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This Week in PNAS: Oct 13, 2015

A study appearing online edition in the Proceedings of the National Academy of Sciences outlines efforts to sequence the genome of the adzuki bean, Vigna angularis, a legume crop believed to have been domesticated in China that's now grown in dozens of countries. Using whole-genome shotgun sequencing, researchers from China and India generated an almost 467 million base draft adzuki bean genome containing more than 34,100 predicted protein-coding genes. The team then compared the genome to soybean sequences and performed a population genomics analysis with 49 more re-sequenced wild, semi-wild, landrace, and improved adzuki bean accessions, uncovering adzuki bean relationships and signals of selection associated with domestication.

An Indiana University team describes spontaneous mutation patterns in Escherichia coli for another PNAS study. Through whole-genome sequencing on three divergent E. coli strains generated using a mutation accumulation protocol in which clonal populations from a single founder are subjected to serial bottlenecks, the researchers uncovered four potential spontaneous mutational forces — from intrinsic DNA polymerase errors and error-prone polymerase activity to endogenously or exogenously induced DNA damage. By analyzing another DNA repair pathway-defective strains, they found that mutation rate and mutation spectra tended to turn up in strains missing pathways for preventing or repairing oxidative DNA damage.

Finally, researchers from the Netherlands assess genetic diversity in tumor organoids and the metastatic colorectal cancer tumor biopsies used to generate them. With the help of SOLiD sequencing, the team examined sequence and copy number patterns across almost 2,000 cancer-related genes in biopsy samples from 14 individuals with metastatic colorectal cancer and in corresponding organoid cultures. The study's authors were able to establish such cultures for more than 70 percent of the biopsy samples and saw some 90 percent concordance between mutations found in biopsy and organoid samples from each individual. "Most importantly," the study's authors say, "none of the mutations that were found exclusively in either the tumor or organoid cultures are in driver genes or gene amenable to drug targeting."