BackgroundAn emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.ResultsThe assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.ConclusionAs the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users.
BackgroundThe Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited.FindingsA total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %.ConclusionsWe report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.
Ferroelectricity and metallicity are usually believed not to coexist because conducting electrons would screen out static internal electric fields. In 1965, Anderson and Blount proposed the concept of ''ferroelectric metal", however, it is only until recently that very rare ferroelectric metals were reported. Here, by combining high-throughput ab initio calculations and data-driven machine learning method with new electronic orbital based descriptors, we systematically investigated a large family (2964) of two-dimensional (2D) bimetal phosphates, and discovered 60 stable ferroelectrics with out-of-plane polarization, including 16 ferroelectric metals and 44 ferroelectric semiconductors that contain seven multiferroics. The ferroelectricity origins from spontaneous symmetry breaking induced by the opposite displacements of bimetal atoms, and the full-d-orbital coinage metal elements cause larger displacements and polarization than other elements. For 2D ferroelectric metals, the odd electrons per unit cell without spin polarization may lead to a half-filled energy band around Fermi level and is responsible for the metallicity. It is revealed that the conducting electrons mainly move on a single-side surface of the 2D layer, while both the ionic and electric contributions to polarization come from the other side and are vertical to the above layer, thereby causing the coexistence of metallicity and ferroelectricity. Van der Waals heterostructures based on ferroelectric metals may enable the change of Schottky barrier height or the Schottky-Ohmic contact type and induce a dramatic change of their vertical transport properties. Our work greatly expands the family of 2D ferroelectric metals and will spur further exploration of 2D ferroelectric metals.
Traditional trial-and-error methods are obstacles for large-scale searching of new optoelectronic materials. Here, we introduce a method combining high-throughput ab initio calculations and machine-learning approaches to predict two-dimensional octahedral oxyhalides with improved optoelectronic properties. We develop an effective machine-learning model based on an expansive dataset generated from density functional calculations including the geometric and electronic properties of 300 two-dimensional octahedral oxyhalides. Our model accelerates the screening of potential optoelectronic materials of 5,000 two-dimensional octahedral oxyhalides. The distorted stacked octahedral factors proposed in our model play essential roles in the machine-learning prediction. Several potential two-dimensional optoelectronic octahedral oxyhalides with moderate band gaps, high electron mobilities, and ultrahigh absorbance coefficients are successfully hypothesized. Supporting information Available: The computational methods, gradient boosted regression, model evaluation, initial features with definition, feature reduction, algorithm selection, comparison with various feature combinations, comparison between Machine-learning-predicted and DFT-calculated band gaps, structural details, electronic structures, phonon dispersions, AIMD evolutions, and carrier mobility. (PDF)
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