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Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Rahma ZOUAGUI, Houda ZOUAGUI, Jamal AURAG, Azeddine IBRAHIMI, Laila SBABOU
Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive
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Phylogeny and expression patterns of ERF genes that are potential reproductive inducers in hybrid larch BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Junfei Hao, Daixi Xu, Chen Wang, Qing Cao, Qingrong Zhao, Miaomiao Xie, Hanguo Zhang, Lei Zhang
Larch is an important component of northern forests and a major cultivated tree species in restoration of forest cover using improved seed material. In recent years, the continuous low seed production has severely affected the production of improved variety seedlings and natural regeneration. However, research on the reproductive growth of gymnosperms is extremely scarce. In this study, based on differential
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Generalizability of machine learning in predicting antimicrobial resistance in E. coli: a multi-country case study in Africa BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Mike Nsubuga, Ronald Galiwango, Daudi Jjingo, Gerald Mboowa
Antimicrobial resistance (AMR) remains a significant global health threat particularly impacting low- and middle-income countries (LMICs). These regions often grapple with limited healthcare resources and access to advanced diagnostic tools. Consequently, there is a pressing need for innovative approaches that can enhance AMR surveillance and management. Machine learning (ML) though underutilized in
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Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Didi Jin, Chao Li, Xiao Chen, Yurui Wang, Khaled A. S. Al-Rasheid, Naomi A. Stover, Chen Shao, Tengteng Zhang
Encystment is an important survival strategy extensively employed by microbial organisms to survive unfavorable conditions. Single-celled ciliated protists (ciliates) are popular model eukaryotes for studying encystment, whereby these cells degenerate their ciliary structures and develop cyst walls, then reverse the process under more favorable conditions. However, to date, the evolutionary basis and
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Mitochondrial genome features and systematic evolution of diospyros kaki thunb 'Taishuu' BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Yunliang Yang, Chao Duan
'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species. The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308 bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three
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Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Fasil Getachew Kebede, Martijn F.L. Derks, Tadelle Dessie, Olivier Hanotte, Carolina Pita Barros, Richard P.M.A. Crooijmans, Hans Komen, John W.M. Bastiaansen
Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic
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Screening and functional analysis of StMYB transcription factors in pigmented potato under low-temperature treatment BMC Genomics (IF 4.4) Pub Date : 2024-03-18 Bi-Cong Chen, Xiao-Jie Wu, Qiu-Ju Dong, Ji-Ping Xiao
MYB transcription factors play an extremely important regulatory role in plant responses to stress and anthocyanin synthesis. Cloning of potato StMYB-related genes can provide a theoretical basis for the genetic improvement of pigmented potatoes. In this study, two MYB transcription factors, StMYB113 and StMYB308, possibly related to anthocyanin synthesis, were screened under low-temperature conditions
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A single workflow for multi-species blood transcriptomics BMC Genomics (IF 4.4) Pub Date : 2024-03-16 Elody Orcel, Hayat Hage, May Taha, Noémie Boucher, Emilie Chautard, Virginie Courtois, Adrien Saliou
Blood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for applications in diagnostics and monitoring of the immune response to vaccines. However, multi-species transcriptomic analysis is still a challenge from a technological point of view and a standardized workflow is urgently needed to allow interspecies comparisons. Here, we
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Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea BMC Genomics (IF 4.4) Pub Date : 2024-03-16 Feng Xiao, Yang Zhao, Xiurong Wang, Xueyan Jian, Yao Yang
Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought
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Serum electrolyte concentrations and risk of atrial fibrillation: an observational and mendelian randomization study BMC Genomics (IF 4.4) Pub Date : 2024-03-16 Yang Wu, Xiang-Jun Kong, Ying-Ying Ji, Jun Fan, Cheng-Cheng Ji, Xu-Miao Chen, Yue-Dong Ma, An-Li Tang, Yun-Jiu Cheng, Su-Hua Wu
