Genomics最新文献

{"title":"Candidate effector proteins revealed by transcriptional profiling during development of Moniliophthora roreri, a fungal pathogen of Theobroma cacao.","authors":"Katiúcia Tícila de Souza de Nascimento, Ícaro Santos Lopes, Ariana Silva Santos, Irma Yuliana Mora-Ocampo, Taís Araújo Santos, Hermanna Vanesca Viana de Oliveira, Larissa Karen Silva Oliveira, Eduardo Almeida Costa, Joise Hander Mares, Maria Zugaib, Karina Peres Gramacho, Daniel Oliveira Jordão do Amaral, Jonathan Javier Mucherino Muñoz, Enrique Arévalo Gardini, Eric Roberto Guimarães Rocha Aguiar, Carlos Priminho Pirovani","doi":"10.1016/j.ygeno.2025.111083","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111083","url":null,"abstract":"<p><p>Frosty pod rot (FPR), caused by Moniliophthora roreri, is one of the most devastating diseases of cocoa plantations in the Americas. This hemibiotrophic fungus only infects the fruits of the cocoa tree. It reduces yields and devalues the fruits, consequently causing economic losses and compromising crops' socioeconomic potential. We analyzed the transcriptome of M. roreri spores and mycelium incubated in a cocoa fruit extract from susceptible plants. A total of 871 differentially expressed genes (DEGs) were identified in spores at different incubation times and in mycelium. The identified DEGs were found to be involved in several biological processes and molecular functions, among them oxidoreductase function, proteolysis, transcriptional regulation, binding processes and stress response. We also explored the repertoire of secreted proteins and putative effectors located in the apoplast and cytoplasm of the host, and found 1075 transcripts encoding secreted proteins, of which 61 were DEGs and 23 were putative effectors, associated with plant cell wall breakdown, oxidative stress, and carbohydrate metabolism. Data also revealed transcripts with up to 50-fold higher expression between the incubation times of non-germinated spores and mycelium, which are considered candidates for marker genes in fungal development. These molecules were related to functions such as growth, pathogenicity, kinase and oxidoreductase activity, playing important roles in the interaction of M. roreri and Theobroma cacao. Functional analysis of three candidate effectors revealed impacts on leaf morphology, mainly leaf drying and wilting, often culminating in necrosis. Our results expand the understanding of the molecular basis of how FPR affects host plants, in addition to identifying a set of secreted proteins that require functional characterization to contribute to disease control.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111083"},"PeriodicalIF":3.4,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotypic and phenotypic characteristics of group B streptococcal isolates from neonates in a tertiary hospital in Qingyang, Gansu Province, China.","authors":"Xinran Li, Lilan Wan, Xiaoyu Zheng, Jilu Song, Yan Yang, Tian Chen, Changjun Wang, Juan Li, Yong Chen, Xiong Liu","doi":"10.1016/j.ygeno.2025.111084","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111084","url":null,"abstract":"<p><p>Group B Streptococcus (GBS) causes severe neonatal infections, leading to high mortality rates. This study aimed to investigate the genetic characteristics of GBS isolates in a hospital setting. Nineteen isolates were identified through a review of preservation and cultivation processes since January 2022, followed by antibiotic susceptibility testing. Whole-genome sequencing (WGS) was used to investigate genetic relationships. Among 19 isolates, serotype V was the most prevalent (n = 7), followed by Ib (n = 6) and III (n = 6). Genomic sequence analysis revealed that 19 isolates belonged to four sequence types (STs) related to four clonal complexes (CCs), namely CC12, CC19, CC327, and CC452. The isolates exhibited high resistance rates to erythromycin (89 %, n = 17), levofloxacin (79 %, n = 15), clindamycin (68 %, n = 13), and tetracycline (53 %, n = 10). The mreA gene was found in all GBS isolates (100 %), while the most prevalent resistance gene was ermB (84 %). Furthermore, the fbsB virulence gene associated with adherence was identified in four serotype V/ST890 GBS isolates. Two isolates with different sequence types (ST10, ST19) were found to have undergone parallel mutations in the gene SE858_09425, which encodes a DNA translocase FtsK. Both exhibited an I259L substitution in a conserved ligand-binding domain, strongly suggesting this site is critical for adaptive evolution. IMPORTANCE: Group B Streptococcus (GBS) is a major pathogen causing severe neonatal infections, such as sepsis and meningitis, with high mortality and morbidity rates. The rising antimicrobial resistance of GBS presents significant challenges for clinical management. This study investigates 19 GBS isolates isolated from neonates in Qingyang, Gansu, focusing on their genetic characteristics and resistance profiles through molecular epidemiological analysis and WGS. The findings offer critical insights into the molecular mechanisms of GBS infections, which can inform infection control measures, improve prevention strategies, and optimize antimicrobial therapies to enhance neonatal healthcare outcomes.