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ImportanceHypertension remains the major cardiovascular disease risk factor globally, but variability in measured blood pressure may result in suboptimal management. Whether genetic contributors to elevated blood pressure may complementarily inform cardiovascular disease risk assessment is unknown.ObjectiveTo examine incident cardiovascular disease by blood pressure polygenic risk score independent of measured blood pressures and antihypertensive medication prescriptions.Design, Setting, and ParticipantsThe cohort study (UK Biobank) recruited UK residents aged 40 to 69 years between March 2006 and August 2010. Participants without a prior physician diagnosis of cardiovascular disease, including myocardial infarction, stroke, or heart failure, were included. Excluded were individuals with mismatch between self-reported and genotypically inferred sex, sex aneuploidy, missing genotype rates of 1% or greater, and excess genotypic heterozygosity. Data analyses were performed from September 25, 2021, to July 21, 2022.ExposuresMeasured blood pressure and externally derived blood pressure polygenic risk score stratified by hypertension diagnosis and management, which included normal blood pressure (Main Outcomes and MeasuresComposite of first incident myocardial infarction, stroke, heart failure, or cardiovascular-related death.ResultsOf the 331 078 study participants included (mean [SD] age at enrollment, 56.9 [8.1] years; 178 824 female [54.0%]), 83 094 (25.1%) had normal blood pressure, 197 597 (59.7%) had untreated hypertension, and 50 387 (15.2%) had treated hypertension. Over a median (IQR) follow-up of 11.1 (10.4-11.8) years, the primary outcome occurred in 15 293 participants. Among those with normal blood pressure, untreated hypertension, and treated hypertension, each SD increase in measured systolic blood pressure was associated with hazard ratios of 1.08 (95% CI, 0.93-1.25), 1.20 (95% CI, 1.16-1.23), and 1.16 (95% CI, 1.11-1.20), respectively, for the primary outcome. Among these same categories, each SD increase in genetically predicted systolic blood pressure was associated with increased hazard ratios of 1.13 (95% CI, 1.05-1.20), 1.04 (95% CI, 1.01-1.07), and 1.06 (95% CI, 1.02-1.10), respectively, for the primary outcome independent of measured blood pressures and other covariates. Findings were similar for measured and genetically predicted diastolic blood pressure.Conclusions and RelevanceBlood pressure polygenic risk score may augment identification of individuals at heightened cardiovascular risk, including those with both normal blood pressure and hypertension. Whether it may also guide antihypertensive initiation or intensification requires further study.

In order to gain a comprehensive understanding of land system changes and regional sustainable development, it is crucial to explore the spatiotemporal distributions of multiple land use functions (LUFs). Therefore, herein, considering the Yangtze River Delta urban agglomeration (YRDUA) as the research object, we constructed an evaluation system based on the perspective of production–living–ecological (PLE) land functions. Furthermore, the coupling coordination model, kernel density curve, trend surface analysis, and spatial autocorrelation model were used to examine the spatial and temporal characteristics of LUFs and their coupling coordination and analyze the spatial clustering of the coupling coordination effect in the urban agglomeration from 2005 to 2020. The following results were obtained: The level of PLE functions and its coupling coordination degree in the YRDUA have been improved in the study period, and the distribution of high value areas of different functions is diverse. In terms of the spatial distribution of the coupling coordination degree, the high value areas of production function (PF)–living function (LF) is distributed in “clusters”, the PF–ecological function (EF) demonstrated a single-polarized development structure, and the LF-EF exhibited a multi-core structure. The coupling coordination of the LUFs demonstrated a “high in the east and low in the west” pattern in the east–west direction and an inverted “U” shape in the north–south direction. Moreover, both high-value and low-value areas exhibited a clustering phenomenon, with an evident spatial positive correlation. The results of this study can serve as a reference for the integrated socioeconomic development of the Yangtze River Delta region and the sustainable development of urban land use.