Atrial fibrillation (AF) is a prevalent arrhythmic condition resulting in increased stroke risk and is associated with high mortality. Electrolyte imbalance can increase the risk of AF, where the relationship between AF and serum electrolytes remains unclear. A total of 15,792 individuals were included in the observational study, with incident AF ascertainment in the Atherosclerosis Risk in Communities
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Molecular adaptations underlying high-frequency hearing in the brain of CF bats species BMC Genomics (IF 4.4) Pub Date : 2024-03-16 Xintong Li, Hui Wang, Xue Wang, Mingyue Bao, Ruyi Sun, Wentao Dai, Keping Sun, Jiang Feng
The majority of bat species have developed remarkable echolocation ability, especially for the laryngeally echolocating bats along with high-frequency hearing. Adaptive evolution has been widely detected for the cochleae in the laryngeally echolocating bats, however, limited understanding for the brain which is the central to echolocation signal processing in the auditory perception system, the laryngeally
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Mitochondrial genome plasticity of mammalian species BMC Genomics (IF 4.4) Pub Date : 2024-03-14 Bálint Biró, Zoltán Gál, Zsófia Fekete, Eszter Klecska, Orsolya Ivett Hoffmann
There is an ongoing process in which mitochondrial sequences are being integrated into the nuclear genome. The importance of these sequences has already been revealed in cancer biology, forensic, phylogenetic studies and in the evolution of the eukaryotic genetic information. Human and numerous model organisms’ genomes were described from those sequences point of view. Furthermore, recent studies were
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Complete chloroplast genome and comparison of herbicides toxicity on Aeschynomene indica (Leguminosae) in upland direct-seeding paddy field BMC Genomics (IF 4.4) Pub Date : 2024-03-14 Yuan Gao, TianYu Chen, Jiaqi Long, Guohui Shen, Zhihui Tian
Indian jointvetch (Aeschynomene indica) is a common and pernicious weed found in the upland direct-seeding rice fields in the lower reaches of the Yangtze River in China. However, there are few reports on the degree of harm, genetic characteristics, and management methods of this weed. The purpose of this study is to clarify the harm of Indian jointvetch to upland direct-seeding rice, analyze the genetic
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Analysis of the complete genome sequence of Paenibacillus sp. lzh-N1 reveals its antagonistic ability BMC Genomics (IF 4.4) Pub Date : 2024-03-13 Ee Li, Kaiquan Liu, Shuhan Yang, Ling Li, Kun Ran, Xiaoli Sun, Jie Qu, Li Zhao, Yuxiu Xin, Feng Zhu, Jingfang Ma, Feng Song, Zhenghua Li
Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina
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De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest BMC Genomics (IF 4.4) Pub Date : 2024-03-13 Claudio Cucini, Sara Boschi, Rebecca Funari, Elena Cardaioli, Nicola Iannotti, Giovanni Marturano, Francesco Paoli, Mirella Bruttini, Antonio Carapelli, Francesco Frati, Francesco Nardi
The spread of Popillia japonica in non-native areas (USA, Canada, the Azores islands, Italy and Switzerland) poses a significant threat to agriculture and horticulture, as well as to endemic floral biodiversity, entailing that appropriate control measures must be taken to reduce its density and limit its further spread. In this context, the availability of a high quality genomic sequence for the species
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Allelic variation in the autotetraploid potato: genes involved in starch and steroidal glycoalkaloid metabolism as a case study BMC Genomics (IF 4.4) Pub Date : 2024-03-12 Hongbo Li, Matthijs Brouwer, Elena Del Pup, Natascha van Lieshout, Richard Finkers, Christian W. B. Bachem, Richard G. F. Visser
Tuber starch and steroidal glycoalkaloid (SGA)-related traits have been consistently prioritized in potato breeding, while allelic variation pattern of genes that underlie these traits is less explored. Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism
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Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome BMC Genomics (IF 4.4) Pub Date : 2024-03-12 Kenyatta C. M. F. Viel, Sreeja Parameswaran, Omer A. Donmez, Carmy R. Forney, Matthew R. Hass, Cailing Yin, Sydney H. Jones, Hayley K. Prosser, Arame A. Diouf, Olivia E. Gittens, Lee E. Edsall, Xiaoting Chen, Hope Rowden, Katelyn A. Dunn, Rui Guo, Andrew VonHandorf, Merrin Man Long Leong, Kevin Ernst, Kenneth M. Kaufman, Lucinda P. Lawson, Ben Gewurz, Bo Zhao, Leah C. Kottyan, Matthew T. Weirauch
There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50%
