BMC Genomics最新文献

{"title":"Discovery of variation in genes related to agronomic traits by sequencing the genome of Cucurbita pepo varieties.","authors":"C Pérez-Moro, D D'Esposito, C Capuozzo, A Guadagno, A Pérez-de-Castro, M R Ercolano","doi":"10.1186/s12864-025-11370-x","DOIUrl":"10.1186/s12864-025-11370-x","url":null,"abstract":"<p><strong>Background: </strong>Cucurbita pepo L. cultivars display high morphological traits variation. In addition, C. pepo faces numerous threats, such as viral and fungal infections, which significantly influence crop cultivation. Recent genomic advancements improved the understanding of genetic diversity and stress responses in this crop. We investigated genetic variations related to plant morphology and quality traits. Additionally, the inclusion of both powdery mildew (PM) and Zucchini yellow mosaic virus (ZYMV) susceptible and tolerant varieties facilitated the examination of genetic diversity concerning biotic stress.</p><p><strong>Results: </strong>The sequencing of eight Cucurbita pepo varieties produced an average of 40 million raw reads with a coverage of reference genome ranging from 22 to 40X. More than 4.7 million genomic variants were identified in all genomes. Based on admixture and PCA analysis, the eight C. pepo genotypes were grouped in two clusters belonging to Cocozelle and Zucchini groups, with \"Whitaker\" separated from the rest of the accessions. Genes involved in pathways related to gibberellin regulation, leaf development, and pigment accumulation resulted highly affected by variation suggesting that the diversity observed among varieties in plant and fruit morphology could be related to variants identified in such genes. Each variety showed its own set of genetic differences. The genomic comparison of 381e, 968Rb and SPQ allowed the identification of variants in chromosome regions affecting response to Zucchini yellow mosaic virus (ZYMV) and powdery mildew (PM). Variants in key genes associated with resistant traits were identified, suggesting potential pathways and mechanisms involved in biotic stress response and plant immunity.</p><p><strong>Conclusions: </strong>Genetic variations affecting morphology and fruit quality in C. pepo emphasize their significance for breeding efforts. Furthermore, the genomic comparison of 381e, 968Rb and SPQ highlighted variants in chromosomal regions influencing zucchini's response to PM and ZYMV. These findings could pave the way for more targeted and effective genetic improvement strategies, thereby potentially leading to increased agricultural productivity and quality.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"335"},"PeriodicalIF":3.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11969804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coupled evolutionary rates shape a Hawaiian insect-symbiont system.","authors":"Patrick H Degnan, Diana M Percy, Allison K Hansen","doi":"10.1186/s12864-025-11514-z","DOIUrl":"10.1186/s12864-025-11514-z","url":null,"abstract":"<p><strong>Background: </strong>The Hawaiian Pariaconus psyllid radiation represents a unique system to study the co-evolution of nuclear, mitochondrial, and endosymbiont genomes. These psyllids, which diversified across the Hawaiian Islands during the last 3-3.5 million years vary with their ecological niches on their plant host 'Ōhi'a lehua (Metrosideros polymorpha) (free-living, open-gall, and closed-gall lifestyles) and harbor one to three beneficial bacterial endosymbionts. Co-evolutionary studies of other multi-endosymbiont insect systems have shown decoupled rates of sequence evolution between mitochondria and endosymbionts. Here we examine the evolutionary trends in Pariaconus psyllids, their mitochondria and their endosymbionts to determine if they fit this paradigm.</p><p><strong>Results: </strong>We sequenced a new Carsonella genome from the ohialoha species group (closed-gall, one symbiont), revealing a remarkable degree of gene conservation between two of the most divergent species from this diverse species group that has dispersed across multiple islands. Further, despite the rapid radiation of psyllid species, we observed complete synteny among mitochondrial genomes from all six Pariaconus species in this study, suggesting the preservation of genome structure due to strong purifying selection. Phylogenetic analyses of the nuclear, mitochondrial, and endosymbiont genomes across these six Pariaconus species revealed correlated rates of substitutions, contrary to prior reports of decoupling between mitochondrial and endosymbiont genomes in other insect systems with multiple symbiont partners. Finally, we found that free-living psyllids with three symbionts exhibited elevated mutation rates (~ 1.2-1.6x) across all genomes and elevated rates of fixation of nonsynonymous substitutions in the insect nuclear genome and one of the endosymbionts.</p><p><strong>Conclusions: </strong>This study highlights the interplay between ecological diversification and genomic evolution in Pariaconus. Further, these data indicate that multiple endosymbiont partners alone are not sufficient to result in decoupling rates of sequence evolution. Future work on basal members of this species radiation will refine our understanding of the mechanisms shaping this dynamic insect-symbiont system and its implications for genome evolution.