Listeria hijacks host mitophagy through a novel mitophagy receptor to evade killing.

Cells use mitophagy to remove damaged or unwanted mitochondria to maintain homeostasis. Here we report that the intracellular bacterial pathogen Listeria monocytogenes exploits host mitophagy to evade killing. We found that L. monocytogenes induced mitophagy in macrophages through the virulence factor listeriolysin O (LLO). We discovered that NLRX1, the only Nod-like receptor (NLR) family member with a mitochondrial targeting sequence, contains an LC3-interacting region (LIR) and directly associated with LC3 through the LIR. NLRX1 and its LIR motif were essential for L. monocytogenes-induced mitophagy. NLRX1 deficiency and use of a mitophagy inhibitor both increased mitochondrial production of reactive oxygen species and thereby suppressed the survival of L. monocytogenes. Mechanistically, L. monocytogenes and LLO induced oligomerization of NLRX1 to promote binding of its LIR motif to LC3 for induction of mitophagy. Our study identifies NLRX1 as a novel mitophagy receptor and discovers a previously unappreciated strategy used by pathogens to hijack a host cell homeostasis system for their survival.

PharmGWAS: a GWAS-based knowledgebase for drug repurposing.

Leveraging genetics insights to promote drug repurposing has become a promising and active strategy in pharmacology. Indeed, among the 50 drugs approved by FDA in 2021, two-thirds have genetically supported evidence. In this regard, the increasing amount of widely available genome-wide association studies (GWAS) datasets have provided substantial opportunities for drug repurposing based on genetics discoveries. Here, we developed PharmGWAS, a comprehensive knowledgebase designed to identify candidate drugs through the integration of GWAS data. PharmGWAS focuses on novel connections between diseases and small-molecule compounds derived using a reverse relationship between the genetically-regulated expression signature and the drug-induced signature. Specifically, we collected and processed 1929 GWAS datasets across a diverse spectrum of diseases and 724 485 perturbation signatures pertaining to a substantial 33609 molecular compounds. To obtain reliable and robust predictions for the reverse connections, we implemented six distinct connectivity methods. In the current version, PharmGWAS deposits a total of 740 227 genetically-informed disease-drug pairs derived from drug-perturbation signatures, presenting a valuable and comprehensive catalog. Further equipped with its user-friendly web design, PharmGWAS is expected to greatly aid the discovery of novel drugs, the exploration of drug combination therapies and the identification of drug resistance or side effects. PharmGWAS is available at https://ngdc.cncb.ac.cn/pharmgwas.

COLOCdb: a comprehensive resource for multi-model colocalization of complex traits.

Large-scale genome-wide association studies (GWAS) have provided profound insights into complex traits and diseases. Yet, deciphering the fine-scale molecular mechanisms of how genetic variants manifest to cause the phenotypes remains a daunting task. Here, we present COLOCdb (https://ngdc.cncb.ac.cn/colocdb), a comprehensive genetic colocalization database by integrating more than 3000 GWAS summary statistics and 13 types of xQTL to date. By employing two representative approaches for the colocalization analysis, COLOCdb deposits results from three key components: (i) GWAS-xQTL, pair-wise colocalization between GWAS loci and different types of xQTL, (ii) GWAS-GWAS, pair-wise colocalization between the trait-associated genetic loci from GWASs and (iii) xQTL-xQTL, pair-wise colocalization between the genetic loci associated with molecular phenotypes in xQTLs. These results together represent the most comprehensive colocalization analysis, which also greatly expands the list of shared variants with genetic pleiotropy. We expect that COLOCdb can serve as a unique and useful resource in advancing the discovery of new biological mechanisms and benefit future functional studies.

Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits.