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Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation BMC Genomics (IF 4.4) Pub Date : 2024-03-12 Pengcheng Lyu, Honglin Jiang
Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite
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Decoding HiPSC-CM’s Response to SARS-CoV-2: mapping the molecular landscape of cardiac injury BMC Genomics (IF 4.4) Pub Date : 2024-03-12 Sicheng Chen, Zhenquan Fu, Kaitong Chen, Xinyao Zheng, Zhenyang Fu
Acute cardiac injury caused by coronavirus disease 2019 (COVID-19) increases mortality. Acute cardiac injury caused by COVID-19 requires understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly infects cardiomyocytes. This study provides a solid foundation for related studies by using a model of SARS-CoV-2 infection in human induced pluripotent stem cell-derived cardiomyocytes
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Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean BMC Genomics (IF 4.4) Pub Date : 2024-03-12 Kevin O. Chiteri, Ashlyn Rairdin, Kulbir Sandhu, Sven Redsun, Andrew Farmer, Jamie A. O’Rourke, Steven B. Cannon, Arti Singh
Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with
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Distribution patterns of molecular markers of antimalarial drug resistance in Plasmodium falciparum isolates on the Thai-Myanmar border during the periods of 1993–1998 and 2002–2008 BMC Genomics (IF 4.4) Pub Date : 2024-03-11 Phunuch Muhamad, Papichaya Phompradit, Wanna Chaijaroenkul, Kesara Na-Bangchang
Polymorphisms of Plasmodium falciparum chloroquine resistance transporter (pfcrt), Plasmodium falciparum multi-drug resistance 1 (pfmdr1) and Plasmodium falciparum kelch 13-propeller (pfk13) genes are accepted as valid molecular markers of quinoline antimalarials and artemisinins. This study investigated the distribution patterns of these genes in P. falciparum isolates from the areas along the Thai-Myanmar
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Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo BMC Genomics (IF 4.4) Pub Date : 2024-03-11 Jessica Iglesias-Moya, Álvaro Benítez, María Segura, Sonsoles Alonso, Dolores Garrido, Cecilia Martínez, Manuel Jamilena
The core regulation of the abscisic acid (ABA) signalling pathway comprises the multigenic families PYL, PP2C, and SnRK2. In this work, we conducted a genome-wide study of the components of these families in Cucurbita pepo. The bioinformatic analysis of the C. pepo genome resulted in the identification of 19 CpPYL, 102 CpPP2C and 10 CpSnRK2 genes. The investigation of gene structure and protein motifs
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Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome BMC Genomics (IF 4.4) Pub Date : 2024-03-11 Steven Tavis, Robert L. Hettich
In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence
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DNA-QLC: an efficient and reliable image encoding scheme for DNA storage BMC Genomics (IF 4.4) Pub Date : 2024-03-09 Yanfen Zheng, Ben Cao, Xiaokang Zhang, Shuang Cui, Bin Wang, Qiang Zhang
DNA storage has the advantages of large capacity, long-term stability, and low power consumption relative to other storage mediums, making it a promising new storage medium for multimedia information such as images. However, DNA storage has a low coding density and weak error correction ability. To achieve more efficient DNA storage image reconstruction, we propose DNA-QLC (QRes-VAE and Levenshtein
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Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows BMC Genomics (IF 4.4) Pub Date : 2024-03-09 Helen Schneider, Ana-Marija Krizanac, Clemens Falker-Gieske, Johannes Heise, Jens Tetens, Georg Thaller, Jörn Bennewitz
Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed
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scFSNN: a feature selection method based on neural network for single-cell RNA-seq data BMC Genomics (IF 4.4) Pub Date : 2024-03-08 Minjiao Peng, Baoqin Lin, Jun Zhang, Yan Zhou, Bingqing Lin
While single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression in individual cells, its unique characteristics like over-dispersion, zero-inflation, high gene-gene correlation, and large data volume with many features pose challenges for most existing feature selection methods. In this paper, we present a feature selection method based on neural network (scFSNN) to solve
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Genome mining of Escherichia coli WG5D from drinking water source: unraveling antibiotic resistance genes, virulence factors, and pathogenicity BMC Genomics (IF 4.4) Pub Date : 2024-03-08 Oluwaseyi Samuel Olanrewaju, Lesego G Molale-Tom, Rinaldo K Kritzinger, Cornelius Carlos Bezuidenhout