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"336"},"PeriodicalIF":3.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing reveals the genetic diversity and structure of Leptosphaeria maculans populations from the Western Cape province of South Africa.","authors":"Huibrecht Maria Schreuder, Beatrix Coetzee, Gerhardus Johannes van Coller, Diane Mostert","doi":"10.1186/s12864-025-11413-3","DOIUrl":"10.1186/s12864-025-11413-3","url":null,"abstract":"<p><strong>Background: </strong>Leptosphaeria maculans is the causal agent of blackleg, a globally important disease of canola. Investigating the genetic diversity and structure of L. maculans populations can provide insight into its evolutionary potential and genetic variability, which is important to develop effective blackleg management strategies. In this study, whole genome sequence data was generated for 230 L. maculans isolates collected between 2020 and 2022 across the canola production regions of the Western Cape of South Africa. A total of 27 419 informative single nucleotide polymorphisms was used to investigate the genetic diversity and structure of the pathogen population.</p><p><strong>Results: </strong>Mating type distribution did not deviate statistically from a 1:1 ratio at any location, indicating no restriction on sexual reproduction. Genetic statistics calculated showed high genotypic diversity and evenness (Lambda and E.5 ≥ 0.98) and low linkage disequilibrium ( ≤ 2.71E-04) which is also associated with sexual reproduction. Discriminative analysis of principal components and sparse nonnegative matrix factorisation revealed genetic differentiation between the Swartland and Southern Cape canola production regions in the Western Cape. Analysis of molecular variance also indicated regions as the most important factor for population differentiation but suggested shallow population structure with only 3,71% of the total variation occurring between regions. To assess the phylogenomic position of South African isolates in the global context, data for 171 international isolates was included, and the clustering analyses repeated. Results showed a high similarity between Australian and Swartland isolates, while isolates from the Southern Cape formed a unique genetic cluster.</p><p><strong>Conclusion: </strong>The results from this study provide the basis for blackleg research in South Africa and enhances understanding of the pathogen, which will assist in developing improved blackleg management strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"334"},"PeriodicalIF":3.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole exome sequencing shows novel COL4A3 and COL4A4 variants as causes of Alport syndrome in Rio Grande do Norte, Brazil.","authors":"Washington Candeia de Araújo, Raul Maia Falcão, Raquel Araujo Costa Uchoa, Carlos Alexandre Garcia, Arthur Quintiliano Bezerra da Silva, Kesia Larissa Medeiros Quirino, Francisco Paulo Freire-Neto, Genilson Pereira Gurgel, Paulo Ricardo Porfirio Nascimento, Leonardo Capistrano Ferreira, Priya Duggal, Jorge Estefano S de Souza, Selma M B Jeronimo","doi":"10.1186/s12864-025-11466-4","DOIUrl":"10.1186/s12864-025-11466-4","url":null,"abstract":"<p><strong>Background: </strong>Alport syndrome is a progressive and hereditary nephropathy characterized by hematuria and proteinuria as well as extra renal manifestations as hearing loss and eye abnormalities. The disease can be expressed as autosomal recessive or autosomal dominant at COL4A3 and COL4A4 loci, respectively, or X-linked at the COL4A5 locus. This study investigated two unrelated families with nephropathy from Brazil with the aim to identify the mutations involved with the disease.</p><p><strong>Methods: </strong>Whole Exome Sequencing was performed for 4 people from each pedigree (case, parents and a sibling). DNA sequences were mapped against the human genome (GRCh38/hg38 build) to identify associated mutations.</p><p><strong>Results: </strong>Two novel deleterious variants in COL4A3 and COL4A4 loci on chromosome 2 were identified. The variants were detected in the probands with mutant alleles in the homozygous state, a premature stop codon at position 481 of COL4A3 protein and a frameshift mutation leading to a stop codon at position 786 of COL4A4 protein. For both Alport cases the putative variants were surrounded by broad Runs of Homozygosity as well as genes associated with other hereditary nephropathies. Genotyping for COL4A3 validated the exome findings.</p><p><strong>Conclusions: </strong>Two novel variants were identified in two unrelated families from northeast of Brazil. The two deleterious variants identified are located on ROH´s locus with all variants in a homozygous state.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"331"},"PeriodicalIF":3.