[观点]的社会法的兴起

Humanity is in the early stages of the rise of social algorithms: programs that size us up, evaluate what we want, and provide a customized experience. This quiet but epic paradigm shift is fraught with social and policy implications. The evolution of Google exemplifies this shift. It began as a simple deterministic ranking system based on the linkage structure among Web sites—the model of algorithmic Fordism, where any color was fine as long as it was black (1). The current Google is a very different product, personalizing results (2) on the basis of information about past searches and other contextual information, like location. On page 1130 of this issue, Bakshy et al. (3) explore whether such personalized curation on Facebook prevents users from accessing posts presenting conflicting political views.

• http://www.sciencemag.org/content/348/6239/1090.abstract?rss=1

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[编辑]保持大量的线粒体基因组的选择

Author: Laura M. Zahn

• http://www.sciencemag.org/content/348/6239/1103.3.full?rss=1

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[研究]综合血清学分析人类使用合成的人类病毒

The human virome plays important roles in health and immunity. However, current methods for detecting viral infections and antiviral responses have limited throughput and coverage. Here, we present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 108 antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system.

• http://www.sciencemag.org/content/348/6239/aaa0698.abstract?rss=1

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[研究]针对使用新的griselimycins结核治疗DNAN

The discovery of Streptomyces-produced streptomycin founded the age of tuberculosis therapy. Despite the subsequent development of a curative regimen for this disease, tuberculosis remains a worldwide problem, and the emergence of multidrug-resistant Mycobacterium tuberculosis has prioritized the need for new drugs. Here we show that new optimized derivatives from Streptomyces-derived griselimycin are highly active against M. tuberculosis, both in vitro and in vivo, by inhibiting the DNA polymerase sliding clamp DnaN. We discovered that resistance to griselimycins, occurring at very low frequency, is associated with amplification of a chromosomal segment containing dnaN, as well as the ori site. Our results demonstrate that griselimycins have high translational potential for tuberculosis treatment, validate DnaN as an antimicrobial target, and capture the process of antibiotic pressure-induced gene amplification.

• http://www.sciencemag.org/content/348/6239/1106.abstract?rss=1

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[在facebook的思想不同的新闻和意见报告]曝光

Exposure to news, opinion, and civic information increasingly occurs through social media. How do these online networks influence exposure to perspectives that cut across ideological lines? Using deidentified data, we examined how 10.1 million U.S. Facebook users interact with socially shared news. We directly measured ideological homophily in friend networks and examined the extent to which heterogeneous friends could potentially expose individuals to cross-cutting content. We then quantified the extent to which individuals encounter comparatively more or less diverse content while interacting via Facebook’s algorithmically ranked News Feed and further studied users’ choices to click through to ideologically discordant content. Compared with algorithmic ranking, individuals’ choices played a stronger role in limiting exposure to cross-cutting content.

• http://www.sciencemag.org/content/348/6239/1130.summary?rss=1

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[报告]基因组特征的进化过渡从孤独的群居生活

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

• http://www.sciencemag.org/content/348/6239/1139.summary?rss=1

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[报告] 2.2Å分辨率冷冻电镜结构与细胞渗透β-半乳糖苷酶抑制剂复合物

Cryo–electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-d-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM.

• http://www.sciencemag.org/content/348/6239/1147.summary?rss=1

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你失去的比我更好：神经网络参与获奖和在实时严格竞争博弈失去

Many situations in daily life require competing with others for the same goal. In this case, the joy of winning is tied to the fact that the rival suffers. In this fMRI study participants played a competitive game against another player, in which every trial had opposite consequences for the two players (i.e., if one player won, the other lost, or vice versa). Our main aim was to disentangle brain activation for two different types of winning. Participants could either win a trial in a way that it increased their payoff; or they could win a trial in a way that it incurred a monetary loss to their opponent. Two distinct brain networks were engaged in these two types of winning. Wins with a monetary gain activated the ventromedial prefrontal cortex, an area associated with the processing of rewards. In contrast, avoidance of loss/other-related monetary loss evoked activation in areas related to mentalizing, such as the temporo-parietal junction and precuneus. However, both types of winnings shared activation in the striatum. Our findings extend recent evidence from neuroeconomics by suggesting that we consider our conspecifics’ payoff even when we directly compete with them.