Escherichia coli, a ubiquitous inhabitant of the gut microbiota, has been recognized as an indicator of fecal contamination and a potential reservoir for antibiotic resistance genes. Its prevalence in drinking water sources raises concerns about the potential dissemination of antibiotic resistance within aquatic ecosystems and the subsequent impact on public health. The ability of E. coli to acquire
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High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China BMC Genomics (IF 4.4) Pub Date : 2024-03-08 Ying Ma, Pengbo Liu, Ziyan Li, Yujuan Yue, Yanmei Zhao, Jian He, Jiaxin Zhao, Xiuping Song, Jun Wang, Qiyong Liu, Liang Lu
Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of
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Genome-wide analysis of acid tolerance genes of Enterococcus faecalis with RNA-seq and Tn-seq BMC Genomics (IF 4.4) Pub Date : 2024-03-08 Zhanyi Chen, Chenguang Niu, Lifan Wei, Zhengwei Huang, Shujun Ran
Enterococcus faecalis, a formidable nosocomial and community-acquired opportunistic pathogen, can persist a wide range of extreme environments, including low pH and nutrient deficiency. Clarifying the survival mechanism of E. faecalis in low-pH conditions is the key to combating the infectious diseases caused by E. faecalis. In this study, we combined transcriptome profiling (RNA-seq) and transposon
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Comparative analysis of the organelle genomes of Aconitum carmichaelii revealed structural and sequence differences and phylogenetic relationships BMC Genomics (IF 4.4) Pub Date : 2024-03-08 Rongxiang Zhang, Niyan Xiang, Changjiang Qian, Shuwen Liu, Yuemei Zhao, Guiyu Zhang, Pei Wei, Jianfeng Li, Tao Yuan
In this study, we conducted an assembly and analysis of the organelle genomes of Aconitum carmichaelii. Our investigation encompassed the examination of organelle genome structures, gene transfer events, and the environmental selection pressures affecting A. carmichaelii. The results revealed distinct evolutionary patterns in the organelle genomes of A. carmichaelii. Especially, the plastome exhibited
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Genome-wide identification of SWEET genes reveals their roles during seed development in peanuts BMC Genomics (IF 4.4) Pub Date : 2024-03-07 Yang Li, Mengjia Fu, Jiaming Li, Jie Wu, Zhenyang Shua, Tiantian Chen, Wen Yao, Dongxin Huai
Sugar Will Eventually be Exported Transporter (SWEET) proteins are highly conserved in various organisms and play crucial roles in sugar transport processes. However, SWEET proteins in peanuts, an essential leguminous crop worldwide, remain lacking in systematic characterization. Here, we identified 94 SWEET genes encoding the conservative MtN3/saliva domains in three peanut species, including 47 in
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Coping with extremes: the rumen transcriptome and microbiome co-regulate plateau adaptability of Xizang goat BMC Genomics (IF 4.4) Pub Date : 2024-03-07 Cheng Pan, Haiyan Li, Shehr Bano Mustafa, Cuomu Renqing, Zhenzhen Zhang, Jingjing Li, Tianzeng Song, Gaofu Wang, Wangsheng Zhao
The interactions between the rumen microbiota and the host are crucial for the digestive and absorptive processes of ruminants, and they are heavily influenced by the climatic conditions of their habitat. Owing to the harsh conditions of the high-altitude habitat, little is known about how ruminants regulate the host transcriptome and the composition of their rumen microbiota. Using the model species
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Bioinformatics analysis identifies a key gene HLA_DPA1 in severe influenza-associated immune infiltration BMC Genomics (IF 4.4) Pub Date : 2024-03-07 Liang Chen, Jie Hua, Xiaopu He
Severe influenza is a serious global health issue that leads to prolonged hospitalization and mortality on a significant scale. The pathogenesis of this infectious disease is poorly understood. Therefore, this study aimed to identify the key genes associated with severe influenza patients necessitating invasive mechanical ventilation. The current study utilized two publicly accessible gene expression
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Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects BMC Genomics (IF 4.4) Pub Date : 2024-03-07 Martin Broberg, Minna Ampuja, Samuel Jones, Tiina Ojala, Otto Rahkonen, Riikka Kivelä, James Priest, Aarno Palotie, Hanna M. Ollila, Emmi Helle
Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk,
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SNP-based and haplotype-based genome-wide association on drug dependence in Han Chinese BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Hanli Xu, Yulin Kang, Tingming Liang, Sifen Lu, Xiaolin Xia, Zuhong Lu, Lingming Hu, Li Guo, Lishu Zhang, Jiaqiang Huang, Lin Ye, Peiye Jiang, Yi Liu, Li Xinyi, Jin Zhai, Zi Wang, Yangyang Liu