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated transcriptomics and metabolomics to explore the mechanisms of Elaeagnus mollis diels seed viability decline.","authors":"Ren Ruifen, Guo Jiayi, Ji Zhe, Du Shuhui, Yang Xiuyun","doi":"10.1186/s12864-025-11483-3","DOIUrl":"10.1186/s12864-025-11483-3","url":null,"abstract":"<p><p>Elaeagnus mollis Diels, is a rare and endangered woody plant endemic to China, which is listed on the IUCN Red List. In the natural state, the viability of its seeds declines very rapidly, which is the key to its endangered status, but the mechanism of E. mollis seed viability decline is still unclear. In order to explore the physiological and molecular mechanism of viability decline of E. mollis seeds, this study used fresh seeds as a control to compare and analyze the changes of seed vitality, antioxidant system, transcription and metabolomics, when seeds were stored for 1 and 3 months at room temperature. The viability of E. mollis seed decreased continuously after 1 month and 3 months of storage. The activities of superoxide dismutase (SOD), monodehydroascorbate reductase (MDHAR), ascorbate (AsA), and glutathione (GSH) decreased significantly, while catalase (CAT) activity increased gradually during the decline of seed viability. Transcriptomic results showed that a total of 801 differentially expressed genes (DEGs) were identified between fresh and 1-month-stored seeds, while 1,524 were identified between fresh and 3-month-stored seeds. Among them, the expression of CAT, MDHAR, GSH and GR were consistent with the results of physiological indicators. Moreover, WRKY, C3H, bZIP, B3, bHLH, NAC and AP2 / ERF-ERF transcription factors are important in regulating seed viability. Metabolomics results showed that the types of differential accumulated metabolites (DAMs) during viability decline were mainly flavonoids, amino acids and derivatives, and phenolic acids. The combined analysis results of transcriptomics and metabolomics further showed that DEGs and DAMs associated with viability were co-enriched in flavonoid biosynthesis and tryptophan metabolism pathways. Also identified were 22 key antioxidant genes, including CAT, ALDH, CHS and C4H, which were identified as participating in the changes of seed viability. This also illustrated that the metabolic pathways of flavonoid biosynthesis and tryptophan metabolism were involved in regulating the decline of seed viability by acting on the antioxidant system. These findings provide new insights into the mechanism of seed viability decline of E. mollis.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"333"},"PeriodicalIF":3.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The comparative genomic analysis provides insight into the divergent inhibitory activity metabolites in pathogen-driven three Pseudomonas palleroniana strains against primary pathogens of Pseudostellaria heterophylla.","authors":"Chunfeng Huang, Xiaoai Wang, Yanping Gao, Xue Jiang, Lingling Wang, Xiaohong Ou, Yanhong Wang, Tao Zhou, Qing-Song Yuan","doi":"10.1186/s12864-025-11527-8","DOIUrl":"10.1186/s12864-025-11527-8","url":null,"abstract":"<p><p>Pseudostellaria heterophylla (Miq.) Pax ex Pax et Hoffm. is a member of the Caryophyllaceae family, in which dried tuberous root is the well-known traditional Chinese medicine (TCM) and a widespread food ingredient in Asia. In recent years, the large-scale cultivation of P. heterophylla has led to frequent infectious diseases caused by multiple pathogens. However, efficient and safe approaches for preventing and managing P. heterophylla diseases have become urgent for this high-quality industrial development. Herein, a culturable microbiome of diseased P. heterophylla rhizosphere soil was constructed, and the broad-spectrum antifungal activity of Pseudomonas was screened. Three P. palleroniana strains, B-BH16-1, B-JK4-1, and HP-YBB-1B, were isolated and identified with vigorous antifungal activity by confrontation method. We employed the PacBio RS II single-molecule real-time (SMRT) sequencing and Illumina sequencing methods to obtain the genome of these three isolates. Phylogenetic, synteny, and ANI analysis showed that the lineage between strain B-JK4-1 with B-BH16-1 or HY-YBB-1B was closer than that between strain B-BH16-1 with HP-YBB-1B. The comparative genome of strains B-BH16-1, B-JK4-1, and HP-YBB-1B showed marked differences in secondary metabolite biosynthesis genes among these three P. palleroniana strains. Strain B-BH16-1, B-JK4-1, and HP-YBB-1 produced tolaasin I/tolaasin F (23 genes), sessilin A (37 genes), and putisolvin (39 genes), respectively. CAZyme analysis showed that 126, 129, and 127 CAZymes were identified in strains B-BH16-1, B-JK4-1, and HP-YBB-1B genomes, which genes in auxiliary activities (AA), carbohydrate esterases (CE), and glycosyl transferases (GT) categories were different among these three strains. These results provide new insights into the divergent antifungal metabolites in pathogen-driven three P. palleroniana strains against primary pathogens of Pseudostellaria heterophylla.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"332"},"PeriodicalIF":3.