Listeriamonocytogenes ( Lm ) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks.

• The aims of this study were to investigate the appearance of strigolactones in the green lineage and to determine the primitive function of these molecules. • We measured the strigolactone content of several isolated liverworts, mosses, charophyte and chlorophyte green algae using a sensitive biological assay and LC‐MS/MS analyses. In parallel, sequence comparison of strigolactone‐related genes and phylogenetic analyses were performed using available genomic data and newly sequenced expressed sequence tags. The primitive function of strigolactones was determined by exogenous application of the synthetic strigolactone analog, GR24, and by mutant phenotyping. • Liverworts, the most basal Embryophytes and Charales, one of the closest green algal relatives to Embryophytes, produce strigolactones, whereas several other species of green algae do not. We showed that GR24 stimulates rhizoid elongation of Charales, liverworts and mosses, and rescues the phenotype of the strigolactone‐deficient Ppccd8 mutant of Physcomitrella patens. • These findings demonstrate that the first function of strigolactones was not to promote arbuscular mycorrhizal symbiosis. Rather, they suggest that the strigolactones appeared earlier in the streptophyte lineage to control rhizoid elongation. They may have been conserved in basal Embryophytes for this role and then recruited for the stimulation of colonization by glomeromycotan fungi.

We have sequenced two complete chloroplast genomes in the Asteraceae, Helianthus annuus (sunflower), and Lactuca sativa (lettuce), which belong to the distantly related subfamilies, Asteroideae and Cichorioideae, respectively. The Helianthus chloroplast genome is 151 104 bp and the Lactuca genome is 152 772 bp long, which is within the usual size range for chloroplast genomes in flowering plants. When compared to tobacco, both genomes have two inversions: a large 22.8‐kb inversion and a smaller 3.3‐kb inversion nested within it. Pairwise sequence divergence across all genes, introns, and spacers in Helianthus and Lactuca has resulted in the discovery of new, fast‐evolving DNA sequences for use in species‐level phylogenetics, such as the trnY‐rpoB, trnL‐rpl32, and ndhC‐trnV spacers. Analysis and categorization of shared repeats resulted in seven classes useful for future repeat studies: double tandem repeats, three or more tandem repeats, direct repeats dispersed in the genome, repeats found in reverse complement orientation, hairpin loops, runs of A's or T's in excess of 12 bp, and gene or tRNA similarity. Results from BLAST searches of our genomic sequence against expressed sequence tag (EST) databases for both genomes produced eight likely RNA edited sites (C → U changes). These detailed analyses in Asteraceae contribute to a broader understanding of plastid evolution across flowering plants.

The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that ‘stoneworts,’ or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as “pond scum”) as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1) the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2) the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.