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Germline genetic regulation of the colorectal tumor immune microenvironment BMC Genomics (IF 4.4) Pub Date : 2024-04-25 Stephanie L. Schmit, Ya-Yu Tsai, Joseph D. Bonner, Rebeca Sanz-Pamplona, Amit D. Joshi, Tomotaka Ugai, Sidney S. Lindsey, Marilena Melas, Kevin J. McDonnell, Gregory E. Idos, Christopher P. Walker, Chenxu Qu, W. Martin Kast, Diane M. Da Silva, Jonathan N. Glickman, Andrew T. Chan, Marios Giannakis, Jonathan A. Nowak, Hedy S. Rennert, Harlan S. Robins, Shuji Ogino, Joel K. Greenson, Victor Moreno, Gad
To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC). Germline DNA samples
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Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance BMC Genomics (IF 4.4) Pub Date : 2024-04-25 Sidra Rahmat Ullah, Sidra Irum, Iqra Mahnoor, Humaira Ismatullah, Mariam Mumtaz, Saadia Andleeb, Abdur Rahman, Muhsin Jamal
Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected
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Effect of metabolically divergent pig breeds and tissues on mesenchymal stem cell expression patterns during adipogenesis BMC Genomics (IF 4.4) Pub Date : 2024-04-25 Siriluck Ponsuksili, Puntita Siengdee, Shuaichen Li, Wannapimol Kriangwanich, Michael Oster, Henry Reyer, Klaus Wimmers
Unraveling the intricate and tightly regulated process of adipogenesis, involving coordinated activation of transcription factors and signaling pathways, is essential for addressing obesity and related metabolic disorders. The molecular pathways recruited by mesenchymal stem cells (MSCs) during adipogenesis are also dependent on the different sources of the cells and genetic backgrounds of donors,
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PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Mingwei Liu, Fan Zhang, Huimin Lu, Hongzhang Xue, Xiaorui Dong, Zhikang Li, Jianlong Xu, Wensheng Wang, Chaochun Wei
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation
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Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Pavel Merkulov, Melania Serganova, Georgy Petrov, Vladislav Mityukov, Ilya Kirov
Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition
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RNA methylation patterns, immune characteristics, and autophagy-related mechanisms mediated by N6-methyladenosine (m6A) regulatory factors in venous thromboembolism BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Deshuai Zhang, Wenxia Fu, Shiwei Zhu, Yitong Pan, Ruogu Li
Recent studies have found a link between deep vein thrombosis and inflammatory reactions. N6-methyladenosine (m6A), a crucial element in immunological regulation, is believed to contribute to the pathophysiology of venous thromboembolism (VTE). However, how the m6A-modified immune microenvironment is involved in VTE remains unclear. In the present study, we identified a relationship between VTE and
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Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Weideng Wei, Xiaoqiang Xia, Taiwen Li, Qianming Chen, Xiaodong Feng
In recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited researchers, without such expertise, exploring information from scRNA-seq data. Therefore, there is a tremendous need to develop easy-to-use software, covering all
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Analysis and prediction of interactions between transmembrane and non-transmembrane proteins BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Chang Lu, Jiuhong Jiang, Qiufen Chen, Huanhuan Liu, Xingda Ju, Han Wang
Most of the important biological mechanisms and functions of transmembrane proteins (TMPs) are realized through their interactions with non-transmembrane proteins(nonTMPs). The interactions between TMPs and nonTMPs in cells play vital roles in intracellular signaling, energy metabolism, investigating membrane-crossing mechanisms, correlations between disease and drugs. Despite the importance of TMP-nonTMP
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Identification of different myofiber types in pigs muscles and construction of regulatory networks BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Chenchen Li, Yinuo Wang, Xiaohui Sun, Jinjin Yang, Yingchun Ren, Jinrui Jia, Gongshe Yang, Mingzhi Liao, Jianjun Jin, Xin’e Shi