Polygenic risk scores (PRS) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. Validation and transferability of existing PRS across independent datasets and diverse ancestries are limited, which hinders the practical utility and exacerbates health disparities. We propose PRSmix, a framework that evaluates and leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture. We applied PRSmix to 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% CI: [1.10; 1.3]; P-value = 9.17 × 10−5) and 1.19-fold (95% CI: [1.11; 1.27]; P-value = 1.92 × 10−6), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI: [1.40; 2.04]; P-value = 7.58 × 10−6) and 1.42-fold (95% CI: [1.25; 1.59]; P-value = 8.01 × 10−7) in European and South Asian ancestries, respectively. Compared to the previously established cross-trait-combination method with scores from pre-defined correlated traits, we demonstrated that our method can improve prediction accuracy for coronary artery disease up to 3.27-fold (95% CI: [2.1; 4.44]; P-value after FDR correction = 2.6 × 10−4). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.

Clonal hematopoiesis of indeterminate potential (CHIP) is associated with an increased risk of cardiovascular diseases (CVD), putatively via inflammasome activation. We pursued an inflammatory gene modifier scan for CHIP-associated CVD risk among 424,651 UK Biobank participants. CHIP was identified using whole exome sequencing data of blood DNA and modeled both as a composite and for common drivers (DNMT3A, TET2, ASXL1, andJAK2) separately. We developed predicted gene expression scores for 26 inflammasome-related genes and assessed how they modify CHIP-associated CVD risk. We identifyIL1RAPas a potential key molecule for CHIP-associated CVD risk across genes and increasedAIM2gene expression leading to heightenedJAK2- andASXL1-associated CVD risks. We show that CRISPR-inducedAsxl1mutated murine macrophages have a particularly heightened inflammatory response to AIM2 agonism. Our study provides new evidence to support gene-specific strategies to address CHIP-associated CVD risk.

Introduction: Hypertension remains the major cardiovascular disease (CVD) risk factor, but variability in blood pressure (BP) may result in suboptimal management. Whether genetic contributors to high BP complementarily inform CVD risk assessment is unknown. We examined CVD risk by BP polygenic risk score (PRS) independent of measured BPs and antihypertensives. Methods: A total of 331,078 unrelated UK Biobank study participants without prior cardiovascular disease were studied. Exposures included measured BP and BP PRS stratified by normal BP (systolic BP [SBP] Results: Of the 331,078 study participants (mean [SD] age at enrollment, 56.9 [8.1] years, and female sex, 178,824 [54.0%]), 83,094 (25.1%) had normal BP, 197,597 (59.7%) had untreated hypertension, and 50,387 (15.2%) had treated hypertension. Over a median follow-up of 11.1 years (IQR, 10.4-11.8), CVD occurred in 15,293 participants. Among normal BP, untreated hypertension, and treated hypertension, a 10 mmHg higher measured SBP was associated with HRs of 1.05 (95% CI, 0.97-1.12), 1.12 (95% CI, 1.11-1.14), and 1.04 (95% CI, 1.02-1.06) for CVD. Among these same categories, a 10 mmHg higher genetically predicted SBP was associated with 1.31 (95% CI, 1.12-1.54), 1.09 (95% CI, 1.02-1.17), and 1.14 (95% CI, 1.05-1.25) increased HR for CVD independent of measured BPs. Conclusions: BP PRS may augment identification of individuals at heightened CVD risk, including those with both normal BP and hypertension.

Polygenic risk scores (PRS) have attenuated cross-population predictive performance. As existing genome-wide association studies (GWAS) were predominantly conducted in individuals of European descent, the limited transferability of PRS reduces its clinical value in non-European populations and may exacerbate healthcare disparities. Recent efforts to level ancestry imbalance in genomic research have expanded the scale of non-European GWAS, although they remain under-powered. Here we present a novel PRS construction method, PRS-CSx, which improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. PRS-CSx couples genetic effects across populations via a shared continuous shrinkage prior, enabling more accurate effect size estimation by sharing information between summary statistics and leveraging linkage disequilibrium (LD) diversity across discovery samples, while inheriting computational efficiency and robustness from PRS-CS. We show that PRS-CSx outperforms alternative methods across traits with a wide range of genetic architectures and cross-population genetic correlations in simulations, and substantially improves the prediction of quantitative traits and schizophrenia risk in non-European populations.

