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This Week in PNAS: Apr 24, 2018

A team led by investigators at the Anhui Agricultural University in China presents findings from a genomic, transcriptomic, and metabolomic analysis of the tea plant Camellia sinensis var. sinensis. Using short- and long-read sequencing, the researchers put together a high-quality draft genome sequence with leaf DNA from the C. sinensis var. sinensis plant cultivar Shuchazao, folding in RNA sequence data from eight tea tissue types to annotate the genome and identify more than 33,900 predicted protein-coding genes. Together with metabolic profiles and comparisons to a previously sequenced draft genome for the Assam type tea plant Camellia sinensis var. assamica, the sequences suggest the tea plant sub-species spring from an ancestral plant that went through two whole-genome duplication events and subsequent paralogous duplications, boosting secondary metabolite gene repertoires.

Researchers from the US and Sweden explore genetic features involved in adaptations to specific local environments by the plant model species Arabidopsis thaliana. By comparing population genomic patterns and quantitative trait loci for several A. thaliana accessions using genome resequencing data, the team identified signs of selection and local adaptation signatures in recombinant inbred A. thaliana populations from Italy and Sweden. "Highly divergent genes between Italy and Sweden populations show evidence of more recent selection in Sweden than Italy," they write, "and the biological annotations of these genes suggest interesting mechanisms underlying local adaptation."

A University of California, Los Angeles-led team characterizes the suite of cell surface proteomic profiles and transcriptomic patterns in a set of prostate cancer samples or cell lines. The researchers used a combination of RNA sequence, microarray profiles, mass spectrometry, and other approaches to assess markers on the surface of prostate adenocarcinoma or neuroendocrine prostate cancer cell lines or xenografts, uncovering "surfaceome" differences between the two advanced prostate cancer subtypes. "[W]e present a generalizable approach to discover cancer subtype-specific target antigens as vulnerabilities amenable to therapeutic exploitation," the authors note. "Our data demonstrate that divergent cancer differentiation states arising during prostate cancer progression are associated with large changes in the repertoire of expressed cell surface proteins (surfaceome)."