A broad range of complex phenotypes are related to dysfunctions in brain (hereafter referred to as brain-related traits), including various mental and behavioral disorders and diseases of the nervous system. These traits in general share overlapping symptoms, pathogenesis, and genetic components. Here, we present Brain Catalog (https://ngdc.cncb.ac.cn/braincatalog), a comprehensive database aiming to delineate the genetic components of more than 500 GWAS summary statistics datasets for brain-related traits from multiple aspects. First, Brain Catalog provides results of candidate causal variants, causal genes, and functional tissues and cell types for each trait identified by multiple methods using comprehensive annotation datasets (58 QTL datasets spanning 6 types of QTLs). Second, Brain Catalog estimates the SNP-based heritability, the partitioning heritability based on functional annotations, and genetic correlations among traits. Finally, through bidirectional Mendelian randomization analyses, Brain Catalog presents inference of risk factors that are likely causal to each trait. In conclusion, Brain Catalog presents a one-stop shop for the genetic components of brain-related traits, potentially serving as a valuable resource for worldwide researchers to advance the understanding of how GWAS signals may contribute to the biological etiology of brain-related traits.

Fever-induced acute sleep terrors in children and adolescents following SARS-CoV-2 infection.

OBJECTIVE: This study aims to provide physicians with insights into the clinical manifestations and outcomes of children and young adolescents experiencing sleep terrors following SARS-CoV-2 infection. METHODS: We enrolled patients who developed new onset sleep terrors after SARS-CoV-2infection fromDecember2022to April 2023 in the Xijing hospital, Xi'an, China. RESULTS: We enrolled six patients who experienced sleep terrors following SARS-CoV-2 infection. Out of these patients, five were children and only one was an adolescent, with a mean age of 9 years. Neuroimaging results were negative for all cases. Sleep terrors occurred during both the active course of COVID-19 illness and the recovery period in all patients. Symptoms included crying or screaming in terror, hyperactivity, inappropriate behavior and periods of mental confusion during sleep. These episodes typically occurred 40 min to 1 h after falling asleep. EEG monitoring confirmed two patients' episodes occurred during non-rapid eye movement (NREM) stage 3 sleep. The duration of sleep terrors ranged from 3mines to30 mines, with each patient experiencing 3-4 to 30-40 instances. Initially, the frequency of episodes was highest at 3-4 times per night, gradually decreasing to once a night, then once a week, until complete disappearance. No medical intervention was required. Clinical follow-up ranged from 6 to 12 months, with spontaneous remission occurring within 1 week to 2 months for different patients. CONCLUSION: SARS-CoV-2 infection may precipitate acute sleep terrors in children and adolescents. The course of these sleep terrors is generally benign, with all patients achieving spontaneous complete remission over time.

Machine learning-based mRNA signature in early acute myocardial infarction patients: the perspective toward immunological, predictive, and personalized.

Patients diagnosed with stable coronary artery disease (CAD) are at continued risk of experiencing acute myocardial infarction (AMI). This study aims to unravel the pivotal biomarkers and dynamic immune cell changes, from an immunological, predictive, and personalized viewpoint, by implementing a machine-learning approach and a composite bioinformatics strategy. Peripheral blood mRNA data from different datasets were analyzed, and CIBERSORT was used for deconvoluting human immune cell subtype expression matrices. Weighted gene co-expression network analysis (WGCNA) in single-cell and bulk transcriptome levels was conducted to explore possible biomarkers for AMI, with a particular emphasis on examining monocytes and their involvement in cell-cell communication. Unsupervised cluster analysis was performed to categorize AMI patients into different subtypes, and machine learning methods were employed to construct a comprehensive diagnostic model to predict the occurrence of early AMI. Finally, RT-qPCR on peripheral blood samples collected from patients validated the clinical utility of the machine learning-based mRNA signature and hub biomarkers. The study identified potential biomarkers for early AMI, including CLEC2D, TCN2, and CCR1, and found that monocytes may play a vital role in AMI samples. Differential analysis revealed that CCR1 and TCN2 exhibited elevated expression levels in early AMI compared to stable CAD. Machine learning methods showed that the glmBoost+Enet [alpha=0.9] model achieved high predictive accuracy in the training set, external validation sets, and clinical samples in our hospital. The study provided comprehensive insights into potential biomarkers and immune cell populations involved in the pathogenesis of early AMI. The identified biomarkers and the constructed comprehensive diagnostic model hold great promise for predicting the occurrence of early AMI and can serve as auxiliary diagnostic or predictive biomarkers.

