In a paper published online in advance in Genome Research this week, researchers report their use of karyotype reconstruction across several ancestral grass species, which they say found "new mechanisms of genome shuffling as a source of plant evolution." Using paleogenomics, the team "delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes" and that "the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events," they write.
Investigators at the University of Chicago describe the "age-dependent chromosomal distribution of male-biased genes in Drosophila" in Genome Research this week. In a genome-wide analysis, Yong Zhang et al. found "an excess of young X-linked male-biased genes," the proportion of which diminishes with time. "These observations revealed that the evolution of male-biased genes is more complicated than the previously detected one-step X→A gene traffic and the enrichment of the male-biased genes on autosomes," Zhang and colleagues write, adding that various evolutionary forces likely affect the chromosomal distribution of male-biased genes.
The University of Maryland's Steven Salzberg and his colleagues describe in a review published in the most recent issue of Genome Research "issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data." In addition, Salzberg's group reviews genome sequences recently assembled by short reads and provides "recommendations for sequencing strategies that will yield a high-quality assembly."
And in an accepted preprint published online recently, investigators at University of Virginia Health Systems show that "RNA synthesis precision is regulated by pre-initiation complex turnover." Specifically, using high-resolution tiling arrays to determine how TATA-binding protein dynamics affect RNA synthesis in Saccharomyces cerevisiae, the team found that "Mot1 plays a broad role in establishing the precision and efficiency of RNA synthesis." Further, the loss of Mot1 showed aberrant transcription initiation and termination in the yeast. "Genetic and genomic analyses support the conclusion that these effects on RNA length are mechanistically tied to dynamic TBP occupancies at certain types of promoters," the authors conclude.