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This Week in Genome Biology: Jul 3, 2013

Researchers with Philip Morris International's R&D branch sequenced and started analyzing the genomes of two South American plants whose ancestors are believed to have donated Nicotiana tabacum's maternal and paternal genomes: the woodland tobacco species N. sylvestris and another diploid species called N. tomentosiformis. The team also tracked down tens of thousands of expressed N. sylvestris and N. tomentosiformis transcripts by sequencing RNA in leaf, root, and flower tissue from the two plants, which belong to the same family as tomato and potato. "Comparisons of the N. sylvestris and N. tomentosiformis genomes with [high quality tomato and potato] reference genomes will improve our understanding of Nicotiana clade evolution," study authors wrote, "and expedite the functional annotation of their genomes."

An international team led by investigators in the US and Germany cataloged the copy-number variation that exists among wild and domestic barley plants and took a peek at the processes behind this type of variation. Using array comparative genomic hybridization, the researchers assessed CNV profiles in barley from eight domesticated barley cultivars and half a dozen types of wild barley. The wild barley plants carried more — and more diverse — CNVs, they found, though almost 15 percent of sequences tested across the barley set showed variable copy number in at least one of the barley genotypes. More than 9 percent of protein-coding gene considered contained CNVs, including genes contributing to disease resistance or the production of certain enzymes.

Italian researchers began teasing apart the impact that growth year, field conditions, and environmental exposures can have on the genes transcribed by grapevine berry. Using array-based gene expression profiling, the team compared berries from one Vitis vinifera clone from a cultivar called Corvina that was vegetatively propagated and grown at 11 Italian vineyards during the course of three years. The analysis revealed sets of genes whose expression remained relatively stable as well as others that have more plastic expression patterns depending on the conditions considered. That latter set tends to include genes involved in secondary metabolite production, study authors note, as well as genes that regulate transcription, translation, and transport.