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111084"},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of two SARS-CoV-2 whole genome amplification and sequencing workflows for genomic surveillance and outbreak analysis in the clinical microbiology laboratory.","authors":"David Panisello Yagüe, Andreu Coello Pelegrin, Laia Soler, Antoni E Bordoy, Sandra Martínez-Puchol, Gemma Clarà, Sara González-Gómez, Alexia Paris de León, Marc Noguera-Julian, Maria Pilar Armengol, Olga Francino, Cristina Casañ, Irma Casas, Pere-Joan Cardona, Montserrat Giménez, Ignacio Blanco, Verónica Saludes, Elisa Martró","doi":"10.1016/j.ygeno.2025.111077","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111077","url":null,"abstract":"<p><p>Whole-genome sequencing (WGS) has become a key element of SARS-CoV-2 genomic epidemiology. In Spain and many other countries, this is mostly driven by Illumina-based sequencing, while Oxford Nanopore Tecnologies' MinION Mk1C is a low-cost, faster, and user-friendly sequencer. We aimed to evaluate the applicability of the Mk1C device with a long-amplicon PCR approach for SARS-CoV-2 rapid genomic surveillance and outbreak characterization. We compared the technical and practical performance of this workflow with the short-amplicon strategy on Illumina's MiSeq platform. We processed 183 PCR-positive nasopharyngeal samples, one positive control derived from a clinical sample, and two synthetic SARS-CoV-2 controls for both sequencing workflows. Good quality sequences were obtained by both methods: their mean breadth coverage was 99 % for both techniques and while mean depth of coverage was 1.78-fold lower for MinION (990× vs 557×), no single nucleotide polymorphism (SNP) differences were observed between paired synthetic controls and neither for most of the clinical samples (149/158, 94.3 %). Pango lineage assignments were totally concordant, which were mainly from the Omicron variant. Only one sample showed differences in sublineage assignment. Nanopore workflow had 1.3-fold shorter turnaround time to results for large batches of surveillance samples (96-well plate), and 4.1-fold for the study of small batches of outbreak-related samples. Nanopore sequencing had also a 4.5-fold lower cost per sample, considering consumables and reagents. These results support the use of MinION-based workflow for a rapid response to nosocomial outbreaks as well for its implementation into SARS-CoV-2 genomic surveillance, as a reliable alternative to Illumina MiSeq-based workflow.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111077"},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through lncRNA genes","authors":"Qi Wang ,&nbsp;Hangyu Chen ,&nbsp;Baopu Du ,&nbsp;Lulu Wang ,&nbsp;Peng Jing ,&nbsp;Haofeng Wu ,&nbsp;Jian Lin ,&nbsp;Yan Gao","doi":"10.1016/j.ygeno.2025.111085","DOIUrl":"10.1016/j.ygeno.2025.111085","url":null,"abstract":"<div><div>This study investigates the role of 5-hydroxymethylcytosine (5hmC) in long non-coding RNA (lncRNA) genes across diverse human tissues, a topic that has remained underexplored despite previous studies highlighting its contributions to development and tissue specificity. We analyzed 15 human tissue samples using 5hmC sequencing (5hmC-seq) to map the distribution of 5hmC across the genome. Specific enrichment of 5hmC was observed in lncRNA genes, particularly those with tissue-specific expression patterns. Bioinformatics analysis revealed strong correlations between the tissue-specific 5hmC-modified lncRNA genes and their respective functional roles in different tissues. Additionally, pathway enrichment and functional annotation analyses of target genes of key 5hmC-modified lncRNA genes provided further insights into their potential involvement in tissue-specific processes. These findings underscore the significant role of 5hmC modifications in regulating the function of lncRNA genes linked to tissue specificity, offering a foundation for future research on the clinical implications of lncRNA 5hmC modifications.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111085"},"PeriodicalIF":3.