Polygenic risk scores (PRS) have attenuated cross-population predictive performance. As existing genome-wide association studies (GWAS) were predominantly conducted in individuals of European descent, the limited transferability of PRS reduces its clinical value in non-European populations and may exacerbate healthcare disparities. Recent efforts to level ancestry imbalance in genomic research have expanded the scale of non-European GWAS, although most of them remain under-powered. Here we present a novel PRS construction method, PRS-CSx, which improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. PRS-CSx couples genetic effects across populations via a shared continuous shrinkage prior, enabling more accurate effect size estimation by sharing information between summary statistics and leveraging linkage disequilibrium (LD) diversity across discovery samples, while inheriting computational efficiency and robustness from PRS-CS. We show that PRS-CSx outperforms alternative methods across traits with a wide range of genetic architectures, cross-population genetic overlaps and discovery GWAS sample sizes in simulations, and improves the prediction of quantitative traits and schizophrenia risk in non-European populations.

Polygenic risk scores (PRS) have attenuated cross-population predictive performance. As existing genome-wide association studies (GWAS) have been conducted predominantly in individuals of European descent, the limited transferability of PRS reduces their clinical value in non-European populations, and may exacerbate healthcare disparities. Recent efforts to level ancestry imbalance in genomic research have expanded the scale of non-European GWAS, although most remain underpowered. Here, we present a new PRS construction method, PRS-CSx, which improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. PRS-CSx couples genetic effects across populations via a shared continuous shrinkage (CS) prior, enabling more accurate effect size estimation by sharing information between summary statistics and leveraging linkage disequilibrium diversity across discovery samples, while inheriting computational efficiency and robustness from PRS-CS. We show that PRS-CSx outperforms alternative methods across traits with a wide range of genetic architectures, cross-population genetic overlaps and discovery GWAS sample sizes in simulations, and improves the prediction of quantitative traits and schizophrenia risk in non-European populations.

Multiple mRNA isoforms can be generated from a single gene locus through alternative splicing. Abnormality in alternative splicing has been linked to many human disorders. Here using RNA-seq data from 48 tissues from GTEx v7 release and summary statistics from GWAS of complex diseases and traits, we present a study to identify genomic variants regulating junction-skipping with the goal to understand their contribution to complex diseases and traits. For each tissue, we found 48 - 575 junction-skipping events regulated by genomic variants. We performed fine-mapping on both the junction-skipping association and 23 complex disease and trait associations and mapped them to 95% credible sets. We found 13 - 279 junction-skipping regulations were mapped to a credible set with ≤5 variants. On the genome-wide scale, we noted a clear disease-tissue specificity. Results from this approach provided critical insights into the functional mechanism of the genetic disease associations and contributed to our understanding of the genetic architecture of human complex disorders.