Skeletal muscle is composed of muscle fibers with different physiological characteristics, which plays an important role in regulating skeletal muscle metabolism, movement and body homeostasis. The type of skeletal muscle fiber directly affects meat quality. However, the transcriptome and gene interactions between different types of muscle fibers are not well understood. In this paper, we selected
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In silico biotechnological potential of Bacillus sp. strain MHSD_37 bacterial endophyte BMC Genomics (IF 4.4) Pub Date : 2024-04-24 Pfariso Maumela, Adivhaho Khwathisi, Ntakadzeni Edwin Madala, Mahloro Hope Serepa-Dlamini
Endophytic bacteria possess a range of unique characteristics that enable them to successfully interact with their host and survive in adverse environments. This study employed in silico analysis to identify genes, from Bacillus sp. strain MHSD_37, with potential biotechnological applications. The strain presented several endophytic lifestyle genes which encode for motility, quorum sensing, stress
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Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings BMC Genomics (IF 4.4) Pub Date : 2024-04-23 Chen Bo, Mengmeng Liu, Qian You, Xiao Liu, Yanfang Zhu, Yongbo Duan, Dexin Wang, Tao Xue, Jianping Xue
Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the “sprout tumble” phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response
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Genome-wide identification of ZmMYC2 binding sites and target genes in maize BMC Genomics (IF 4.4) Pub Date : 2024-04-23 Lijun Liu, Yuhan Zhang, Chen Tang, Jine Wu, Jingye Fu, Qiang Wang
Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified. To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the
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The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Xiaolin Gu, Lingling Li, Xiaona Zhong, Yingjuan Su, Ting Wang
While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study
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Multiple transcriptome analyses reveal mouse testis developmental dynamics BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Anqi Chen, Chaoneng Ji, Chengtao Li, Beate Brand-Saberi, Suhua Zhang
The testes are the organs of gamete production and testosterone synthesis. Up to date, no model system is available for mammalian testicular development, and only few studies have characterized the mouse testis transcriptome from no more than three postnatal ages. To describe the transcriptome landscape of the developing mouse testis and identify the potential molecular mechanisms underlying testis
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Metabolomics and proteomics insights into subacute ruminal acidosis etiology and inhibition of proliferation of yak rumen epithelial cells in vitro BMC Genomics (IF 4.4) Pub Date : 2024-04-22 JunMei Wang, Liyuan Shi, Xiaohong Zhang, Rui Hu, Ziqi Yue, Huawei Zou, Quanhui Peng, Yahui Jiang, Zhisheng Wang
Untargeted metabolomics and proteomics were employed to investigate the intracellular response of yak rumen epithelial cells (YRECs) to conditions mimicking subacute rumen acidosis (SARA) etiology, including exposure to short-chain fatty acids (SCFA), low pH5.5 (Acid), and lipopolysaccharide (LPS) exposure for 24 h. These treatments significantly altered the cellular morphology of YRECs. Metabolomic
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scGAL: unmask tumor clonal substructure by jointly analyzing independent single-cell copy number and scRNA-seq data BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Ruixiang Li, Fangyuan Shi, Lijuan Song, Zhenhua Yu
Accurately deciphering clonal copy number substructure can provide insights into the evolutionary mechanism of cancer, and clustering single-cell copy number profiles has become an effective means to unmask intra-tumor heterogeneity (ITH). However, copy numbers inferred from single-cell DNA sequencing (scDNA-seq) data are error-prone due to technically confounding factors such as amplification bias
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Key mRNAs and lncRNAs of pituitary that affect the reproduction of FecB + + small tail han sheep BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Jianqi Yang, Jishun Tang, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Wenping Hu, Mingxing Chu