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating multi-omics analysis to uncover the impact of PLXNA1 on the progression of esophageal cancer cells","authors":"Zhichao Hou ,&nbsp;Tangjuan Zhang ,&nbsp;Chunyang Zhang ,&nbsp;Zheng Ding ,&nbsp;Peng Wang ,&nbsp;Xue Pan ,&nbsp;Xiangnan Li","doi":"10.1016/j.ygeno.2025.111081","DOIUrl":"10.1016/j.ygeno.2025.111081","url":null,"abstract":"<div><div>Transcriptomics, proteomics, phosphoproteomics, and comprehensive multi-omics analysis were conducted to investigate the relationship between Plexin A1 (PLXNA1) and esophageal cancer (EC) cells. The positive rate of PLXNA1 in EC tissues was significantly high than in adjacent normal tissue. Knocking down PLXNA1 in EC cells led to increased apoptosis and decreased proliferation, invasion, and migration. Analyses revealed that PLXNA1 knockdown influenced cellular transcriptional regulation and cancer-related pathways. Elevated expression of PLXNA1 in patients with EC correlates with survival outcomes. PLXNA1 plays a crucial role in transcriptional regulation and cancer pathways in EC. The expression of PLXNA1 was elevated in patients with EC and might play a key role in EC by regulating the transcriptional process and carcinogenic pathways.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111081"},"PeriodicalIF":3.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global transcriptome characterization of peripheral blood mononuclear cells in individuals with chronic HIV infection","authors":"Han-Ying Wang ,&nbsp;Xi Wang ,&nbsp;Qian-Qian Zhang ,&nbsp;Xing-Zhong Miao ,&nbsp;Liang-Juan Chen ,&nbsp;Li-Jun Sun ,&nbsp;Hong-Bo Shi","doi":"10.1016/j.ygeno.2025.111082","DOIUrl":"10.1016/j.ygeno.2025.111082","url":null,"abstract":"<div><h3>Background</h3><div>Acquired Immune Deficiency Syndrome (AIDS), resulting from Human Immunodeficiency Virus (HIV) infection, is one of the most severe infectious diseases worldwide. The current state of prevention and control remains critical. Recent studies have increasingly highlighted the significant role of cellular metabolism in regulating immune responses and managing infections. However, whether distinct immunometabolic profiles exist among different groups infected with HIV remains to be investigated. In this study, we employed RNA-seq technology to explore the differential characterization of immune metabolism across various HIV infections.</div></div><div><h3>Methods</h3><div>To investigate the metabolic differences in peripheral blood mononuclear cells (PBMCs) from HIV-infected populations, we obtained PBMCs from 18 individuals diagnosed with HIV. This cohort included four Immune Responders (IRs), five Immune Non-Responders (INRs), five typical progressors (TPs) who maintained high viral loads, and four Elite Controllers (ECs) who sustained low levels of viral replication without treatment. We conducted single-cell sequencing on the PBMCs derived from these patients and compared the results between IRs and INRs, as well as ECs and TPs.</div></div><div><h3>Results</h3><div>Our findings revealed significant metabolic dysregulation and altered inflammatory states in INRs compared to IRs. These alterations were primarily observed in purine metabolism, oxidative phosphorylation (OXPHOS) and glycolysis pathways, as well as modifications in amino acid and fatty acid metabolism pathways. Furthermore, we identified variations within a subset of CD8⁺ T-cell populations characterized by high expression of GNLY, which predominantly exerts cytotoxic effects. Differences in metabolic pathways were also noted between ECs and TPs; however, these changes mainly focused on OXPHOS and pentose phosphate pathways while no significant differences were observed in glycolysis pathway.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111082"},"PeriodicalIF":3.4,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of Bacillus anthracis A and B-clades reveals genetic variation in genes responsible for spore germination","authors":"Sankwetea P. Mokgokong ,&nbsp;Ayesha Hassim ,&nbsp;Tendo Mafuna ,&nbsp;Wendy C. Turner ,&nbsp;Henriette van Heerden ,&nbsp;Kgaugelo E. Lekota","doi":"10.1016/j.ygeno.2025.111074","DOIUrl":"10.1016/j.ygeno.2025.111074","url":null,"abstract":"<div><div><em>Bacillus anthracis</em>, the causative agent of anthrax, is composed of three genetic clades (A, B, and C). Clade-A is the most common and distributed worldwide, B-clade has a narrow geographic distribution, and C-clade is rare. South Africa's Kruger National Park (KNP) has high diversity of <em>B. anthracis</em>, with strains from A and B clades described from its northernmost region, Pafuri. We employed whole genome