Background Brachydactyly type A1 (BDA1, OMIM 112500) is a rare inherited malformation characterized primarily by shortness or absence of middle bones of fingers and toes. It is the first recorded disorder of the autosomal dominant Mendelian trait. Indian hedgehog (IHH) gene is closely associated with BDA1, which was firstly mapped and identified in Chinese families in 2000. Previous studies have demonstrated that BDA1-related mutant IHH proteins affected interactions with its receptors and impaired IHH signaling. However, how the altered signaling pathway affects downstream transcriptional regulation remains unclear. Results Based on the mouse C3H10T1/2 cell model for IHH signaling activation, two recombinant human IHH-N proteins, including a wild type protein (WT, amino acid residues 28–202) and a mutant protein (MT, p.E95k), were analyzed. We identified 347, 47 and 4 Gli1 binding sites in the corresponding WT, MT and control group by chromatin immunoprecipitation and the overlapping of these three sets was poor. The putative cis regulated genes in WT group were enriched in sensory perception and G-protein coupled receptor-signaling pathway. On the other hand, putative cis regulated genes were enriched in Runx2-related pathways in MT group. Differentially expressed genes in WT and MT groups indicated that the alteration of mutant IHH signaling involved cell-cell signaling and cellular migration. Cellular assay of migration and proliferation validated that the mutant IHH signaling impaired these two cellular functions. Conclusions In this study, we performed integrated genome-wide analyses to characterize differences of IHH/Gli1 downstream regulation between wild type IHH signaling and the E95K mutant signaling. Based on the cell model, our results demonstrated that the E95K mutant signaling altered Gli1-DNA binding pattern, impaired downstream gene expressions, and leaded to weakened cellular proliferation and migration. This study may help to deepen the understanding of pathogenesis of BDA1 and the role of IHH signaling in chondrogenesis. Electronic supplementary material The online version of this article (10.1186/s12863-018-0697-5) contains supplementary material, which is available to authorized users.

Pathway Analysis of Predicted Gli1 target genes in WT. Top 25 pathway analysis of predicted Gli1 target genes in WT. (PDF 1618 kb)

Pathway Analysis of Predicted Gli1 target genes in MT. Top 25 pathway analysis of predicted Gli1 target genes in MT. (PDF 1633 kb)

Background As the scale and power of GWAS have increased to detect the small genetic effect sizes involved in complex polygenic traits, the results of GWAS, especially SNP effect size estimates, are increasingly utilised for prediction. A popular approach is the application of Polygenic Risk Scores (PRS). However, the effect size estimates are inherently prone to overfit the specific samples on which the GWAS were performed (e.g. “the Winner's Curse”). The inflation of effect size estimation reduces the out-of-sample accuracy of prediction based on GWAS results. Many shrinkage methods have been developed to correct for such inflation. As GWAS results and large individual genotype data sets become widely available, there is greater opportunity to accurately evaluate effect size inflation and compare the performance of different shrinkage methods. Methods We develop a novel permutation-based shrinkage method and compare its performance with previously developed methods based on local false discovery rate and the LASSO. We evaluate the performance of the methods across a wide range of phenotypes and investigate different factors (e.g. phenotype heritability) that influence their impact on the predictive power of polygenic risk scores. Results Using large-scale real genotype data, we show that SNP effect sizes are markedly overfit even in relatively large samples, but that our permutation-based shrinkage approach can improve PRS prediction dramatically. Discussion Our results suggest that GWAS results can be adjusted using an efficient empirical approach to provide more accurate effect size estimates and thus greater downstream predictive power. This approach could be applied to a wide variety of big data settings.

In this study, the performance of 33 Coupled Model Intercomparison Project 5 (CMIP5) global climate models (GCMs) in simulating precipitation over the Tibetan Plateau (TP) was assessed using data from 1961 to 2005 by an improved score-based method, which adopts multiple criteria to achieve a comprehensive evaluation. The future precipitation change was also estimated based on the Delta method by selecting the submultiple model ensemble (SMME) in the near-term (2006&ndash, 2050) and far future (2051&ndash, 2095) periods under Representative Concentration Pathways (RCP) scenarios RCP4.5 and RCP8.5. The results showed that most GCMs can reasonably simulate the precipitation pattern of an annual cycle, however, all GCMs overestimated the precipitation over TP, especially in spring and summer. The GCMs generally provide good simulations of the temporal characteristics of precipitation, while they did not perform as well in reproducing its spatial distributions. Different assessment criteria lead to inconsistent results, however, the improved rank score method, which adopts multiple criteria, provided a robust assessment of GCMs performance. The future annual precipitation was projected to increase by ~6% in the near-term with respect to the period 1961&ndash, 2005, whereas increases of 12.3% and 16.7% are expected in the far future under RCP4.5 and RCP8.5 scenarios, respectively. Similar spatial distributions of future precipitation changes can be seen in the near-term and far future periods under the two scenarios, and indicate that the most predominant increases occurred in the north of TP. The results of this study are expected to provide valuable information on climate change, and for water resources and agricultural management in TP.