Expanded Salinity Window of Middle-Phase Microemulsions and Reduced Surfactant Adsorption by Hydrotrope.

Using surfactant blends to mobilize residual oil offers a promising technique for enhanced oil recovery (EOR) and surfactant-enhanced aquifer remediation (SEAR). A major financial setback for broader application of this method is the loss of surfactants, as they get absorbed onto reservoir mineral surfaces. This loss becomes even more costly in oil fields with high-salinity formation water. Our research delved into the use of hydrotropes to minimize the surfactant absorption. The impacts of surfactant adsorption with hydrotrope additives were quantified and compared to three representative porous media. Initial tests studied the ideal salinity range influenced by hydrotropes with the observations of Winsor Type III microemulsions with selected surfactants, and four specific hydrocarbons were confirmed through interfacial tension measurements. When tested on three types of porous media, the presence of hydrotropes reduced the adsorption rates: up to 65% on Indiana limestone, 21% on Ottawa sand, and 53% on activated carbon. Notably, our study revealed urea's role in reducing surfactant retention in porous media. This discovery can help modify the salinity range of middle-phase microemulsions, which is crucial for EOR by easing salinity constraints of target reservoirs. The large middle-phase microemulsion window is also very advantageous for other potential applications. Moreover, urea proves to be more effective than typical sacrificial agents for reservoirs, as it binds the surfactant to the liquid rather than acting as a mere sacrificial component. Our research underscores the potential of improving surfactant flooding results by integrating hydrotropes, offering substantial cost savings in surfactant consumption and enhancing the overall efficiency of EOR and SEAR projects.

Short-term intensive fasting enhances the immune function of red blood cells in humans.

BACKGROUND: Fasting is known to influence the immune functions of leukocytes primarily by regulating their mobilization and redistribution between the bone marrow and the peripheral tissues or circulation, in particular via relocalization of leukocytes back in the bone marrow. However, how the immune system responds to the increased risk of invasion by infectious pathogens with fewer leukocytes in the peripheral blood during fasting intervention remains an open question. RESULTS: We used proteomic, biochemical and flow cytometric tools to evaluate the impact of short-term intensive fasting (STIF), known as beego, on red blood cells by profiling the cells from the STIF subjects before and after 6 days of fasting and 6 days of gradual refeeding. We found that STIF, by triggering the activation of the complement system via the complement receptor on the membrane of red blood cells, boosts fairly sustainable function of red blood cells in immune responses in close relation to various pathogens, including viruses, bacteria and parasites, particularly with the pronounced capacity to defend against SARS-CoV-2, without compromising their oxygen delivery capacity and viability. CONCLUSION: STIF fosters the immune function of red blood cells and therefore, it may be considered as a nonmedical intervention option for the stronger capacity of red blood cells to combat infectious diseases.

The association between sleep architecture, quality of life, and hypertension in patients with obstructive sleep apnea.