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Caregiver-child interaction and early childhood development among preschool children in rural China: the possible role of blood epigenome-wide DNA methylation.","authors":"Mengna Wei, Rui Chang, Chunan Li, Yanfen Jiang, Jianduan Zhang","doi":"10.1186/s12864-025-11406-2","DOIUrl":"10.1186/s12864-025-11406-2","url":null,"abstract":"<p><strong>Background: </strong>While the association between caregiver-child interaction and early childhood development (ECD) has been observed, the underlying biological mechanism remains to be elucidated.</p><p><strong>Objective: </strong>This study aimed to examine the potential role of epigenome-wide DNA methylation in the association between caregiver-child interaction and ECD among preschool children living in rural China.</p><p><strong>Methods: </strong>This study was conducted in a rural area in Central China. ECD was evaluated with the Gesell Development Diagnosis Scale (Chinese version), yielding a developmental quotient (DQ), i.e. global neurodevelopmental score (NDS). Caregiver-child interaction was assessed using the Brigance Parent-Child Interaction Scale. Of the 171 children aged 3-6 years who participated in ECD assessment and blood samples collection, a total of 64 were selected for epigenome-wide association study with Illumina Infinium MethylationEPIC v1.0 BeadChip array (850 K). The linear regression model in the R package \"CpGassoc\"was applied to identify CpG sites associated with global NDS and caregiver-child interaction. The causal inference test (CIT) was utilized to explore the potential mediation effect of DNA methylation.</p><p><strong>Results: </strong>Our epigenome-wide DNA methylation analysis revealed 844 CpG sites significantly associated with children's global NDS (P_FDR<0.05), while no CpG sites were found to be directly related to caregiver-child interaction after FDR correction. Mediation analysis indicated that 395 CpG sites mediated the association between caregiver-child interaction and children's ECD before FDR correction; and among the genes with top 20 CpG sites, genes CFAP45 (cg07740897), PCDH9 (cg20666533), LAMC3 (cg14447608), FAM19A5 (cg13192640), PRKG1 (cg09071556), PLEKHG5 (cg05151739), TCERG1 (cg09189322), and MTRR (cg08075506) have been reported to be associated with neurodevelopment and related diseases.</p><p><strong>Conclusions: </strong>Blood DNA methylation may mediate the association between caregiver-child interaction and ECD in preschool children. This provides population-level epigenetic evidence supporting parenting interventions for vulnerable preschool children who experience poor caregiver-child interaction, aiming to ensure optimal early development potential. However, future studies in diverse populations are needed to validate these findings.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"329"},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LoniComp: a platform for gene function comparison and analysis between Lonicera japonica and Lonicera macranthoides.","authors":"Jingjie Zhang, Bingbing Pan, Jiangxin Yang, Qi Pan, Panpan Zhu, Jiaotong Yang, Mian Zhang, Qiaoqiao Xiao","doi":"10.1186/s12864-025-11507-y","DOIUrl":"10.1186/s12864-025-11507-y","url":null,"abstract":"<p><p>Lonicera japonica and L. macranthoides are popular medicinal plants used for treating various diseases. Recently, new chromosome level genomes of Lonicera have provided a huge resource for understanding gene function. Although LjaFGD was created for analyzing L. japonica gene functions, it is now outdated due to updated genomes and more transcriptome data. Utilizing new chromosome-level genomic and transcriptomic data, we developed co-expression networks of L. japonica and L. macranthoides. Gene annotations were performed by comparing sequences with NR, TAIR, Swissprot, and trEMBL databases. GO and KEGG annotations were predicted using InterProScan and GhostKOALA software, while gene families were identified with iTAK, HMMER, and InParanoid. To fully leverage the utilization value of public resources and data, we developed LoniComp ( www.gzybioinformatics.cn/LoniComp ) as a newer and information-rich alternative, a platform for gene function comparison and analysis by integrating genomic, transcriptomic data and processed functional annotations. It features tools like BLAST, Extract Sequence, Enrichment, Heatmap, DEG, and JBrowse2. We demonstrated its use with examples like LjFT and LjMYB12. It offers superior genomic data, transcriptomic resources, and analysis tools compared to LjaFGD, aiding researchers in gene function studies and comparison.