sequencing to investigate the genomic diversity of <em>B. anthracis</em> strains isolated from animal carcasses (<em>n</em> = 34) during the 2012–2015 outbreaks. Whole-genome single-nucleotide polymorphism (wgSNP) analysis assigned the 2012–2015 <em>B. anthracis</em> genomes to the A-clade branch, distributed across the branch's two minor sub-clades A.Br.005/006. Additionally, pan-genomic analysis distinguished the A- and B-clade genomes, identifying unique accessory genes. Notable genetic differences include the biosynthetic spore cell wall genes; long-chain fatty acid CoA ligases (<em>FaD13</em>), <em>Bacillus</em> collagen-like protein of <em>anthracis</em> (BclA) involved in the exosporium germination, as well as a truncated murein DD-endopeptidase (<em>mepH</em>) found in the pXO2 plasmid of the B-clade strains. The tryptophan synthase subunit alpha gene (<em>trpA</em>), which results in a pseudogene in B-clade genomes separates the A- and B-clade genomes. These differences in biosynthetic cell wall genes suggest variation in adaptability or cell growth of the B-clade strains in the environment, further influenced by the truncation of the <em>trpA</em> gene involved in spore germination. The A.Br.005/006-clade strains in KNP exhibit higher genetic diversity, which may enhance their resilience to environmental stressors. In contrast, the KNP B-clade (B.Br.001/002) strains show limited genetic variation, potentially reducing their adaptability. This pattern is evident through whole-genome SNP analysis and pan-genomics investigating the evolution of <em>B. anthracis</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111074"},"PeriodicalIF":3.4,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144580860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome and lipid metabolome of the subcutaneous fat of Tibetan sheep: A comprehensive analysis of the reduction in fat deposition upon resveratrol and β-hydroxy-β-methyl butyric acid supplementation","authors":"Xuan Chen ,&nbsp;Yu Zhang ,&nbsp;Xiaohong Wang ,&nbsp;Zhenling Wu ,&nbsp;Quyangangmao ,&nbsp;Qiurong Ji ,&nbsp;Tingli He ,&nbsp;Kaina Zhu ,&nbsp;Feng shuo Zhang ,&nbsp;Shengzhen Hou ,&nbsp;Linsheng Gui","doi":"10.1016/j.ygeno.2025.111078","DOIUrl":"10.1016/j.ygeno.2025.111078","url":null,"abstract":"<div><div>Previous research studies confirmed that resveratrol (RES) and β-hydroxy-β-methyl butyric acid (HMB) regulated the glucolipid metabolism. However, the mechanism underlying of RES and HMB on subcutaneous fat remains unclear in ruminant. This study investigated the effects of dietary RES and HMB supplementation on immune, oxidative, and morphological changes in subcutaneous fat of Tibetan sheep using transcriptomics and metabolomics analysis. One hundred and twenty male Tibetan lambs of similar initial weight (15.5 ± 0.14 kg) were randomly divided into four groups of 30 lambs each: 1) H group (basal diet without RES or HMB); 2) H-RES group (1.5 g/day RES); 3) H-HMB group (1250 mg/day HMB); and 4) H-RES-HMB group (1.5 g/day RES and 1250 mg/day HMB). The study included a pre-test period of 10 days and a formal experimental period of 90 days. The results showed that, the supplementation of RES and HMB in combination reduced the backfat thickness and adipocyte diameter (<em>P</em> &lt; 0.05). Notably, dietary RES and HMB significantly influenced the composition of fatty acid in subcutaneous fat, including increased monounsaturated fatty acid (MUFA), such as C16:1 N7, C18:1 N9, C20:1 N9, C22:1 N9, C24:1 N9, C24:1 N, and decreased saturated fatty acid (SFA), such as C8:0, C10:0, C11:0, C24:0. The H-RES-HMB group enriched in the lipid-related signaling pathways, including “linoleic acid”, “arachidonic acid”, “tyrosine” and “retinol”. The transcriptome and metabolome indicated ten key genes including <em>PLA2G5</em>, <em>PLA2G2D</em>, <em>PTGES</em>, <em>TBXAS1</em>, <em>ALOX5</em>, <em>MAOA</em>, <em>TYR</em>, <em>UGT1A4</em>, <em>RDH5</em>, and <em>DHRS9</em>) and five metabolites including PC(33:4), LPC(22:0), LPC(15:0), LPC(16:1), PC(42:8) were identified as key biomarkers. In conclusion, dietary RES and HMB supplementation regulated the lipid metabolism by modulating gene transcription and metabolism in Tibetan sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111078"},"PeriodicalIF":3.4,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144600004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of microRNA-mRNA regulatory network associated with microplastic exposure in Mytilus galloprovincialis","authors":"Giovanni Annona ,&nbsp;Concetta Montanino ,&nbsp;Bruna De Felice ,&nbsp;Pasquale De