Drug addiction is a serious problem worldwide and is influenced by genetic factors. The present study aimed to investigate the association between genetics and drug addiction among Han Chinese. A total of 1000 Chinese users of illicit drugs and 9693 healthy controls were enrolled and underwent single nucleotide polymorphism (SNP)-based and haplotype-based association analyses via whole-genome genotyping
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Integrated analysis reveals the regulatory mechanism of the neddylation inhibitor MLN4924 on the metabolic dysregulation in rabbit granulosa cells BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Mengjuan Chen, Yuqing Liu, Mingzhong Zuo, Meina Zhang, Zhitong Wang, Xin Li, Dongdong Yuan, Huifen Xu, Guangqing Yu, Ming Li
Neddylation, an important post-translational modification (PTM) of proteins, plays a crucial role in follicular development. MLN4924 is a small-molecule inhibitor of the neddylation-activating enzyme (NAE) that regulates various biological processes. However, the regulatory mechanisms of neddylation in rabbit ovarian cells have not been emphasized. Here, the transcriptome and metabolome profiles in
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A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Xingguang Zhai, Dandan Wu, Chen Chen, Xunzhe Yang, Shaobo Cheng, Lina Sha, Shuhan Deng, Yiran Cheng, Xing Fan, Houyang Kang, Yi Wang, Dengcai Liu, Yonghong Zhou, Haiqin Zhang
The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as “St”, accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data
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Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Huifang Zheng, Yali Xie, Changhong Mu, Wenlong Cheng, Yucong Bai, Jian Gao
The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study
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Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Timothy J. Peters, Braydon Meyer, Lauren Ryan, Joanna Achinger-Kawecka, Jenny Song, Elyssa M. Campbell, Wenjia Qu, Shalima Nair, Phuc Loi-Luu, Phillip Stricker, Elgene Lim, Clare Stirzaker, Susan J. Clark, Ruth Pidsley
The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend
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Integrated analysis reveals FLI1 regulates the tumor immune microenvironment via its cell-type-specific expression and transcriptional regulation of distinct target genes of immune cells in breast cancer BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Jianying Pei, Ying Peng, Kexin Ma, Chunyan Lan, Tingting Zhang, Yan Li, Xiaofang Chen, Huafang Gao
Immunotherapy is a practical therapeutic approach in breast cancer (BRCA), and the role of FLI1 in immune regulation has gradually been unveiled. However, the specific role of FLI1 in BRCA was conflicted; thus, additional convincing evidence is needed. We explored the upstream regulation of FLI1 expression via summary data-based Mendelian randomization (SMR) analysis and ncRNA network construction
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Iron-related gene mutations driving global Mycobacterium tuberculosis transmission revealed by whole-genome sequencing BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Yameng Li, Yifan Li, Yao Liu, Xianglong Kong, Ningning Tao, Yawei Hou, Tingting Wang, Qilin Han, Yuzhen Zhang, Fei Long, Huaichen Li
Iron plays a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism governing this system requires further elucidation. Additionally, limited studies have examined the impact of gene mutations related to iron on the transmission of M. tuberculosis globally. This research aims to investigate the correlation between mutations in iron-related
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Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata BMC Genomics (IF 4.4) Pub Date : 2024-03-06 Ana Paula Zotta Mota, Komivi Dossa, Mathieu Lechaudel, Denis Cornet, Pierre Mournet, Sylvain Santoni, David Lopez, Hana Chaïr
Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the
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Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae) BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Lei Zhang, Ying Meng, Da Wang, Guan-Hao He, Jun-Ming Zhang, Jun Wen, Ze-Long Nie
Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three
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The first Cyclospora cayetanensis lineage A genome from an isolate from Mexico BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Monica Santin, Aleksey Molokin, Guadalupe E. Orozco-Mosqueda, Sonia Almeria, Jenny Maloney
