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This Week in PNAS: May 31, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, an international team reports on findings from a genome sequencing study of Arachis duranensis, the presumed progenitor for the A sub-genome of the cultivated peanut plant A. hypogaea. The researchers used shotgun sequencing to tackle the nearly 1.4 billion base A. duranensis genome, producing a draft genome assembly that contained 50,324 predicted protein-coding genes. They also sequenced six diploid parent plants and several synthetic tetraploids for the analysis to take a look at peanut evolution and biology. Earlier this year, members of the International Peanut Genome Initiative presented findings from their own sequencing study of A. duranensis, as well as the A. ipaensis species that's similar to the cultivated peanut's B genome.

Researchers from France, the UK, US, and Morocco explore the feasibility of doing homozygosity mapping and linkage analyses using whole-exome sequencing data rather than genome-wide array-based genotyping results. Starting with data for 110 individuals from Western Europe, the Middle East, North Africa, Sub-Saharan African, or Central and South America, the team found that the exome sequences compared favorably with SNP data for predicting population structure and homozygosity rates. In a subsequent analysis of 15 consanguineous families, the investigators found that linkage information declined genome-wide when using exome sequences alone, though linkage profiles were substantially bolstered across the protein-coding portions of the genome.

Finally, a Stanford University-led team assesses the consequences of genetic variation in the different parts of the protein encoded by the beta-cardiac myosin gene MYH. Using MYH7 gene sequences from more than 2,900 individuals with a heritable heart condition called hypertrophic cardiomyopathy, which can stem from MYH alterations, the researchers searched for clues to the heart condition using structural modeling and computational approaches that took into account different stages of the myosin protein's motor function. When they compared genetic and phenotypic patterns in cases with those in data from the ExAC and SHaRe cohorts — together containing exome sequences for more than 103,000 individuals — the investigators found that hypertrophic cardiomyopathy-associated variants were enriched in a region of the beta-cardiac myosin protein called the converter domain and/or sites on a surface on the myosin head.