OBJECTIVE: The aim of this study was to investigate the association between hypertension and overnight polysomnography measures of sleep duration, sleep architecture, and quality of life (QoL) in patients with obstructive sleep apnea (OSA). METHODS: Participants were patients suspected of having OSA with or without hypertension. All patients underwent overnight polysomnography and completed the Epworth Sleepiness Scale (ESS), Self-Rating Anxiety Scale, Self-Rating Depression Scale, and 12-item Short-Form Health Survey. RESULTS: Of 128 patients (mean age 46.2 ± 12.5 years), 53% had hypertension. The average total sleep duration was 344 min (standard deviation 90) or 5.7 h and sleep efficiency was < 70%. There was no significant difference between patients with OSA with/without hypertension in total sleep duration, sleep architecture, anxiety, depression, ESS scores, or QoL. In patients with OSA, nocturnal minimum oxygen saturation was significantly negatively correlated with bodily pain and physical component summary (PCS) scores; mean nocturnal saturation was negatively correlated with bodily pain and social function; anxiety showed a significant negative correlation with role emotional; and depression was significantly negatively correlated with physical function, role physical, general health, role emotional, PCS, and mental component summary (MCS) scores. In the group with OSA and hypertension, N3 duration was negatively correlated with social function, mental health, and MCS scores. Anxiety was significantly negatively correlated with physical function, role physical, vitality, mental health, role emotional, PCS, and MCS scores. Depression was significantly negatively correlated with physical function, role physical, vitality, mental health, role emotional, PCS, and MCS scores. In patients with mild, moderate, and severe OSA, QoL was associated with depression. In mild OSA, PCS was correlated with ESS and anxiety. In moderate OSA, MCS was correlated with apnea-hypopnea index scores. In severe OSA, MCS and PCS were correlated with anxiety. CONCLUSIONS: There were no significant associations between the presence of hypertension and total sleep duration, sleep architecture, or QoL in patients with OSA. However, hypertension may affect the influencing factors of QoL in patients with OSA. Further cohort studies are needed to confirm these findings.

CircUsp9x/miR-599/stim1 axis regulates proliferation and migration in vascular smooth muscle cells induced by oxidized-low density lipoprotein.

Circular RNAs (circRNAs) regulate the function of vascular smooth muscle cells (VSMCs) in atherosclerosis (AS) progression. We aimed to explore the role of circUSP9X in oxidized low-density lipoprotein (ox-LDL)-induced VSMCs. Cell proliferation was assessed using cell counting kit-8 and EDU assays. Cell migration was evaluated using Transwell and wound healing assays. The interaction between circUSP9X or STIM1 and miR-599 was analyzed using dual-luciferase reporter and RNA pull-down assays. Their levels were examined using quantitative real-time PCR. CircUSP9X and STIM1 expression was increased, whereas miR-599 expression was reduced in the serum of patients with AS and ox-LDL-stimulated VSMCs. Overexpression of circUSP9X facilitated the proliferation and migration of VSMCs induced by ox-LDL. CircUSP9X sponged miR-599, which targeted STIM1. MiR-599 reversed the effects induced by circUSP9X, and STIM1 reversed the effects induced by miR-599. Taken together, CircUSP9X promoted proliferation and migration in ox-LDL-treated VSMCs via the miR-599/STIM1 axis, providing a theoretical basis for the role of circUSP9X/miR-599/STIM1 axis in AS.

Evidence for CAT gene being functionally involved in the susceptibility of COVID-19.

Novel coronary pneumonia (COVID-19) is a respiratory distress syndrome caused by a new type of coronavirus. Understanding the genetic basis of susceptibility and prognosis to COVID-19 is of great significance to disease prevention, molecular typing, prognosis, and treatment. However, so far, there have been only two genome-wide association studies (GWASs) on the susceptibility of COVID-19. Starting with these reported DNA variants, we found the genes regulated by these variants through cis-eQTL and cis-meQTL acting. We further did a series of bioinformatics analysis on these potential risk genes. The analysis shows that the genetic variants on EHF regulate the expression of its neighbor CAT gene via cis-eQTL. There was significant evidence that CAT and the SARS-CoV-2-related S protein binding protein ACE2 interact with each other. Intracellular localization results showed that CAT and ACE2 proteins both exists in the cell membrane and extracellular area and their interaction could have an impact on the cell invasion ability of S protein. In addition, the expression of these three genes showed a significant positive correlation in the lungs. Based on these results, we propose that CAT plays a crucial intermediary role in binding effectiveness of ACE2, thereby affecting the susceptibility to COVID-19.