• http://feeds.nature.com/~r/srep/rss/current/~3/P4YTUext7Ng/srep11017

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贝塞尔梁车轴结构的样品

We report about a Bessel beam CARS approach for axial profiling of multi-layer structures. This study presents an experimental implementation for the generation of CARS by Bessel beam excitation using only passive optical elements. Furthermore, an analytical expression is provided describing the generated anti-Stokes field by a homogeneous sample. Based on the concept of coherent transfer functions, the underling resolving power of axially structured geometries is investigated. It is found that through the non-linearity of the CARS process in combination with the folded illumination geometry continuous phase-matching is achieved starting from homogeneous samples up to spatial sample frequencies at twice of the pumping electric field wave. The experimental and analytical findings are modeled by the implementation of the Debye Integral and scalar Green function approach. Finally, the goal of reconstructing an axially layered sample is demonstrated on the basis of the numerically simulated modulus and phase of the anti-Stokes far-field radiation pattern.

• http://feeds.nature.com/~r/srep/rss/current/~3/q_XDwGtIths/srep10991

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在活细胞的选择性识别唾液酸转移酶的活性无创成像

To elucidate the biological and pathological functions of sialyltransferases (STs), intracellular ST activity evaluation is necessary. Focusing on the lack of noninvasive methods for obtaining the dynamic activity information, this work designs a sensing platform for in situ FRET imaging of intracellular ST activity and tracing of sialylation process. The system uses tetramethylrhodamine isothiocyanate labeled asialofetuin (TRITC-AF) as a ST substrate and fluorescein isothiocyanate labeled 3-aminophenylboronic acid (FITC-APBA) as the chemoselective recognition probe of sialylation product, both of which are encapsulated in a liposome vesicle for cellular delivery. The recognition of FITC-APBA to sialylated TRITC-AF leads to the FRET signal that is analyzed by FRET efficiency images. This strategy has been used to evaluate the correlation of ST activity with malignancy and cell surface sialylation, and the sialylation inhibition activity of inhibitors. This work provides a powerful noninvasive tool for glycan biosynthesis mechanism research, cancer diagnostics and drug development.

• http://feeds.nature.com/~r/srep/rss/current/~3/w0b4ubehkCs/srep10947

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与钻石中的氮空缺中心解决单分子结构

We present theoretical proposals for two-dimensional nuclear magnetic resonance spectroscopy protocols based on Nitrogen-vacancy (NV) centers in diamond that are strongly coupled to the target nuclei. Continuous microwave and radio-frequency driving fields together with magnetic field gradients achieve Hartmann-Hahn resonances between NV spin sensor and selected nuclei for control of nuclear spins and subsequent measurement of their polarization dynamics. The strong coupling between the NV sensor and the nuclei facilitates coherence control of nuclear spins and relaxes the requirement of nuclear spin polarization to achieve strong signals and therefore reduced measurement times. Additionally, we employ a singular value thresholding matrix completion algorithm to further reduce the amount of data required to permit the identification of key features in the spectra of strongly sub-sampled data. We illustrate the potential of this combined approach by applying the protocol to a shallowly implanted NV center addressing a small amino acid, alanine, to target specific hydrogen nuclei and to identify the corresponding peaks in their spectra.

