Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness

Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success.

The Asteraceae (Compositae), a large plant family of approximately 24 000-35 000 species, accounts for $10% of all angiosperm species and contributes a lot to plant diversity. The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.) that diversified through reticulate evolution. Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication (WGD) or polyploidization and locally repetitive genome expansion. However, the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification. Here, we used Oxford Nanopore long-read technology to sequence the diploid Chrysanthemum nankingense genome, which represents one of the progenitor genomes of domesticated chrysanthemums. Our analysis revealed that the evolution of the C. nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recent WGD that distinguishes chrysanthemum from sunflower, which diverged from chrysanthemum approximately 38.8 million years ago. Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication. Collectively, our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants, and also to accelerate their breeding and improvement.

BackgroundElevated plasma homocysteine (Hcy) levels have been indicated as a strong and modifiable risk factor of ischemic stroke; the previous studies have shown that exposure to Hcy activates cultured microglia. However, whether neurotoxicity of Hcy involves microglia activation following brain ischemia and the underlying mechanisms remains incompletely understood.MethodsThe cerebral damage was evaluated by staining with 2,3,5-triphenyltetrazolium chloride, hematoxylin-eosin, and Fluoro Jade B. The activation state of microglia was assessed via immunoreaction using the microglial markers Iba1 and OX-42. Then, the inflammatory factors such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and phosphorylated signal transducer and activator of transcription 3 (pSTAT3) were examined by Western blot analysis and fluorescence immunohistochemistry.ResultsElevated Hcy level augmented brain damage and neural cell toxicity in the brain cortex and the dentate gyrus region of the hippocampus after cerebral ischemia/reperfusion. Meanwhile, Hcy activated microglia and induced the expression of the inflammatory factors such as TNF-α and IL-6. Moreover, Hcy caused an increase in pSTAT3 expression which occurs in microglial cells. AG490, a JAK2-STAT3 inhibitor, effectively inhibited the phosphorylation of STAT3, microglial cell activation and the secretion of IL-6, TNF-α raised by Hcy treatment.ConclusionsSTAT3 signaling pathway located in microglia plays a critical role in mediating Hcy-induced activation of microglia and neuroinflammation in rat MCAO model. This suggests the feasibility of targeting the JAK2/STAT3 pathway as an effective therapeutic strategy to alleviate the progression of Hcy-associated ischemia stroke.Electronic supplementary materialThe online version of this article (10.1186/s12974-017-0963-x) contains supplementary material, which is available to authorized users.

Various studies have evaluated the significance of PTEN (phosphatase and tensin homolog deleted from chromosome 10) expression in breast cancer, but their results remain controversial. We conducted a meta-analysis to evaluate the associations of PTEN expression with clinicopathological characteristics and prognosis in breast cancer. PubMed, Embase, Web of Science, and China National Knowledge Infrastructure were searched to identify relevant publications. The associations between PTEN expression and clinicopathological parameters, disease-free survival (DFS), and overall survival (OS) were then assessed via meta-analyses of odds ratio (ORs) and hazard ratio (HRs) with 95% confidence intervals (CIs). Based on 27 studies involving 10,231 patients, the pooled results revealed that PTEN loss was significantly more common in breast cancer than in normal tissues (OR = 12.15, 95% CI = 6.48–22.79, P < 0.00001) and that PTEN loss had clear associations with larger tumor size (> 2 cm, OR = 0.62, 95% CI = 0.48–0.82, P = 0.0006), lymph node metastasis(OR = 0.61, 95% CI = 0.45–0.82, P = 0.0001), later TNM stage(stage III–IV, OR = 0.55, 95% CI = 0.35–0.86, P = 0.009), poor differentiation(OR = 0.37, 95% CI = 0.24–0.59, P < 0.0001), and the highly aggressive triple-negative phenotype (OR = 1.62, 95% CI = 1.23–2.12, P = 0.0005). Moreover, patients with PTEN loss exhibited significantly worse DFS and OS(HR = 1.63, 95% CI = 1.04–2.22, P < 0.00001; HR = 1.41, 95% CI = 1.08–1.73, P < 0.0001; respectively). In conclusion, PTEN loss might predict more aggressive behavior and worse outcomes in patients with breast cancer.

