BackgroundThere is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.FindingsTo overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.ConclusionsBenchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.Oceans cover approximately 71% of the Earth's surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species 1 . Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change 2,3 . As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world's oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation 4 . Understanding biomineralization and molluscan shell formation is, thus, a major area of interest 5 . Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more th...

Efforts to understand the influence of historical global warming on individual extreme climate events have increased over the past decade. However, despite substantial progress, events that are unprecedented in the local observational record remain a persistent challenge. Leveraging observations and a large climate model ensemble, we quantify uncertainty in the influence of global warming on the severity and probability of the historically hottest month, hottest day, driest year, and wettest 5-d period for different areas of the globe. We find that historical warming has increased the severity and probability of the hottest month and hottest day of the year at >80% of the available observational area. Our framework also suggests that the historical climate forcing has increased the probability of the driest year and wettest 5-d period at 57% and 41% of the observed area, respectively, although we note important caveats. For the most protracted hot and dry events, the strongest and most widespread contributions of anthropogenic climate forcing occur in the tropics, including increases in probability of at least a factor of 4 for the hottest month and at least a factor of 2 for the driest year. We also demonstrate the ability of our framework to systematically evaluate the role of dynamic and thermodynamic factors such as atmospheric circulation patterns and atmospheric water vapor, and find extremely high statistical confidence that anthropogenic forcing increased the probability of record-low Arctic sea ice extent. event attribution | climate extremes | climate change | global warming T he last decade has witnessed increasing interest in possible connections between historical global warming and individual extreme climate events (1-9). This interest is grounded in both scientific and practical motivations. First, extremes underlie many of the most acute stresses on natural and human systems (10, 11). Understanding the influence of historical warming on extremes is therefore critical for detecting climate change impacts (12, 13). Second, trends in the frequency and/or intensity of extremes have already been detected (10, 11), implying increasing probability of events that are unprecedented in the observed record. Third, continued global warming is likely to cause widespread emergence of unprecedented events in the future (e.g., refs. 10 and 14).Effective management of climate-related risks therefore requires robust quantification of the probability of extremes in the current and future climate (10). For example, quantification of risk and liability (8,15), and design of resilient infrastructure and resource management systems (16), must account for both historical nonstationarity and the likelihood of future changes. Similarly, the United Nations mechanisms for climate change compensation, adaptation, and preparation create a practical need to quantify the contribution of historical emissions to individual extreme events (e.g., ref. 17). Finally, connections between historical warming and individual events have b...

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Bulk-like molybdenum disulfide (MoS2) thin films were deposited on the surface of p-type Si substrates using dc magnetron sputtering technique and MoS2/Si p-n junctions were formed. The vibrating modes of E12g and A1g were observed from the Raman spectrum of the MoS2 films. The current density versus voltage (J-V) characteristics of the junction were investigated. A typical J-V rectifying effect with a turn-on voltage of 0.2 V was shown. In different voltage range, the electrical transporting of the junction was dominated by diffusion current and recombination current, respectively. Under the light illumination of 15 mW cm−2, the p-n junction exhibited obvious photovoltaic characteristics with a short-circuit current density of 3.2 mA cm−2 and open-circuit voltage of 0.14 V. The fill factor and energy conversion efficiency were 42.4% and 1.3%, respectively. According to the determination of the Fermi-energy level (∼4.65 eV) and energy-band gap (∼1.45 eV) of the MoS2 films by capacitance-voltage curve and ultraviolet-visible transmission spectra, the mechanisms of the electrical and photovoltaic characteristics were discussed in terms of the energy-band structure of the MoS2/Si p-n junctions. The results hold the promise for the integration of MoS2 thin films with commercially available Si-based electronics in high-efficient photovoltaic devices.

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