The pituitary directly regulates the reproductive process through follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Transcriptomic research on the pituitaries of ewes with different FecB (fecundity Booroola) genotypes has shown that some key genes and lncRNAs play an important role in pituitary function and sheep fecundity. Our previous study found that ewes with FecB + + genotypes (without
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Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Heqian Ma, Lina Zhu, Xiao Yang, Meng Ao, Shunxiang Zhang, Meizhen Guo, Xuelin Dai, Xiuwei Ma, Xiaoying Zhang
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1–2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent
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Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Sara Lamei Javan, Arman Beyraghdar Kashkooli, AbdolAli Shojaeiyan, Sina Majidian
Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting
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Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Xiaokun Xu, Mengdan He, Qingjie Xue, Xiuzhen Li, Ang Liu
The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion
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Evolution of myxozoan mitochondrial genomes: insights from myxobolids BMC Genomics (IF 4.4) Pub Date : 2024-04-22 Tatiana Orli Milkewitz Sandberg, Dayana Yahalomi, Noam Bracha, Michal Haddas-Sasson, Tal Pupko, Stephen D. Atkinson, Jerri L. Bartholomew, Jin Yong Zhang, Dorothée Huchon
Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging
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GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes BMC Genomics (IF 4.4) Pub Date : 2024-04-20 Doyoung Kim, Jeong-Ih Shin, In Young Yoo, Sungjin Jo, Jiyon Chu, Woo Young Cho, Seung-Hun Shin, Yeun-Jun Chung, Yeon-Joon Park, Seung-Hyun Jung
Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC)
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GbyE: an integrated tool for genome widely association study and genome selection based on genetic by environmental interaction BMC Genomics (IF 4.4) Pub Date : 2024-04-19 Xinrui Liu, Mingxiu Wang, Jie Qin, Yaxin Liu, Shikai Wang, Shiyu Wu, Ming Zhang, Jincheng Zhong, Jiabo Wang
The growth and development of organism were dependent on the effect of genetic, environment, and their interaction. In recent decades, lots of candidate additive genetic markers and genes had been detected by using genome-widely association study (GWAS). However, restricted to computing power and practical tool, the interactive effect of markers and genes were not revealed clearly. And utilization
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Genome-wide identification, characterization and expression of C2H2 zinc finger gene family in Opisthopappus species under salt stress BMC Genomics (IF 4.4) Pub Date : 2024-04-19 Xiaojuan Zhou, Ting Gao, Yimeng Zhang, Mian Han, Yuexin Shen, Yu Su, Xiaolong Feng, Qi Wu, Genlou Sun, Yiling Wang
The C2H2 zinc finger protein family plays important roles in plants. However, precisely how C2H2s function in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear. In this study, a total of 69 OpC2H2 zinc finger protein genes were identified and clustered into five Groups. Seven tandem and ten fragment repeats were found in OpC2H2s, which underwent robust purifying
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Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome BMC Genomics (IF 4.4) Pub Date : 2024-04-18 Shuilian He, Bin Xu, Siyun Chen, Gengyun Li, Jie Zhang, Junqiang Xu, Hang Wu, Xuejiao Li, Zhengan Yang
Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. We investigated
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Screening of temperature-responsive signalling molecules during sex differentiation in Asian yellow pond turtle (Mauremys mutica) BMC Genomics (IF 4.4) Pub Date : 2024-04-18 Xiaoli Liu, Haoyang Xu, Mingwei Peng, Chenyao Zhou, Chengqing Wei, Xiaoyou Hong, Wei Li, Chen Chen, Liqin Ji, Xinping Zhu
The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than females and exhibits temperature-dependent sex determination (TSD), in which the incubation temperature during embryonic development determines the sexual fate. However, the mechanisms of the
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Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress BMC Genomics (IF 4.4) Pub Date : 2024-04-18 Jinqing Zhang, Shuxia Li, Xueqin Gao, Yaling Liu, BingZhe Fu
Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families
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Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Souradeep Das, Anish K. Pandey, Denise E Morris, Rebecca Anderson, Victor Lim, Chong Chun Wie, Ivan Kok Seng Yap, Ahmed Ghazi Alattraqchi, Hafis Simin, Ramle Abdullah, Chew Chieng Yeo, Stuart C. Clarke, David W. Cleary
Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both healthcare associated infections (HAI) and community acquired infections (CAI) due to extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae (CRKp) are of concern
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Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Hadil A. Alkathiry, Samia Q. Alghamdi, Amit Sinha, Gabriele Margos, Alexandr A. Stekolnikov, Abdulaziz N. Alagaili, Alistair C. Darby, Benjamin L. Makepeace, Jing Jing Khoo
Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic
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Integrated analysis of single-cell and bulk RNA sequencing data reveals prognostic characteristics of lysosome-dependent cell death-related genes in osteosarcoma BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Yueshu Wu, Jun Yang, Gang Xu, Xiaolin Chen, Xiaochen Qu
Tumor cells exhibit a heightened susceptibility to lysosomal-dependent cell death (LCD) compared to normal cells. However, the role of LCD-related genes (LCD-RGs) in Osteosarcoma (OS) remains unelucidated. This study aimed to elucidate the role of LCD-RGs and their mechanisms in OS using several existing OS related datasets, including TCGA-OS, GSE16088, GSE14359, GSE21257 and GSE162454. Analysis identified
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Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022 BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Qiang Yin, Wei Liu, Yajuan Jiang, Qiang Feng, Xiaoyu Wang, Huixin Dou, Zanzan Liu, Feifei He, Yingying Fan, Baihai Jiao, Boyan Jiao
This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. All 87 SARS-CoV-2 whole-genome
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Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Robert Dagostino, Assaf Gottlieb
Deciphering gene regulation is essential for understanding the underlying mechanisms of healthy and disease states. While the regulatory networks formed by transcription factors (TFs) and their target genes has been mostly studied with relation to cis effects such as in TF binding sites, we focused on trans effects of TFs on the expression of their transcribed genes and their potential mechanisms.
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Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Hyun-Eui Park, Kyu-Min Kim, Jeong-Ih Shin, Jeong-Gyu Choi, Won-Jun An, Minh Phuong Trinh, Kyeong-Min Kang, Jung-Wan Yoo, Jung-Hyun Byun, Myung Hwan Jung, Kon-Ho Lee, Hyung-Lyun Kang, Seung Cheol Baik, Woo-Kon Lee, Min-Kyoung Shin
Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated
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Multi-trait GWAS for diverse ancestries: mapping the knowledge gap BMC Genomics (IF 4.4) Pub Date : 2024-04-17 Lucie Troubat, Deniz Fettahoglu, Léo Henches, Hugues Aschard, Hanna Julienne
Approximately 95% of samples analyzed in univariate genome-wide association studies (GWAS) are of European ancestry. This bias toward European ancestry populations in association screening also exists for other analyses and methods that are often developed and tested on European ancestry only. However, existing data in non-European populations, which are often of modest sample size, could benefit from
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Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Yong Cui, Meng Ru, Yujie Wang, Linjian Weng, Ramlat Ali Haji, Haiping Liang, Qingjie Zeng, Qing Wei, Xianhua Xie, Chao Yin, Jianzhen Huang
Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunop
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Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Kui Ding, Qinzeng Xu, Liyuan Zhao, Yixuan Li, Zhong Li, Wenge Shi, Qianhui Zeng, Xianyan Wang, Xuelei Zhang
The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close
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Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Nanbo Jiao, Jieru Xu, Yue Wang, Dunxi Li, Feifei Chen, Yu Chen, Jinhui Chen
Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio’s
