In this week's PNAS Early Edition, an international research team reports its sequencing of two rust fungi, Melampsora larici-populina — the causal agent of poplar leaf rust — and Puccinia graminis f. sp. Tritici — the causal agent of wheat and barley stem rust. In a comparative analysis, the team identified genomic features in both fungi "related to their obligate biotrophic lifestyle," including the "dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters," which the team suggests may "play a role in host infection and nutrient acquisition."
A team led by investigators at New York University this week presents molecular evidence to support a single evolutionary origin of domesticated Asian rice, Oryza sativa. By re-sequencing 630 gene fragments on chromosomes 8, 10, and 12 for a diverse set of rice accessions, the team identified "20 putative selective sweeps on these chromosomes in cultivated rice" as well as SNP data to strongly suggest a single domestication event around 8,200 to 13,500 years ago.
The J. Craig Venter Institute's Gregory Sims and Sung-Hou Kim at the University of California, Berkeley, report in PNAS this week a "whole-genome phylogeny of [the] Escherichia coli/Shigella group by feature frequency profiles." Using this approach, to infer phylogenetic distances based on the I-mer features of whole genomes, Sims and Kim found that Shigella consists of at least two distantly related subclades and that "the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains." Further, Sims and Kim say that their results suggest the E. coli/Shigella ancestor "was likely a facultative or opportunistic pathogen." Our sister publication GenomeWeb Daily News has more on this study.
Harvard Medical School's Shobha Vasudevan and her colleagues this week show that in immature Xenopus laevis oocytes, microRNA-mediated up-regulated reporter expression depends on Xenopus AGO or human AGO2 and FXR1. Additionally, Vasudevan et al. report that Myt1 kinase is "an important, endogenous cell state regulator" as well as a "natural target of microRNA-mediated up-regulation in response to xlmiR16, ensuring maintenance of oocyte immaturity."