In this study, we assessed the performance of 34 Coupled Model Intercomparison Project Phase 5 (CMIP5) general climate models (GCMs) for simulating the observed temperature over the Lower Mekong Basin (LMB) in 1961&ndash, 2004. An improved score-based method was used to rank the performance of the GCMs over the LMB. Two methods of multi-model ensemble (MME), sub-ensemble from the top 25% ranked GCMs and full ensemble from the entire GCMs, were calculated using arithmetic mean (AM) method and downscaled using the Delta method to project future temperature change during two future time periods, the near future (2006&ndash, 2049) and the far future (2050&ndash, 2093), under representative concentration pathways (RCP2.6, RCP4.5, and RCP8.5 scenarios) over the LMB. The improved score-based method combining multiple criteria showed a robust assessment of the GCMs performance over the LMB, which can provide good information for projecting future temperature change. The results showed a significant increase in temperature over the LMB under the two ensembles. However, there were differences in the magnitudes of the future temperature increase between the two ensemble methods, with a higher mean annual temperature increase from full ensemble and sub-ensemble at 1.26 &deg, C (1.09 &deg, C), 1.90 &deg, C (1.70 &deg, C), and 2.97 &deg, C (2.78 &deg, C) during 2050&ndash, 2093 under the RCP2.6, RCP4.5, and RCP8.5 scenarios compared to the values at 0.93 &deg, C (0.87 &deg, C), 0.99 &deg, C (0.95 &deg, C), and 1.09 &deg, C (1.06 &deg, C) during 2006&ndash, 2049, respectively, relative to the reference time period of 1961&ndash, 2004. In the future (2006&ndash, 2093), the temperature is likely to increase at 0.04 &deg, C, 0.16 &deg, C, and 0.37 &deg, C decade-1 under the RCP2.6, RCP4.5, and RCP8.5 scenarios by the sub-ensemble, while a higher temperature increase at 0.05 &deg, C, 0.17 &deg, C, and 0.39 &deg, C was found by the full ensemble over the LMB, relative to the reference time period of 1961&ndash, 2004. On the whole, the higher warming mainly occurred in the northern and central areas over the LMB, while the lower warming mainly occurred in the southeast and the southwest, especially under the RCP4.5 and RCP8.5 scenarios, with the warming increased with increasing RCP for both ensembles. Moreover, in order to reduce the uncertainty of temperature projection in further studies in the LMB, multiple methods of GCMs ensemble should be considered and compared.

Sand-binding vegetation is effective in stabilizing sand dunes and reducing soil erosion, thus helps minimize the detrimental effects of desertification. The aim of this study is to better understand the relationships between water and nutrient usage of sand-binding species, and the effects of succession and rainfall variability on plants’ water–nutrient interactions. We examined the effects of long-term succession (50 years), inter-annual rainfall variability (from 65% of the mean annual precipitation in 2004 to 42% in 2005) and seasonality on water–nutrient interactions of three major sand-binding species ( Artemisia ordosica , Hedysarum scoparium and Caragana korshinskii ) by measuring foliar δ 13 C, δ 15 N and [N]. Long-term succession in general did not significantly alter δ 13 C, δ 15 N and [N] of the three species. Short-term rainfall variability, however, significantly increased foliar δ 13 C levels of all three species by 1.0–1.8‰ during the severely dry year. No significant seasonal patterns were found in foliar δ 13 C and δ 15 N values of the three species, whereas foliar [N] varied by season. For the two leguminous shrubs, the correlations between δ 13 C and δ 15 N were positive in both sampling years, and the positive correlation between [N] and δ 13 C was only found in the severely dry year. The results indicate that these sand-binding plants have developed into a relatively stable stage and they are able to regulate their nitrogen and water use in responding to environmental conditions, which reinforces the effectiveness of plantation of native shrubs without irrigation in degraded areas. However, the results also indicate that short-term climate variability could have severe impact on the vegetation functions.