Cyclospora cayetanensis is a protozoan parasite that causes intestinal illness in humans worldwide. Despite its global distribution, most genomic data for C. cayetanensis has been obtained from isolates collected in the United States, leaving genetic variability among globally distributed isolates underexplored. In the present study, the genome of an isolate of C. cayetanensis obtained from a child
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Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Godstime Taiwo, Olanrewaju B. Morenikeji, Modoluwamu Idowu, Taylor Sidney, Ajiboye Adekunle, Andres Pech Cervantes, Sunday Peters, Ibukun M. Ogunade
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = − 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred
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Vitamin a potentiates sheep myoblasts myogenic differentiation through BHLHE40-modulated ID3 expression BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Pengkang Song, Jiamin Zhao, Weipeng Zhang, Xuying Li, Bingzhen Ji, Junxing Zhao
Vitamin A and retinoic acid (RA, a metabolite of vitamin A), are inextricably involved to the development of skeletal muscle in animals. However, the mechanisms regulating skeletal muscle development by vitamin A remain poorly reported. The current study designed to investigate the underlying mechanism of vitamin A affecting myogenic differentiation of lamb myoblasts through transcriptome sequencing
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Loss of chromosome Y in regulatory T cells BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Jonas Mattisson, Jonatan Halvardson, Hanna Davies, Bożena Bruhn-Olszewska, Paweł Olszewski, Marcus Danielsson, Josefin Bjurling, Amanda Lindberg, Ammar Zaghlool, Edyta Rychlicka-Buniowska, Jan P. Dumanski, Lars A. Forsberg
Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher
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i5mC-DCGA: an improved hybrid network framework based on the CBAM attention mechanism for identifying promoter 5mC sites BMC Genomics (IF 4.4) Pub Date : 2024-03-05 Jianhua Jia, Rufeng Lei, Lulu Qin, Xin Wei
5-Methylcytosine (5mC) plays a very important role in gene stability, transcription, and development. Therefore, accurate identification of the 5mC site is of key importance in genetic and pathological studies. However, traditional experimental methods for identifying 5mC sites are time-consuming and costly, so there is an urgent need to develop computational methods to automatically detect and identify
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Correction: Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Daniel Gaspar, Catarina Ginja, Nuno Carolino, Célia Leão, Helena Monteiro, Lino Tábuas, Sandra Branco, Ludovina Padre, Pedro Caetano, Ricardo Romão, Claudino Matos, António Marcos Ramos, Elisa Bettencourt, Ana Usié
Correction: BMC Genomics 25, 100 (2024) https://doi.org/10.1186/s12864-023-09844-x Following publication of the original article an error in the affiliation listing was reported. The incorrect affiliation distribution is shown below: Daniel Gaspar1,2,3, Catarina Ginja2,3,4, Nuno Carolino4,5,6, Célia Leão1,5,7, Helena Monteiro7, Lino Tábuas7, Sandra Branco8,9, Ludovina Padre8, Pedro Caetano8, Ricardo
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Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Indrawati Sendow, Irene Kasindi Meki, Ni Luh Putu Indi Dharmayanti, Heri Hoerudin, Atik Ratnawati, Tirumala Bharani K. Settypalli, Hatem Ouled Ahmed, Harimurti Nuradji, Muharam Saepulloh, Rahmat Setya Adji, Nuha Fairusya, Faralinda Sari, Katamtama Anindita, Giovanni Cattoli, Charles Euloge Lamien
Lumpy skin disease (LSD) is a transboundary viral disease of cattle and water buffaloes caused by the LSD virus, leading to high morbidity, low mortality, and a significant economic impact. Initially endemic to Africa only, LSD has spread to the Middle East, Europe, and Asia in the past decade. The most effective control strategy for LSD is the vaccination of cattle with live-attenuated LSDV vaccines
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Integrated Metabolomic and transcriptomic analyses reveal deoxycholic acid promotes transmissible gastroenteritis virus infection by inhibiting phosphorylation of NF-κB and STAT3 BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Yajing Zhou, Chao Xu, Shanshen Gu, Yeyi Xiao, Shenglong Wu, Haifei Wang, Wenbin Bao
Acute diarrhea, dehydration and death in piglets are all symptoms of transmissible gastroenteritis virus (TGEV), which results in significant financial losses in the pig industry. It is important to understand the pathogenesis and identify new antiviral targets by revealing the metabolic interactions between TGEV and host cells. We performed metabolomic and transcriptomic analyses of swine testicular
