We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locati...

Significance: This research uncovers the mechanisms of an ancient arms race between butterflies and plants, seen today in countless gardens as caterpillars of cabbage butterflies that devour cabbage crop varieties. Nearly 90 million years ago, the ancestors of Brassica (mustards, cabbage) and related plants developed a chemical defense called glucosinolates. While very toxic to most insects, humans experience glucosinolates as the sharp taste in wasabi, horseradish and mustard. Here we report that this triggered a chemical arms race that escalated in complexity over time. By investigating the evolutionary histories of these plants and insects, we found that major increases in chemical defense complexity were followed by butterflies evolving countertactics to allow them to continue to attack and feed on the plants.

The shift from outcrossing to selfing is common in flowering plants^1,2, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

Mathieu Blanchette and colleagues report whole-genome sequencing of three Brassicaceae species, Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum. They include comparative genomic analysis with 6 additional crucifier genomes, identify and characterize over 90,000 conserved noncoding sequences and provide a map of functional noncoding regions in plant genomes.

Subgenome differences in levels of transposon methylation mirror increases in subgenome-specific expression bias observed over generations following hybridizati

During the haploid phase of mammalian spermatogenesis, nucleosomal chromatin is ultimately repackaged by small, highly basic protamines to generate an extremely compact, toroidal chromatin architecture that is critical to normal spermatozoal function. In common with several species, however, the human spermatozoon retains a small proportion of its chromatin packaged in nucleosomes. As nucleosomal chromatin in spermatozoa is structurally more open than protamine-packaged chromatin, we considered it likely to be more accessible to exogenously applied endonucleases. Accordingly, we have used this premise to identify a population of endonuclease-sensitive DNA sequences in human and murine spermatozoa. Our results show unequivocally that, in contrast to the endonuclease-resistant sperm chromatin packaged by protamines, regions of increased endonuclease sensitivity are closely associated with gene regulatory regions, including many promoter sequences and sequences recognized by CCCTC-binding factor (CTCF). Similar differential packaging of promoters is observed in the spermatozoal chromatin of both mouse and man. These observations imply the existence of epigenetic marks that distinguish gene regulatory regions in male germ cells and prevent their repackaging by protamines during spermiogenesis. The ontology of genes under the control of endonuclease-sensitive regulatory regions implies a role for this phenomenon in subsequent embryonic development.