Mn2O3 as an Electron Shuttle between Peroxymonosulfate and Organic Pollutants: The Dominant Role of Surface Reactive Mn(IV) Species.

The environmentally benign Mn oxides play a crucial role in the transformation of organic contaminants, either through catalytically decomposing oxidants, e.g., peroxymonosulfate (PMS), or through directly oxidizing the target pollutants. Because of their dual roles and the complex surface chemical reactions, the mechanism involved in Mn oxide-catalyzed PMS activation processes remains obscure. Here, we clearly elucidate the mechanism involved in the Mn2O3 catalyzed PMS activation process by means of separating the PMS activation and the pollutant oxidation process. Mn2O3 acts as a shuttle that mediates the electron transfer from organic substrates to PMS, accompanied by the redox cycle of surface Mn(IV)/Mn(III). Multiple experimental results indicate that PMS is bound to the surface of Mn2O3 to form an inner-sphere complex, which then decomposes to form long-lived surface reactive Mn(IV) species, without the generation of sulfate radicals (SO4•-) and hydroxyl radicals (HO•). The surface reactive Mn(IV) species are proposed to be responsible for the degradation of organic contaminants (e.g., phenol) and the formation of singlet oxygen (1O2), followed by the regeneration of the surface Mn(III) sites on Mn2O3. This study advances the fundamental understanding of the underlying mechanism involved in transition metal oxide-catalyzed PMS activation processes.

RETRACTED: CGVD: a genomic variation database for Chinese populations.

Precision medicine calls upon deeper coverage of population-based sequencing and thorough gene-content and phenotype-based analysis, which lead to a population-associated genomic variation map or database. The Chinese Genomic Variation Database (CGVD; https://bigd.big.ac.cn/cgvd/) is such a database that has combined 48.30 million (M) SNVs and 5.77 M small indels, identified from 991 Chinese individuals of the Chinese Academy of Sciences Precision Medicine Initiative Project (CASPMI) and 301 Chinese individuals of the 1000 Genomes Project (1KGP). The CASPMI project includes whole-genome sequencing data (WGS, 25-30×) from ∼1000 healthy individuals of the CASPMI cohort. To facilitate the usage of such variations for pharmacogenomics studies, star-allele frequencies of the drug-related genes in the CASPMI and 1KGP populations are calculated and provided in CGVD. As one of the important database resources in BIG Data Center, CGVD will continue to collect more genomic variations and to curate structural and functional annotations to support population-based healthcare projects and studies in China and worldwide.

ITGA7, CD133, ALDH1 are inter-correlated, and linked with poor differentiation, lymph node metastasis as well as worse survival in surgical cervical cancer.

AIM: Integrin alpha 7 (ITGA7) regulates cancer stemness and metastasis in several malignancies, while its role in cervical cancer is obscure. Therefore, the current study aimed to investigate the correlation among ITGA7, cluster of differentiation 133 (CD133), and aldehyde dehydrogenase isoform 1 (ALDH1), as well as their relation to tumor features and survival in cervical cancer patients. METHODS: A total of 133 surgical cervical cancer patients were enrolled. Tumor ITGA7, CD133, and ALDH1 expressions were determined by immunohistochemistry (IHC). Furthermore, the clinicopathological features, disease-free survival (DFS), and overall survival (OS) were collected. RESULTS: ITGA7 expression positively related to CD133 expression (p = 0.040) and ALDH1 expression (p < 0.001). Besides, ITGA7 (p = 0.001), CD133 (p = 0.016), and ALDH1 (p = 0.009) high expressions linked with poor tumor differentiation; meanwhile, ITGA7 (p = 0.010) and ALDH1 (p = 0.004) high expressions correlated with more prevalence of lymph node metastasis. However, ITGA7, CD133, or ALDH1 expression was not associated with other clinicopathological features. Inspiringly, it was worth noting that ITGA7 (p = 0.009), CD133 (p = 0.041), and ALDH1 (p = 0.035) high expressions predicted unfavorable DFS; meanwhile, both ITGA7 (p = 0.021) and ALDH1 (p = 0.023) high expressions but not CD133 expression (p = 0.169) forecasted exasperated OS. CONCLUSION: ITGA7, CD133, ALDH1 are inter-correlated, and linked with poor differentiation, lymph node metastasis as well as worse survival in surgical cervical cancer.