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Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Numrah Fadra, Laura E Schultz-Rogers, Pritha Chanana, Margot A Cousin, Erica L Macke, Alejandro Ferrer, Filippo Pinto e Vairo, Rory J Olson, Gavin R Oliver, Lindsay A Mulvihill, Garrett Jenkinson, Eric W Klee
X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females
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Genome-wide identification of polyamine metabolism and ethylene synthesis genes in Chenopodium quinoa Willd. and their responses to low-temperature stress BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Xiaoxue Zhao, Shiyu Wang, Fenggen Guo, Pan Xia
Quinoa (Chenopodium quinoa Willd.) is valued for its nutritional richness. However, pre-harvest sprouting poses a significant threat to yield and grain quality. This study aims to enhance our understanding of pre-harvest sprouting mitigation strategies, specifically through delayed sowing and avoiding rainy seasons during quinoa maturation. The overarching goal is to identify cold-resistant varieties
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Investigating pigeon circovirus infection in a pigeon farm: molecular detection, phylogenetic analysis and complete genome analysis BMC Genomics (IF 4.4) Pub Date : 2024-04-16 Xiaobo Li, Shujing Wang, Wei Li, Shasha Wang, Xiao Qin, Ji Wang, Rui Fu
Pigeon circovirus infections in pigeons (Columba livia domestica) have been reported worldwide. Pigeons should be PiCV-free when utilized as qualified experimental animals. However, pigeons can be freely purchased as experimental animals without any clear guidelines to follow. Herein, we investigated the status quo of PiCV infections on a pigeon farm in Beijing, China, which provides pigeons for experimental
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Common occurrence of hotspots of single strand DNA breaks at transcriptional start sites BMC Genomics (IF 4.4) Pub Date : 2024-04-15 Huifen Cao, Yufei Zhang, Tianrong Song, Lu Xia, Ye Cai, Philipp Kapranov
We recently developed two high-resolution methods for genome-wide mapping of two prominent types of DNA damage, single-strand DNA breaks (SSBs) and abasic (AP) sites and found highly complex and non-random patterns of these lesions in mammalian genomes. One salient feature of SSB and AP sites was the existence of single-nucleotide hotspots for both lesions. In this work, we show that SSB hotspots are
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Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes BMC Genomics (IF 4.4) Pub Date : 2024-04-15 Kai-Xiong Qing, Amy C. Y. Lo, Siduo Lu, You Zhou, Dan Yang, Di Yang
The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time. In this study, we screened
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Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations BMC Genomics (IF 4.4) Pub Date : 2024-04-15 Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Large-scale copy number variants (CNVs) are structural alterations in the genome that involve the duplication or deletion of DNA segments, contributing to genetic diversity and playing a crucial role in the evolution and development of various diseases and disorders, as they can lead to the dosage imbalance of one or more genes. Massively parallel sequencing (MPS) has revolutionized the field of genetic
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Many purported pseudogenes in bacterial genomes are bona fide genes BMC Genomics (IF 4.4) Pub Date : 2024-04-15 Nicholas P. Cooley, Erik S. Wright
Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed to result from gene degradation during evolution but could also be technical artifacts of genome sequencing or assembly. Using a combination of observational and experimental data, we show that many putative pseudogenes
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New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56 BMC Genomics (IF 4.4) Pub Date : 2024-04-13 Desy Putri Handayani, Alim Isnansetyo, Indah Istiqomah
Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive
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Comparative transcriptomic analysis delineates adaptation strategies of Rana kukunoris toward cold stress on the Qinghai-Tibet Plateau BMC Genomics (IF 4.4) Pub Date : 2024-04-12 Tao Zhang, Lun Jia, Zhiyi Niu, Xinying Li, Shengkang Men, Lu Jiang, Miaojun Ma, Huihui Wang, Xiaolong Tang, Qiang Chen
Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter. Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing
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Cotyledonary somatic embryo is one kind of intermediate material similar to callus in the process of in vitro tissue culture from Rosa hybrida ‘John F. Kennedy’ BMC Genomics (IF 4.4) Pub Date : 2024-04-12 Li Du, Xiaoling Kang, Haoran Guo, Zhongfeng Zhu, Rui Wu, Meijing Yuan, Chuanyu Ding
Rose is recognized as an important ornamental plant worldwide, and it is also one of the most widely used flowers in gardens. At present, the improvement of rose traits is still difficult and uncertain, and molecular breeding can provide new ideas for the improvement of modern rose varieties. Somatic embryos are quite good receptors for genetic transformation. However, little is known about the molecular
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Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison BMC Genomics (IF 4.4) Pub Date : 2024-04-12 Lucas Kuijpers, Bastian Hornung, Mirjam C. G. N. van den Hout - van Vroonhoven, Wilfred F. J. van IJcken, Frank Grosveld, Eskeatnaf Mulugeta
Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based
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Mitotic gene regulation by the N-MYC-WDR5-PDPK1 nexus BMC Genomics (IF 4.4) Pub Date : 2024-04-11 Sarah A. Streeter, Alexandria G. Williams, James R. Evans, Jing Wang, Alissa D. Guarnaccia, Andrea C. Florian, Rafet Al-Tobasei, Qi Liu, William P. Tansey, April M. Weissmiller
During mitosis the cell depends on proper attachment and segregation of replicated chromosomes to generate two identical progeny. In cancers defined by overexpression or dysregulation of the MYC oncogene this process becomes impaired, leading to genomic instability and tumor evolution. Recently it was discovered that the chromatin regulator WDR5—a critical MYC cofactor—regulates expression of genes
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A murine model for the del(GJB6-D13S1830) deletion recapitulating the phenotype of human DFNB1 hearing impairment: generation and functional and histopathological study BMC Genomics (IF 4.4) Pub Date : 2024-04-11 María Domínguez-Ruiz, Silvia Murillo-Cuesta, Julio Contreras, Marta Cantero, Gema Garrido, Belén Martín-Bernardo, Elena Gómez-Rosas, Almudena Fernández, Francisco J. del Castillo, Lluís Montoliu, Isabel Varela-Nieto, Ignacio del Castillo
Inherited hearing impairment is a remarkably heterogeneous monogenic condition, involving hundreds of genes, most of them with very small (< 1%) epidemiological contributions. The exception is GJB2, the gene encoding connexin-26 and underlying DFNB1, which is the most frequent type of autosomal recessive non-syndromic hearing impairment (ARNSHI) in most populations (up to 40% of ARNSHI cases). DFNB1
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HOXA9 gene inhibits proliferation and differentiation and promotes apoptosis of bovine preadipocytes BMC Genomics (IF 4.4) Pub Date : 2024-04-11 Lixia He, Xue Feng, Chunli Hu, Shuang Liu, Hui Sheng, Bei Cai, Yun Ma
Hox gene family is an important transcription factor that regulates cell process, and plays a role in the process of adipocytes differentiation and fat deposition. Previous transcriptome sequencing studies have indicated that the Homeobox A9 gene (HOXA9) is a candidate gene for regulating the process of bovine lipid metabolism, but the function and specific mechanism of action remain unclear. Therefore
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Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson) BMC Genomics (IF 4.4) Pub Date : 2024-04-10 Yuting Tan, Yunyan Huang, Chunhui Xu, Xuan Huang, Shibao Li, Zhaozheng Yin
Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of
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Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae BMC Genomics (IF 4.4) Pub Date : 2024-04-10 Bo Wang, Yanyan Jia, Ningxin Dang, Jie Yu, Stephen J. Bush, Shenghan Gao, Wenxi He, Sirui Wang, Hongtao Guo, Xiaofei Yang, Weimin Ma, Kai Ye
Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown. We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 and Chlorella pyrenoidosa DBH, with chromosome numbers of 12 and 13, and genome sizes
