Abundance and diversity of bees visiting flowering pennycress, a new oilseed crop in the midwestern USA

Oilseed pennycress (Thlaspi arvense) is a new, autumn-sown, “cash cover crop” for the Midwestern USA and elsewhere. Anthesis occurs in early spring when few other plants bloom, and its flowers attract early-emerging bees. However, the taxonomic composition of these bees was unknown. Consequently, we systematically captured and identified the genera and species of bees visiting pennycress flowers throughout anthesis at five site-years: two in Illinois and three in Minnesota. A cumulative total of 28 bee species were found across site-years. The most common genera were Andrena (10 species), Lasioglossum (12 species), and Halictus (2 species). Rarer genera were Apis, Ceratina, Hylaeus, and Nomada. Bee abundance and diversity were related closely and in a negative exponential manner with percent land area devoted to annual cropping. The inclusion of new early flowering crops, such as pennycress, may enhance bee abundance and diversity, especially if even small areas of uncropped land are nearby

The Genome of Austrofundulus Limnaeus Offers Insights into Extreme Vertebrate Stress Tolerance and Embryonic Development

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system. Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection. Conclusion: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

High-density single-nucleotide polymorphism (SNP) arrays have revolutionized the ability of genome-wide association studies to detect genomic regions harboring sequence variants that affect complex traits. Extensive numbers of validated SNPs with known allele frequencies are essential to construct genotyping assays with broad utility. We describe an economical, efficient, single-step method for SNP discovery, validation and characterization that uses deep sequencing of reduced representation libraries (RRLs) from specified target populations. Using nearly 50 million sequences generated on an Illumina Genome Analyzer from DNA of 66 cattle representing three populations, we identified 62,042 putative SNPs and predicted their allele frequencies. Genotype data for these 66 individuals validated 92% of 23,357 selected genome-wide SNPs, with a genotypic and sequence allele frequency correlation of r = 0.67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome