooling as a cost-effective strategy for rare variant detection and provide general guidelines for how best to utilize this method. The authors report that "the optimal number of individuals in a pool is indifferent to the [minor allele frequency] at the same coverage depth and detection threshold. In addition, when the individual contributions to each pool are equal, the total number of individuals across different pools required in an optimal design to detect a variant with a desired power is similar at different coverage depths."

Mouse Transciptome
Diez-Roux G, Banfi S, Sultan M, et al. (2011). A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biology. 9(1): e1000582.

Using RNA in situ hybridization, the authors generated the first genome-wide transcriptome atlas of an entire mammalian organism — the developing mouse at 14.5 embryonic days. The researchers created anatomy-based expression profiles for more than 18,000 coding genes and more than 400 microRNAs, and identified 1,002 genes that are a source of novel, tissue-specific markers for 37 different anatomical structures. "The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease," they write in the paper.

Pine Pathogen
DiGuistini S, Wang Y, Liao NY, et al. (2011). Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. PNAS. Epub: doi 10.1371/pnas.1011289108.

A team led by researchers at the University of British Columbia describes an effort to sequence Grosmannia clavigera, a symbiont of the mountain pine beetle that is currently destroying wide areas of lodgepole pine forest in western North America. The team used genome and transcriptome analyses to report insights into how G. clavigera tolerates conifer-defense chemicals, including oleoresin terpenoids, as they colonize a host tree. "RNA-seq data indicate that terpenoids induce a substantial antimicrobial stress in Gc, and suggest that the fungus may detoxify these chemicals by using them as a carbon source," the team reports.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.