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Genome-wide identification, expression profiling, and protein interaction analysis of the CCoAOMT gene family in the tea plant (Camellia sinensis) BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Yiqing Wang, Tao Wang, Siyu Qi, Jiamin Zhao, Jiumei Kong, Zhihui Xue, Weijiang Sun, Wen Zeng
The caffeoyl-CoA-O methyltransferase (CCoAOMT) family plays a crucial role in the oxidative methylation of phenolic substances and is involved in various plant processes, including growth, development, and stress response. However, there is a limited understanding of the interactions among CCoAOMT protein members in tea plants. In this study, we identified 10 members of the CsCCoAOMT family in the
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RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Hosein Ahmadi, Reza Fatahi, Zabihollah Zamani, Majid Shokrpour, Morteza Sheikh-Assadi, Peter Poczai
Here, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes ‘Zagheh-11’ (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and ‘Malayer-21’ (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated
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Identification and validation of RNA-binding protein SLC3A2 regulates melanocyte ferroptosis in vitiligo by integrated analysis of single-cell and bulk RNA-sequencing BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Jingzhan Zhang, Fang Xiang, Yuan Ding, Wen Hu, Hongjuan Wang, Xiangyue Zhang, Zixian Lei, Tingting Li, Peng Wang, Xiaojing Kang
The pathogenesis of vitiligo remains unclear. The genes encoding vitiligo-related RNA-binding proteins (RBPs) and their underlying pathogenic mechanism have not been determined. Single-cell transcriptome sequencing (scRNA-seq) data from the CNCB database was obtained to identify distinct cell types and subpopulations and the relative proportion changes in vitiligo and healthy samples. We identified
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The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Guangyan Feng, Yongjuan Jiao, Huizhen Ma, Haoyang Bian, Gang Nie, Linkai Huang, Zheni Xie, Qifan Ran, Wenwen Fan, Wei He, Xinquan Zhang
Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in
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An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Kate Keogh, D. A. Kenny, P. A. Alexandre, M. McGee, A. Reverter
Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene
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De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome BMC Genomics (IF 4.4) Pub Date : 2024-03-04 David Ryder, David Stone, Diana Minardi, Ainsley Riley, Justin Avant, Lisa Cross, Marta Soeffker, Deborah Davidson, Andrew Newman, Peter Thomson, Chris Darby, Ronny van Aerle
Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key
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Evaluation of aphid resistance on different rose cultivars and transcriptome analysis in response to aphid infestation BMC Genomics (IF 4.4) Pub Date : 2024-03-04 Wenqi Dong, Lei Sun, Bo Jiao, Pu Zhao, Chunhong Ma, Junping Gao, Shuo Zhou
The rose is one of the most important ornamental flowers in the world for its aesthetic beauty but can be attacked by many pests such as aphids. Aphid infestation causes tremendous damage on plant tissues leading to harmed petals and leaves. Rose cultivars express different levels of resistance to aphid infestation yet the information remains unclear. Not only that, studies about the transcriptional
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Insight into telomere regulation: road to discovery and intervention in plasma drug-protein targets BMC Genomics (IF 4.4) Pub Date : 2024-03-02 Kaixi Ding, Juejue Zhangwang, Ming Lei, Chunping Xiong
Telomere length is a critical metric linked to aging, health, and disease. Currently, the exploration of target proteins related to telomere length is usually limited to the context of aging and specific diseases, which limits the discovery of more relevant drug targets. This study integrated large-scale plasma cis-pQTLs data and telomere length GWAS datasets. We used Mendelian randomization(MR) to
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Targeted next-generation sequencing and long-read HiFi sequencing provide novel insights into clinically significant KLF1 variants BMC Genomics (IF 4.4) Pub Date : 2024-03-01 Luyi Ye, Chen Wang, Aijing Li, Minghao Li, Yan Pi, Jingmin Yang, Ziyan Zhu, Daru Lu
Krüppel-like factor 1 (KLF1), a crucial erythroid transcription factor, plays a significant role in various erythroid changes and haemolytic diseases. The rare erythrocyte Lutheran inhibitor (In(Lu)) blood group phenotype serves as an effective model for identifying KLF1 hypomorphic and loss-of-function variants. In this study, we aimed to analyse the genetic background of the In(Lu) phenotype in a