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This Week in PLOS: Dec 1, 2014

In PLOS One, Chinese researchers report on the chloroplast sequences for two species of Echinochloa, a genus in the Poaceae family that contains plant pests known for causing crop yield losses. By sequencing DNA from the leaves of E. oryzicola and E. crus-galli plants, the team produced chloroplast genomes spanning nearly 140,000 bases in each species. Both genomes contained 131 protein-coding genes, though the study's authors also identified 466 base substitutions between the chloroplast genomes, along with 79 small insertion and deletion differences. From these and other data, they estimated that the two Echinochloa species diverged from one another some 3.3 million years ago.

A University of California, San Diego-led team used mass spectrometry to profile proteomic patterns in kidney tissue from an isolated population of island foxes in California that is particularly prone to a chronic inflammatory disease called amyloid A amyloidosis that can affect the kidney, spleen, oral cavity, or vasculature. As they reported in PLOS One, the researchers found high levels of serum amyloid A — a protein associated with the condition in the past. In addition to delineating the amino acid sequence for the fox SAA protein, investigators identified several other proteins found at higher-than-usual levels in kidney samples from the sickly island foxes.

Finally, investigators from the Baylor College of Medicine and centers around the world describe findings from their effort to sequence and analyze the genome sequence of the centipede, Strigamia maritima, in PLOS Biology. The team put together a 176 million base genome assembly for S. maritima using DNA from wild Scottish centipedes before re-sequencing four more centipede individuals to evaluate variant patterns in the insect. Together with new clues to the centipede's protein-coding potential and alternative splicing patterns, the study offered new information on its evolutionary relationships, revealing apparent similarities between centipedes and the ancestor to all arthropod insects. GenomeWeb has more on the study here.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.