Variability in activity of CYP2C9, which is involved in the metabolism of approximately 15% of current therapeutic drugs, is an important contributor to interindividual differences in drug response. To evaluate the functional alternations of CYP2C9(*)2, CYP2C9(*)3, CYP2C9(*)8, CYP2C9(*)11 and CYP2C9(*)31, identified in our previous study in Chinese Han population, allelic variants as well as the wild-type CYP2C9 were transiently expressed in COS-7 cells. Kinetic parameters (Km, Vmax, and Clint) for S-warfarin 7-hydroxylation by these recombinant CYP2C9s were determined. Relative to CYP2C9.1, recombinant CYP2C9.3 and CYP2C9.11 exhibited significantly higher Km values, and all allelic variants showed significantly decreased Vmax and Clint values. Among all allelic variants, catalytic activity of CYP2C9.3 and CYP2C9.11 reduced the most (8.2% and 9.8% of Clint ratio, respectively; P0.001). These findings should be useful for predicting the phenotype profiles of CYP2C9 in Chinese Han population, comparing the functional results of these alleles accurately, and finally optimizing pharmacotherapy of drug treatment.

Epidermal growth factor receptor (EGFR) Tyrosine kinase inhibitor (TKI) is an effective targeted therapy for advanced non-small cell lung cancer (NSCLC) but also causes adverse drug reactions (ADRs) e.g., skin rash and diarrhea. SNPs in the EGFR signal pathway, drug metabolism/ transport pathways and miRNA might contribute to the interpersonal difference in ADRs but biomarkers for therapeutic responses and ADRs to TKIs in Chinese population are yet to be fully investigated. We recruited 226 Chinese advanced NSCLC patients who received TKIs erlotinib, gefitinib and icotinib hydrochloride and systematically studied the genetic factors associated with therapeutic responses and ADRs. Rs884225 (T > C) in EGFR 3′ UTR was significantly associated with lower risk of ADRs to erlotinib (p value = 0.0010, adjusted p value = 0.042). A multivariant interaction four-SNP model (rs884225 in EGFR 3′UTR, rs7787082 in ABCB1 intron, rs38845 in MET intron and rs3803300 in AKT1 5′UTR) was associated with ADRs in general and the more specific drug induced skin injury. The SNPs associated with both therapeutic responses and ADRs indicates they might share a common genetic basis. Our study provided potential biomarkers and clues for further research of biomarkers for therapeutic responses and ADRs in Chinese NSCLC patients.

Rare codons generally arrest translation due to rarity of their cognate tRNAs. This property of rare codons can be utilized to regulate protein expression. In this study, a linear relationship was found between expression levels of genes and copy numbers of rare codons inserted within them. Based on this discovery, we constructed a molecular device in Escherichia coli using the rare codon AGG, its cognate tRNA (tRNAArg (CCU)), modified tRNAAsp (GUC → CCU), and truncated aspartyl-tRNA synthetase (TDRS) to switch the expression of reporter genes on or off as well as to precisely regulate their expression to various intermediate levels. To underscore the applicability of our work, we used the rare codon device to alter the expression levels of four genes of the fatty acid synthesis II (FASII) pathway (i.e. fabZ, fabG, fabI, and tesA’) in E. coli to optimize steady-state kinetics, which produced nearly two-fold increase in fatty acid yield. Thus, the proposed method has potential applications in regulating target protein expression at desired levels and optimizing metabolic pathways by precisely tuning in vivo molar ratio of relevant enzymes.

Background Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella. Results The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades. Conclusions Prevotella intermedia ZT belongs to a genus marked with highly dynamic genomes. The specific genes of Prevotella intermedia indicate that adhesion, competing with surrounding microbes and horizontal gene transfer are the main drive of the evolution of Prevotella intermedia. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1272-3) contains supplementary material, which is available to authorized users.