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"328"},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity.","authors":"Loizos Savva, Anthony Bryan, Dominik Vinopal, Oscar E Gonzalez-Navarro, Zennah Kosgey, Kimani Cyrus Ndung'u, Jemal Tola Horo, Kitessa Gutu Danu, Messele Molla, Yoseph Alemayehu, David P Hodson, Diane G O Saunders","doi":"10.1186/s12864-025-11428-w","DOIUrl":"10.1186/s12864-025-11428-w","url":null,"abstract":"<p><strong>Background: </strong>Fungal plant disease outbreaks are increasing in both scale and frequency, posing severe threats to agroecosystem stability, native biodiversity and food security. Among these, the notorious wheat stem rust fungus, Puccinia graminis f.sp. tritici (Pgt), has threatened wheat production since the earliest days of agriculture. New Pgt strains continue to emerge and quickly spread over vast distances through the airborne dispersal of asexual urediniospores, triggering extensive disease outbreaks as these exotic Pgt strains often overcome resistance in dominant crop varieties of newly affected regions. This highlights the urgent need for a point-of-care, real-time Pgt genotyping platform to facilitate early detection of emerging Pgt strains.</p><p><strong>Results: </strong>In this study, we developed a simple amplicon-based re-sequencing platform for rapid genotyping of Pgt isolates. This system is built around a core set of 276 Pgt genes that we found are highly polymorphic between Pgt isolates and showed that the sequence of these genes alone could be used to accurately type Pgt strains to particular lineages. We also developed a simplistic DNA preparation method and an automated bioinformatic pipeline, to enable these Pgt gene markers to be sequenced and analysed rapidly using the MinION nanopore sequencing device. This approach successfully enabled the typing of Pgt strains within approximately 48 h of collecting Pgt-infected wheat samples, even in resource-limited locations in Kenya and Ethiopia. In addition, we incorporated monitoring capabilities for sequence variations in Pgt genes that encode targets of the azole and succinate dehydrogenase inhibitor fungicides, enabling real-time tracking of potential shifts in fungicide sensitivity.</p><p><strong>Conclusion: </strong>The newly developed Pgt Mobile And Real-time, PLant disEase (MARPLE) diagnostics platform we established, now allows precise typing of individual Pgt strains while simultaneously tracking changes in fungicide sensitivity, providing an early warning system for potential indicators of changes in the Pgt population and emerging fungicide resistance. Further integration of this Pgt MARPLE diagnostics platform into national surveillance programmes will support more informed management decisions and timely responses to Pgt disease outbreaks, helping reduce the devastating crop losses currently caused by this 'cereal killer'.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"327"},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The potential mechanism of MicroRNA involvement in the regulation of muscle development in weaned piglets by tryptophan and its metabolites.","authors":"Tianle He, Qingyun Chen, Huifeng Li, Jiani Mao, Ju Luo, Dengjun Ma, Zhenguo Yang","doi":"10.1186/s12864-025-11424-0","DOIUrl":"10.1186/s12864-025-11424-0","url":null,"abstract":"<p><strong>Background: </strong>Muscle development is a key factor influencing the growth performance of piglets. Optimizing this developmental process is crucial for enhancing breeding efficiency and economic profitability. Tryptophan (Trp) is considered one of the key limiting amino acids for weaned piglets, plays an essential role in regulating feed intake, growth, and muscle development. However, the regulatory mechanisms by which Trp and its derivatives influence muscle development in weaned piglets remain unclear.</p><p><strong>Methods: </strong>The aim of this study was to investigate the regulatory pathways and potential mechanisms of Trp and its metabolites on muscle development in weaned piglets. In this study, 10 healthy castrated male piglets, 28 days old and weaned, were selected and randomly assigned to a control group (CON, 0.14% Trp) and a high tryptophan group (HT, 0.35% Trp), with 5 in each group. After a 7-day pre-feeding period, the formal feeding began, and after 28 days, the pigs were slaughtered and the longissimus dorsi muscles was collected for transcriptome sequencing.</p><p><strong>Results: </strong>The results indicated that different dietary Trp levels led to the identification of sixteen differentially expressed microRNAs (DE miRNAs) in the longissimus dorsi muscle of the weaned piglets. Target gene functional enrichment analysis showed that these DE miRNAs are involved in muscle cell proliferation, differentiation, protein deposition, and muscle development through multiple biological pathways. Furthermore, we constructed a protein-protein interaction (PPI) network for the target genes, with the enriched core gene cluster functions associated with cellular proliferation, signaling pathways, hormone release, and muscle development. Finally, qRT-PCR validated the reliability and accuracy of the RNA-seq results, revealing a correlation coefficient of 0.97 between the two methods.</p><p><strong>Conclusions: </strong>This study uncovers the potential mechanisms by which miRNAs participate in the regulation of muscle development in weaned piglets mediated by Trp and its metabolites, providing a theoretical basis and practical guidance for optimizing piglet management and health improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"330"},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}