Luca","doi":"10.1016/j.ygeno.2025.111080","DOIUrl":"10.1016/j.ygeno.2025.111080","url":null,"abstract":"<div><div>The ever-growing plastics production and their natural fragmentation in micro- and nanoparticles have made plastic debris ubiquitous, with aquatic environments as the final collection basin. Plastic pollution is responsible for physical damage and biological pathways disruption in marine animals at almost all trophic levels, interfering with primary processes as development, growth, and reproduction. Micro- and nanoplastics accumulate in the food chain and represent a concrete risk for human health. Mussels have a worldwide spread and, as a starring seafood product, may constitute an important vehicle for microplastic uptake in humans.</div><div>Micro- and nanoplastics affect biological processes at the nuclear level, altering DNA methylation and gene regulators, including long non-coding (lncRNAs) and microRNAs (miRNAs). MicroRNAs, interacting with several mRNA targets, can prompt several processes, including antioxidant responses, inflammation, immune system cell recruitment, up to apoptosis.</div><div>The present study investigates the impact of microplastic particles on the modulation of microRNAs in adult mussels <em>Mytilus galloprovincialis</em> and the identification of microRNA-mRNA regulatory network. In this work, we exposed adult mussels to different concentrations and several temporal window to polystyrene monodispersed microparticles and analysed the expression of selected microRNAs and related target genes. Our results revealed that microplastic exposure induces miRNAs modulation and target genes associated with the activation of specific regulatory networks, including immune response, cellular stimuli response, protein interactions, apoptosis, and cell death.</div><div>This study provides new insights into the microplastic capability to affect gene expression and regulatory pathways mRNA miRNA-regulated, contributing to wider knowledge about the adverse effects of plastic pollution and providing useful data for further trials, not just in nature, but also in human health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111080"},"PeriodicalIF":3.4,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level genome assembly and evolutionary analysis of the Nao-zhou stock of large yellow croaker (Larimichthys crocea)","authors":"Hao-jie Wang ,&nbsp;Jing-hui Jin ,&nbsp;Eric Amenyogbe ,&nbsp;Yue Liu ,&nbsp;Shu-pei Huang ,&nbsp;Yi Lu ,&nbsp;Ren-xie Wu ,&nbsp;Zhong-liang Wang ,&nbsp;Grace Afumwaa Boamah ,&nbsp;Jian-sheng Huang","doi":"10.1016/j.ygeno.2025.111075","DOIUrl":"10.1016/j.ygeno.2025.111075","url":null,"abstract":"<div><div>The Nao-zhou stock of large yellow croaker is an indigenous population in the South China Sea and is phenotypically different from the population on the eastern coast of China. The chromosome-level genome assembly presented in this study significantly advances the understanding of <em>Larimichthys crocea</em> by surpassing previous fragmented genome assemblies and genome-wide RAD marker studies. While earlier studies have provided foundational insights into the genetic diversity and population structure of the species, they lack the resolution necessary for in-depth evolutionary, functional, and applied genomic analyses. In this study, the chromosome-level genome assembly of the Nao-zhou stock was constructed by combining MGI (MGISEQ-2000), and PacBio (Pacific Biosciences) HiFi and Hi-C sequencing methods. The results showed that the assembled genome size was 726 Mb, of which 98.27 % (723 Mb) of the sequences were anchored to 24 chromosomes and the proportion of complete genes reached 98.7 %. In the genome annotation, 31.04 % of the repetitive sequences in the genome were identified, with 24,796 protein-coding genes predicted, of which 99.47 % (24,664 genes) were successfully annotated. A total of 867 positively selected genes were identified in the environmental adaptation of the Nao-zhou stock. Gene Ontology (GO) enrichment of these genes showed that they were mainly enriched in DNA replication, rRNA processing, and ubiquinone biosynthesis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that these genes were mainly involved in cytokine receptor interactions, ribosome generation in eukaryotes, DNA replication, and RNA degradation. These genomic data provide valuable genetic resources for more in-depth evolutionary and functional studies in the future, as well as a basis for molecular breeding and protection of this economically important species.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 5","pages":"Article 111075"},"PeriodicalIF":3.4,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}