Novel cinnamic acid magnolol derivatives as potent α-glucosidase and α-amylase inhibitors: Synthesis, in vitro and in silico studies.

In this study, twenty novel cinnamic acid magnolol derivatives were synthesized, and screened for their anti-hyperglycemic potential. All synthesized compounds exhibited good to moderate α-glucosidase and α-amylase inhibitory activities with IC50 values: 5.11 ± 1.46-90.26 ± 1.85 µM and 4.27 ± 1.51-49.28 ± 2.54 µM as compared to the standard acarbose (IC50: 255.44 ± 1.89 µM and 80.33 ± 2.95 µM, respectively). Compound 6j showed the strongest inhibitory activity against α-glucosidase (IC50 = 5.11 ± 1.46 µM) and α-amylase (IC50 = 4.27 ± 1.51 µM). Kinetic study indicated that compound 6j was reversible and a mixed type inhibitor against α-glucosidase and α-amylase. In silico studies revealed the binding interaction between 6j and two enzymes, respectively. Finally, cells cytotoxicity assay revealed that compound 6j showed low toxicity against 3 T3-L1 cells and HepG2 cells.

Aberrant expression of HIF3A in plasma of patients with non-small cell lung cancer and its clinical significance.

BACKGROUND: Hypoxia-inducible factors (HIFs) have been evaluated in various cancers and diseases. However, the specific role of hypoxia-inducible factor 3 alpha (HIF3A) in non-small cell lung cancer (NSCLC) remains controversial. MATERIALS AND METHODS: We investigated HIF3A mRNA expression in the plasma and tumor tissues of patients with NSCLC and explored its clinical significance. Plasma samples from 103 cases of lung adenocarcinoma (LUAD) and 96 cases of lung squamous cell carcinoma (LUSC), and tumor-adjacent normal tissues from 58 LUAD and 62 LUSC cases were retrospectively evaluated at the No.8 People's Hospital of Qing Dao. HIF3A expression was explored using RT-qPCR. The clinical significance of HIF3A was evaluated in the plasma and tumor tissues using the receiver operating curve (ROC) and the area under the curve (AUC). RESULTS: Hypoxia-inducible factor 3 alpha expression was notably downregulated in the plasma or tumor tissues of patients with LUAD and LUSC, compared with the healthy control group or adjacent normal tissues. Furthermore, HIF3A expression had a significant positive correlation in the plasma and tumor tissues of LUAD and LUSC patients. Meanwhile, the ROC-AUCs achieved a significantly higher range, from 0.84 to 0.93, with the plasma or tumor tissues of NSCLC patients. Thus, HIF3A expression was not only correlated with plasma and tumor tissues, but also showed potential significance in NSCLC. CONCLUSION: Hypoxia-inducible factor 3 alpha is aberrantly detectable in NSCLC patients in the plasma and tumor tissues. HIF3A may be involved in hypoxic responses during the development and occurrence of NSCLC.

MiR-186-3p attenuates tumorigenesis of cervical cancer by targeting IGF1.