• http://feeds.nature.com/~r/srep/rss/current/~3/vXCHvJTIpxg/srep11007

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许多类使用递归自适应分区离散变量之间的互信息

Mutual information, a general measure of the relatedness between two random variables, has been actively used in the analysis of biomedical data. The mutual information between two discrete variables is conventionally calculated by their joint probabilities estimated from the frequency of observed samples in each combination of variable categories. However, this conventional approach is no longer efficient for discrete variables with many categories, which can be easily found in large-scale biomedical data such as diagnosis codes, drug compounds, and genotypes. Here, we propose a method to provide stable estimations for the mutual information between discrete variables with many categories. Simulation studies showed that the proposed method reduced the estimation errors by 45 folds and improved the correlation coefficients with true values by 99 folds, compared with the conventional calculation of mutual information. The proposed method was also demonstrated through a case study for diagnostic data in electronic health records. This method is expected to be useful in the analysis of various biomedical data with discrete variables.

• http://feeds.nature.com/~r/srep/rss/current/~3/jliL5GFdHkI/srep10981

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通过集成的决策确定超声与乳腺癌分子亚型的临床特征

Breast cancer is molecularly heterogeneous and categorized into four molecular subtypes: Luminal-A, Luminal-B, HER2-amplified and Triple-negative. In this study, we aimed to apply an ensemble decision approach to identify the ultrasound and clinical features related to the molecular subtypes. We collected ultrasound and clinical features from 1,000 breast cancer patients and performed immunohistochemistry on these samples. We used the ensemble decision approach to select unique features and to construct decision models. The decision model for Luminal-A subtype was constructed based on the presence of an echogenic halo and post-acoustic shadowing or indifference. The decision model for Luminal-B subtype was constructed based on the absence of an echogenic halo and vascularity. The decision model for HER2-amplified subtype was constructed based on the presence of post-acoustic enhancement, calcification, vascularity and advanced age. The model for Triple-negative subtype followed two rules. One was based on irregular shape, lobulate margin contour, the absence of calcification and hypovascularity, whereas the other was based on oval shape, hypovascularity and micro-lobulate margin contour. The accuracies of the models were 83.8%, 77.4%, 87.9% and 92.7%, respectively. We identified specific features of each molecular subtype and expanded the scope of ultrasound for making diagnoses using these decision models.

• http://feeds.nature.com/~r/srep/rss/current/~3/XLrpHD38Als/srep11085

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呆在一个β倒塌/单体40的构象平衡和β42扩展变化概率

In present study, we set out to investigate the conformation dynamics of Aβ40 and Aβ42 through exploring the impact of intra-molecular interactions on conformation dynamics using equilibrium molecular dynamics simulations. Our 40 microsecond-scale simulations reveal heterogeneous conformation ensembles of Aβ40 and Aβ42 that encompass ~35% β-strand and ~60% unstructured coils. Two conformational states were identified in both alloforms: a collapsed state (CS) that resembles the structural motif of face-to-face hydrophobic clustering in amyloid fibrils, and an extended state (ES) that features the structural characteristics of anti-parallel β-sheets in amyloid oligomers. In Aβ40, the C-terminus remains unstructured and rarely interacts with other parts, thereof the hydrophobic clustering is in loose contact and the peptide assumes ES with high probability. In contrast, the C-terminus of Aβ42 adopts a β-strand structure that strongly interacts with segments E3-R5 and V18-A21. The active association leads to a more compact hydrophobic collapse and refrain the alloform from ES. Based on the structural characterization, we propose that the fibril and oligomer assembly pathways could respectively take off from CS and ES, and their aggregation propensity may be governed by the probability of visiting the corresponding conformational states at the equilibrium.

• http://feeds.nature.com/~r/srep/rss/current/~3/KYyLCwtzjNg/srep11024

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DNA双链断裂改变同源基因在植物细胞中的空间布局

Chromatin dynamics and arrangement are involved in many biological processes in nuclei of eukaryotes including plants. Plants have to respond rapidly to various environmental stimuli to achieve growth and development because they cannot move. It is assumed that the alteration of chromatin dynamics and arrangement support the response to these stimuli; however, there is little information in plants. In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO/LacI-EGFP system and simulation analysis. It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. These results suggest that homologous loci approach each other to repair DSBs, and AtRAD54 mediates these phenomena.