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A chromosome-level genome assembly of the soybean pod borer: insights into larval transcriptional response to transgenic soybean expressing the pesticidal Cry1Ac protein BMC Genomics (IF 4.4) Pub Date : 2024-04-09 Yangzhou Wang, Yao Yao, Yunyue Zhang, Xueyan Qian, Dongquan Guo, Brad S. Coates
Genetically modified (GM) crop plants with transgenic expression of Bacillus thuringiensis (Bt) pesticidal proteins are used to manage feeding damage by pest insects. The durability of this technology is threatened by the selection for resistance in pest populations. The molecular mechanism(s) involved in insect physiological response or evolution of resistance to Bt is not fully understood. To investigate
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Genome-wide analysis and expression profiling of the HD-ZIP gene family in kiwifruit BMC Genomics (IF 4.4) Pub Date : 2024-04-09 Kai-yu Ye, Jie-wei Li, Fa-ming Wang, Jian-you Gao, Cui-xia Liu, Hong-juan Gong, Bei-bei Qi, Ping-ping Liu, Qiao-sheng Jiang, Jian-min Tang, Quan-hui Mo
The homeodomain-leucine zipper (HD-Zip) gene family plays a pivotal role in plant development and stress responses. Nevertheless, a comprehensive characterization of the HD-Zip gene family in kiwifruit has been lacking. In this study, we have systematically identified 70 HD-Zip genes in the Actinidia chinensis (Ac) genome and 55 in the Actinidia eriantha (Ae) genome. These genes have been categorized
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The transcriptional response in mosquitoes distinguishes between fungi and bacteria but not Gram types BMC Genomics (IF 4.4) Pub Date : 2024-04-09 Bretta Hixson, Louise Huot, Bianca Morejon, Xiaowei Yang, Peter Nagy, Kristin Michel, Nicolas Buchon
Mosquitoes are prolific vectors of human pathogens, therefore a clear and accurate understanding of the organization of their antimicrobial defenses is crucial for informing the development of transmission control strategies. The canonical infection response in insects, as described in the insect model Drosophila melanogaster, is pathogen type-dependent, with distinct stereotypical responses to Gram-negative
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Transcriptome exploration of ferroptosis-related genes in TGFβ- induced lens epithelial to mesenchymal transition during posterior capsular opacification development BMC Genomics (IF 4.4) Pub Date : 2024-04-09 Cong Fan, Chao Wang, Yan Wang, Jian Jiang
Posterior capsular opacification (PCO) is the main reason affecting the long-term postoperative result of cataract patient, and it is well accepted that fibrotic PCO is driven by transforming growth factor beta (TGFβ) signaling. Ferroptosis, closely related to various ocular diseases, but has not been explored in PCO. RNA sequencing (RNA-seq) was performed on both TGF-β2 treated and untreated primary
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Correction: Transcriptomics and metabolomics of blood, urine and ovarian follicular fuid of yak at induced estrus stage BMC Genomics (IF 4.4) Pub Date : 2024-04-08 Huangqing Zhao, Yongzhen Huang, Shi Shu, Guowen Wang, Changqi Fu, Rong Huang, Jun Zhang, Huawei Su, Yang He, Chuzhao Lei, Lei Du, Jiahao Zhao, Wei Peng
Correction: BMC Genomics 25, 201 (2024) https://doi.org/10.1186/s12864-024-10079-7 Following publication of the original article it was reported that the ‘Availability of data and materials’, ‘Funding’ and ‘Ethics approval and consent to participate’ declarations were missing. The correct declarations are given in this Correction and the original article has been updated. Funding This research has
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Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals BMC Genomics (IF 4.4) Pub Date : 2024-04-08 Tao Xiong, Zaibao Zhang, Tianyu Fan, Fan Ye, Ziyi Ye
In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs
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Accuracy of Genomic prediction for fleece traits in Inner Mongolia Cashmere goats BMC Genomics (IF 4.4) Pub Date : 2024-04-08 Xiaochun Yan, Jinquan Li, Libing He, Oljibilig Chen, Na Wang, Shuai Wang, Xiuyan Wang, Zhiying Wang, Rui Su
The fleece traits are important economic traits of goats. With the reduction of sequencing and genotyping cost and the improvement of related technologies, genomic selection for goats has become possible. The research collect pedigree, phenotype and genotype information of 2299 Inner Mongolia Cashmere goats (IMCGs) individuals. We estimate fixed effects, and compare the estimates of variance components