Finding the missing honey bee genes: lessons learned from a genome upgrade

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.Funding for the project was provided by a grant to RG from the National Human Genome Research Institute, National Institutes of Health (NHGRI, NIH) U54 HG003273. Contributions from members of the CGE lab were supported by Agriculture and Food Research Initiative Competitive grant no. 2010- 65205-20407 from the USDA National Institute of Food Agriculture. AKB was supported by a Clare Luce Booth Fellowship at Georgetown University

Red mangroves emit hydrocarbons

The objective of this study is to investigate hydrocarbon species and amounts released by red mangrove foliage and determine if these quantities warrant future research on atmospheric chemical processing of these compounds. The field investigation took place during July 2001 at Key Largo, Florida Bay, Florida. Foliage still attached to plants was enclosed in cuvettes while air of known flow rates circulated around leaves to study, hydrocarbon emissions. Cuvette air samples underwent gas chromatographic analyses to determine species and amounts of hydrocarbons released by mangrove foliage. Red mangrove foliage emits isoprene and trace amounts of the monoterpenes of alpha-pinene, beta-pinene, camphene, and d-limonene. The mangrove flowers released these latter compounds in amounts ranging from 0.5 to 10 mg (monoterpene) per gram of dry biomass per hour. These fluxes are normalized to, the foliage temperature of 30 degreesC. When normalized to the foliage temperature of 30 degreesC and light levels of 1000 mumol m(-2) s(-1), isoprene emission rates as high as 0.092 +/- 0.109 mug (isoprene) per gram of dry biomass per hour were measured. Compared to terrestrial forest ecosystems, red mangroves are low isoprene emitters. During peak flowering periods in the summertime, however, red mangroves may emit sufficient amounts of monoterpenes to alter ground-level ozone concentrations and contribute to biogenic aerosol formation

2006 Whole Earth Telescope observations of GD358 : a new look at the prototype DBV

We report on the analysis of 436.1 hr of nearly continuous high-speed photometry on the pulsating DB white dwarf GD358 acquired with the Whole Earth Telescope (WET) during the 2006 international observing run, designated XCOV25. The Fourier transform (FT) of the light curve contains power between 1000 and 4000 μHz, with the dominant peak at 1234 μHz. We find 27 independent frequencies distributed in 10 modes, as well as numerous combination frequencies. Our discussion focuses on a new asteroseismological analysis of GD358, incorporating the 2006 data set and drawing on 24 years of archival observations. Our results reveal that, while the general frequency locations of the identified modes are consistent throughout the years, the multiplet structure is complex and cannot be interpreted simply as l =l modes in the limit of slow rotation. The high-k multiplets exhibit significant variability in structure, amplitude and frequency. Any identification of the m components for the high-k multiplets is highly suspect. The k = 9 and 8 modes typically do show triplet structure more consistent with theoretical expectations. The frequencies and amplitudes exhibit some variability, but much less than the high-k modes. Analysis of the k = 9 and 8 multiplet splittings from 1990 to 2008 reveal a long-term change in multiplet splittings coinciding with the 1996 sforzando event, where GD358 dramatically altered its pulsation characteristics on a timescale of hours. We explore potential implications, including the possible connections between convection and/or magnetic fields and pulsations.We suggest future investigations, including theoretical investigations of the relationship between magnetic fields, pulsation, growth rates, and convection

2006 Whole Earth Telescope observations of GD358 : a new look at the prototype DBV

We report on the analysis of 436.1 hr of nearly continuous high-speed photometry on the pulsating DB white dwarf GD358 acquired with the Whole Earth Telescope (WET) during the 2006 international observing run, designated XCOV25. The Fourier transform (FT) of the light curve contains power between 1000 and 4000 μHz, with the dominant peak at 1234 μHz. We find 27 independent frequencies distributed in 10 modes, as well as numerous combination frequencies. Our discussion focuses on a new asteroseismological analysis of GD358, incorporating the 2006 data set and drawing on 24 years of archival observations. Our results reveal that, while the general frequency locations of the identified modes are consistent throughout the years, the multiplet structure is complex and cannot be interpreted simply as l =l modes in the limit of slow rotation. The high-k multiplets exhibit significant variability in structure, amplitude and frequency. Any identification of the m components for the high-k multiplets is highly suspect. The k = 9 and 8 modes typically do show triplet structure more consistent with theoretical expectations. The frequencies and amplitudes exhibit some variability, but much less than the high-k modes. Analysis of the k = 9 and 8 multiplet splittings from 1990 to 2008 reveal a long-term change in multiplet splittings coinciding with the 1996 sforzando event, where GD358 dramatically altered its pulsation characteristics on a timescale of hours. We explore potential implications, including the possible connections between convection and/or magnetic fields and pulsations.We suggest future investigations, including theoretical investigations of the relationship between magnetic fields, pulsation, growth rates, and convection