• http://feeds.nature.com/~r/srep/rss/current/~3/Zu5YYxNQo_g/srep11058

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EGCG对非小细胞肺癌JWA和拓扑异构酶IIα之间的串扰（NSCLC）细胞

(-)-epigallocatechin-3-gallate (EGCG) is a well-known cancer chemopreventive agent. The potential mechanisms include regulation of multiple molecules. Carcinogenesis in lung cancer is related to the imbalance of tumor suppressor and oncogene. JWA is a structurally novel microtubule-binding protein and is a potential tumor suppressor. DNA topoisomerase IIα is a nuclear enzyme that governs DNA topology and is usually highly expressed in many types of cancer. It serves as a target of anticancer drugs. In the current study, the regulation of JWA and topoisomerase IIα by EGCG, and thereafter the mutual interaction between them was investigated. The results revealed that EGCG up-regulated JWA while decreased topoisomerase IIα expression in both human non-small cell lung cancer (NSCLC) cells and an NSCLC xenograft mice model. There was a negative correlation between JWA and topoisomerase IIα in NSCLC as well as in human NSCLC tissue specimens. Topoisomerase IIα overexpression reduced JWA at the translational level. Meanwhile, JWA-induced topoisomerase IIα degradation was regulated both in the transcriptional and post-translational level. Interestingly, JWA and topoisomerase IIα regulated each other in the cells arrested in G2/M. Furthermore, JWA and topoisomerase IIα synergistically affected NCI-H460 cells invasion. These results may serve a novel mechanism for cancer prevention.

• http://feeds.nature.com/~r/srep/rss/current/~3/mrUEgTM0VKU/srep11009

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染色体水平的基因图谱的药用真菌，灵芝提供了不同的防御机制

Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms.

• http://feeds.nature.com/~r/srep/rss/current/~3/rqma4Y5Dn7Y/srep11087

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小的组织样本的一个有效的质膜蛋白质组学的方法

Advancing the quest for new drug targets demands the development of innovative plasma membrane proteome research strategies applicable to small, functionally defined tissue samples. Biotinylation of acute tissue slices and streptavidin pull-down followed by shotgun proteomics allowed the selective extraction and identification of >1,600 proteins of which >60% are associated with the plasma membrane, including (G-protein coupled) receptors, ion channels and transporters, and this from mm3-scale tissue.

• http://feeds.nature.com/~r/srep/rss/current/~3/hUqlJLZ7EBA/srep10917

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控制杂草的新策略：选择有价值的乡土植物来打败他们

To explore replacement control of the invasive weed Ipomoea cairica, we studied the competitive effects of two valuable natives, Pueraria lobata and Paederia scandens, on growth and photosynthetic characteristics of I. cairica, in pot and field experiments. When I. cairica was planted in pots with P. lobata or P. scandens, its total biomass decreased by 68.7% and 45.8%, and its stem length by 33.3% and 34.1%, respectively. The two natives depressed growth of the weed by their strong effects on its photosynthetic characteristics, including suppression of leaf biomass and the abundance of the CO2-fixing enzyme RUBISCO. The field experiment demonstrated that sowing seeds of P. lobata or P. scandens in plots where the weed had been largely cleared produced 11.8-fold or 2.5-fold as much leaf biomass of the two natives, respectively, as the weed. Replacement control by valuable native species is potentially a feasible and sustainable means of suppressing I. cairica.

• http://feeds.nature.com/~r/srep/rss/current/~3/rmHIO8fmI60/srep11004

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用单光子ququart演示量子置换算法

We report an experiment to demonstrate a quantum permutation determining algorithm with linear optical system. By employing photon's polarization and spatial mode, we realize the quantum ququart states and all the essential permutation transformations. The quantum permutation determining algorithm displays the speedup of quantum algorithm by determining the parity of the permutation in only one step of evaluation compared with two for classical algorithm. This experiment is accomplished in single photon level and the method exhibits universality in high-dimensional quantum computation.