Aims  Little is known about the relation between the long-term joint exposure to various ambient air pollutants and the incidence of heart failure (HF). We aimed to assess the joint association of various air pollutants with HF risk and examine the modification effect of the genetic susceptibility. Methods and results  This study included 432 530 participants free of HF, atrial fibrillation, or coronary heart disease in the UK Biobank study. All participants were enrolled from 2006 to 2010 and followed up to 2018. The information on particulate matter (PM) with diameters ≤2.5 µm (PM2.5), ≤10 µm (PM10), and between 2.5 and 10 µm (PM2.5–10) as well as nitrogen oxides (NO2 and NOx) was collected. We newly proposed an air pollution score to assess the joint exposure to the five air pollutants through summing each pollutant concentration weighted by the regression coefficients with HF from single-pollutant models. We also calculated the weighted genetic risk score of HF. During a median of 10.1 years (4 346 642 person-years) of follow-up, we documented 4201 incident HF. The hazard ratios (HRs) [95% confidence interval (CI)] of HF for a 10 µg/m3 increase in PM2.5, PM10, PM2.5–10, NO2, and NOx were 1.85 (1.34–2.55), 1.61 (1.30–2.00), 1.13 (0.80–1.59), 1.10 (1.04–1.15), and 1.04 (1.02–1.06), respectively. We found that the air pollution score was associated with an increased risk of incident HF in a dose–response fashion. The HRs (95% CI) of HF were 1.16 (1.05–1.28), 1.19 (1.08–1.32), 1.21 (1.09–1.35), and 1.31 (1.17–1.48) in higher quintile groups compared with the lowest quintile of the air pollution score (P trend &lt;0.001). In addition, we observed that the elevated risk of HF associated with a higher air pollution score was strengthened by the genetic susceptibility to HF. Conclusion  Our results indicate that the long-term joint exposure to various air pollutants including PM2.5, PM10, PM2.5–10, NO2, and NOx is associated with an elevated risk of incident HF in an additive manner. Our findings highlight the importance to comprehensively assess various air pollutants in relation to the HF risk.

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BackgroundThe effects of ambient particulate matter (PM) pollution on pneumonia in adults are inconclusive, and few scientific data on a national scale have been generated in low- or middle-income countries, despite their much higher PM concentrations. We aimed to examine the association between PM levels and hospital admissions for pneumonia in Chinese adults.Methods and findingsA nationwide time series study was conducted in China between 2014 and 2017. Information on daily hospital admissions for pneumonia for 2014–2017 was collected from the database of Urban Employee Basic Medical Insurance (UEBMI), which covers 282.93 million adults. Associations of PM concentrations and hospital admissions for pneumonia were estimated for each city using a quasi-Poisson regression model controlling for time trend, temperature, relative humidity, day of the week, and public holiday and then pooled by random-effects meta-analysis. Meta-regression models were used to investigate potential effect modifiers, including cities’ annual-average air pollutants concentrations, temperature, relative humidity, gross domestic product (GDP) per capita, and coverage rates by the UEBMI. More than 4.2 million pneumonia admissions were identified in 184 Chinese cities during the study period. Short-term elevations in PM concentrations were associated with increased pneumonia admissions. At the national level, a 10-μg/m3 increase in 3-day moving average (lag 0–2) concentrations of PM2.5 (PM ≤2.5 μm in aerodynamic diameter) and PM10 (PM ≤10 μm in aerodynamic diameter) was associated with 0.31% (95% confidence interval [CI] 0.15%–0.46%, P < 0.001) and 0.19% (0.11%–0.30%, P < 0.001) increases in hospital admissions for pneumonia, respectively. The effects of PM10 were stronger in cities with higher temperatures (percentage increase, 0.031%; 95% CI 0.003%–0.058%; P = 0.026) and relative humidity (percentage increase, 0.011%; 95% CI 0%–0.022%; P = 0.045), as well as in the elderly (percentage increase, 0.10% [95% CI 0.02%–0.19%] for people aged 18–64 years versus 0.32% [95% CI 0.22%–0.39%] for people aged ≥75 years; P < 0.001). The main limitation of the present study was the unavailability of data on individual exposure to PM pollution.ConclusionsOur findings suggest that there are significant short-term associations between ambient PM levels and increased hospital admissions for pneumonia in Chinese adults. These findings support the rationale that further limiting PM concentrations in China may be an effective strategy to reduce pneumonia-related hospital admissions.