Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences ...remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Clean and spiked sediment formulations of various silt sand and clay sand ratios were tested for toxicity using a bioassay that utilizes bioluminescent bacteria Measured toxicities of clean and ...copper sulfate–spiked sediments were negatively but nonlinearly related with percent silt and percent clay, but no significant relationship existed between measured toxicity and sediment composition for methyl parathion–spiked formulations Results suggest that solid phase sediment bioassays using bioluminescent bacteria may be useful for testing the toxicities of single contaminants in formulated artificial sediments of known particle size composition, and for repeated samples collected from the same site However, extreme caution must be taken when testing sediments of varying composition or which may be differentially contaminated or contain a suite of contaminants.
Studies were conducted at sites in south‐east Queensland, Australia, to investigate the effect of habitat modification for mosquito control on the distribution of eggshells of the salt marsh ...mosquito, Ochlerotatus vigilax (Skuse). Modifications were
mainly runnelling, but an Open Marsh Water Management (OMWM) site and a grid‐ditched
site were also included. There were two separate experimental designs: one was data
collected Before and After (BA) modification and the other was for other sites with
a Treatment and Control (TC) experimental design. For the BA data, there were significant
reductions in eggshells after modification. Eggshells were generally fewer after
modification in areas which were close to unrestricted tidal flushing. A sandy substrate
and vegetation changes which resulted in reduced Sporobolus virginicus or
mixed Sporobolus and Sarcocornia quinqueflora also contributed to the effect. In the TC experiment, there was no effect of modification at the runnelled site, eggshells were fewer at the OMWM site, but there were more eggshells at the grid‐ditched site. There was some general indication that recent oviposition activity was reduced in sites that had been modified, evidenced by a relatively small proportion of young (dark coloured) eggshells.
Abstract Background The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in ...non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from 'knocking down' expression of the actin gene. Conclusion This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals.