• http://feeds.nature.com/~r/srep/rss/current/~3/v0NnoJB6LYI/srep10995

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多维TOF-SIMS分析有效分析疾病相关的离子从组织表面

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

• http://feeds.nature.com/~r/srep/rss/current/~3/LnbjGUm5Pbo/srep11077

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激光引起的热效应可引起触觉

Humans process a plethora of sensory information that is provided by various entities in the surrounding environment. Among the five major senses, technology for touch, haptics, is relatively young and has relatively limited applications largely due to its need for physical contact. In this article, we suggest a new way for non-contact haptic stimulation that uses laser, which has potential advantages such as mid-air stimulation, high spatial precision, and long working distance. We demonstrate such tactile stimulation can be enabled by laser-induced thermoelastic effects by means of physical and perceptual studies, as well as simulations. In the physical study, the mechanical effect of laser on a human skin sample is detected using low-power radiation in accordance with safety guidelines. Limited increases (< ~2.5 °C) in temperature at the surface of the skin, examined by both thermal camera and the Monte Carlo simulation, indicate that laser does not evoke heat-induced nociceptive sensation. In the human EEG study, brain responses to both mechanical and laser stimulation are consistent, along with subjective reports of the non-nociceptive sensation of laser stimuli.

• http://feeds.nature.com/~r/srep/rss/current/~3/VZMHLQg8fVg/srep11016

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加强抗菌活性的天然提取的合成超小型金属纳米粒子

The use of Catechin as an antibacterial agent is becoming ever-more common, whereas unstable and easy oxidation, have limited its application. A simple and low-energy-consuming approach to synthesize highly stable and dispersive Catechin-Cu nanoparticles(NPs) has been developed, in which the stability and dispersivity of the NPs are varied greatly with the pH value and temperature of the reaction. The results demonstrate that the optimal reaction conditions are pH 11 at room temperature. As-synthesized NPs display excellent antimicrobial activity, the survival rates of bacterial cells exposed to the NPs were evaluated using live/dead Bacterial Viability Kit. The results showed that NPs at the concentration of 10 ppm and 20 ppm provided rapid and effective killing of up to 90% and 85% of S. aureus and E. coli within 3 h, respectively. After treatment with 20 ppm and 40 ppm NPs, the bacteria are killed completely. Furthermore, on the basis of assessing the antibacterial effects by SEM, TEM, and AFM, it was found the cell membrane damage of the bacteria caused by direct contact of the bacteria with the NPs was the effective mechanism in the bacterial inactivation.

• http://feeds.nature.com/~r/srep/rss/current/~3/HlgXuhuu15E/srep11033

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从头组装和美洲大蠊的EST-SSR标记睾丸转录组和发展特征

The cockroach Periplaneta americana is a notorious pest and threat to health worldwide, with a high reproductive ability. However, a limited amount of data is available on the developmental stage-specific transcriptomes of P. americana. To identify genes involved in developmental processes and to develop additional SSR markers in P. americana, we carried out de novo assembly of the P. americana transcriptome using Illumina sequencing. After removing low-quality sequences, we obtained 64,954,709 contigs, which were further assembled into 125,390 unigenes with an average length of 711 bp. Based on similarity searches against known proteins, we identified 48,300 unigenes based on a cut-off E-value of 10−5. The assembled sequences were annotated according to gene descriptions, gene ontology and clusters of orthologous groups. A total of 14,195 potential SSRs were identified, and 41 of 63 randomly chosen primer pairs successfully amplified the predicted SSR markers, seven of which were polymorphic in size in P. americana. Furthermore, the Spag6 gene was confirmed to be testes specific, and the fru and RPSA genes were related to the development of the testis. This is the special report of a P. americana transcriptome obtained using Illumina sequencing technology, and a large number of molecular markers were developed.

• http://feeds.nature.com/~r/srep/rss/current/~3/ZRT-Rxt5Mcs/srep11144

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