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This Week in PNAS: Jan 22, 2019

In the early version of the Proceedings of the National Academy of Sciences, researchers from the University of Missouri and elsewhere describe chromosomal features detected by painting all 10 maize plant chromosomes with whole-chromosome oligonucleotide fluorescence in situ hybridization painting, The probes were developed with the help of shotgun sequences from an inbred maize line called B73, the team says, revealing everything from recombination to cell division patterns in the plant. "Combined with other chromosome-labeling techniques, a complete set of whole-chromosome oligonucleotide paints lays the foundation for future studies of the structure, organization, and evolution of genomes," the authors write.

A University of California, Los Angeles-led team presents findings from expression and metabolic analysis of unicellular Chlamydomonas reinhardtii green algae grown over time in a specific light and dark cycle in bioreactors. Using RNA sequencing, liquid chromatography-mass spectrometry, and other approaches, the researchers saw light cycle-related differential expression for almost 85 percent of the green algae's genes, along with a dip in respiratory pathways and rising levels of other metabolic pathways at night. "We report that the majority of the algal genome is differentially expressed over the course of the day and the timing of specific genes is dictated by their biological function," the authors report.

Researchers from Taiwan, China, and the US suggest that adaptations in the vinous-throated parrotbill, Sinosuthora webbiana, largely stem from standing genetic variation. In addition to producing a 1.06 billion base de novo reference genome for the Taiwanese vinous-throated parrotbill, which contained an estimated 20,149 protein-coding genes and ome 72 million bases of repetitive sequences, the team re-sequenced 40 parrotbills from two high-altitude and two low-altitude populations in Taiwan. By comparing the Taiwan parrotbills to another 40 re-sequenced parrotbills from mainland China, the investigators identified two dozen sites of standing variation in non-coding parts of the genome that primarily appear to serve as the source of local adaptation in the island parrotbill birds.