BACKGROUND: Mounting evidence in the cancer literature suggests that microRNAs (miRNAs) influence the progression of human cancer cells by targeting protein-coding genes. How insulin-like growth factor 1(IGF1) and miR-186-3p contribute to the development of cervical cancer (CC) remains unclear. This study examined the regulatory roles of miR-186-3p and IGF1 in CC development. METHODS: Gene expression levels were determined by qRT-PCR. Proliferation, migration, and apoptosis of CC and normal cells were determined by MTT, Transwell, and caspase-3 activity assays, respectively. Dual-luciferase reporter activity and RNA pull-down assays were performed to identify the target gene of miR-186-3p. RESULTS: IGF1 was the target of miR-186-3p. The expression of miR-186-3p inhibited cell proliferation and migration abilities of CC cell lines, but induced the apoptosis rate of CC cells. IGF1 could restore the inhibitory effects of miR-186-3p on the proliferation, migration, and apoptosis abilities of CC cells. Experimental results revealed that miR-186-3p could inhibit IGF1 expression, thereby reducing the viability of CC cells. CONCLUSIONS: The data suggest that targeting of IGF1 by miR-186-3p could be crucial in regulating the progression of CC.

De novo transcriptome assembly and population genetic analyses of an important coastal shrub, Apocynum venetum L.

BACKGROUND: Apocynum venetum L. is an important medicinal plant that is mainly distributed in the coastal areas and northwest of China. In addition to its high medical and economic value, its adaptation to saline-alkali and coastal saline lands makes A. venetum an ideal candidate for use in vegetation restoration. To date, the study of A. venetum has been limited in the northwest region of China, little attention has been paid to the genetic diversity and population structure of A. venetum populations in the coastal region. Here, we performed transcriptome sequencing of total RNA from A. venetum leaves and developed efficient expressed sequence tag-simple sequence repeat (EST-SSR) markers for analyzing the genetic diversity and population structure of A. venetum in the coastal region. RESULTS: A total of 86,890 unigenes were generated after de novo assembly, and 68,751 of which were successfully annotated by searching against seven protein databases. Furthermore, 14,072 EST-SSR loci were detected and 10,243 primer pairs were successfully designed from these loci. One hundred primer pairs were randomly selected and synthesized, twelve primer pairs were identified as highly polymorphic and further used for population genetic analysis. Population genetic analyses showed that A. venetum exhibited low level of genetic diversity (mean alleles per locus, NA = 3.3; mean expected heterozygosity, HE = 0.342) and moderate level of genetic differentiation among the populations (genetic differentiation index, FST = 0.032-0.220) in the coastal region. Although the contemporary (mean mc = 0.056) and historical (mean mh = 0.106) migration rates among the six A. venetum populations were moderate, a decreasing trend over the last few generations was detected. Bayesian structure analysis clustered six populations into two major groups, and genetic bottlenecks were found to have occurred in two populations (QG, BH). CONCLUSIONS: Using novel EST-SSR markers, we evaluated the genetic variation of A. venetum in the coastal region and determined conservation priorities based on these findings. The large dataset of unigenes and SSRs identified in our study, combining samples from a broader range, will support further research on the conservation and evolution of this important coastal plant and its related species.

Correction: Comprehensively benchmarking applications for detecting copy number variation.

[This corrects the article DOI: 10.1371/journal.pcbi.1007069.].

Comprehensively benchmarking applications for detecting copy number variation.

MOTIVATION: Recently, copy number variation (CNV) has gained considerable interest as a type of genomic variation that plays an important role in complex phenotypes and disease susceptibility. Since a number of CNV detection methods have recently been developed, it is necessary to help investigators choose suitable methods for CNV detection depending on their objectives. For this reason, this study compared ten commonly used CNV detection applications, including CNVnator, ReadDepth, RDXplorer, LUMPY and Control-FREEC, benchmarking the applications by sensitivity, specificity and computational demands. Taking the DGV gold standard variants as a standard dataset, we evaluated the ten applications with real sequencing data at sequencing depths from 5X to 50X. Among the ten methods benchmarked, LUMPY performs the best for both high sensitivity and specificity at each sequencing depth. For the purpose of high specificity, Canvas is also a good choice. If high sensitivity is preferred, CNVnator and RDXplorer are better choices. Additionally, CNVnator and GROM-RD perform well for low-depth sequencing data. Our results provide a comprehensive performance evaluation for these selected CNV detection methods and facilitate future development and improvement in CNV prediction methods.