BMC Genomics最新文献

{"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":"","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":"","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":"https://doi.org/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":"","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":"","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":"https://doi.org/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":"","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":"","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":"","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":"","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":"","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":"","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":"https://doi.org/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":"","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":"","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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive genomic epidemiology and antimicrobial resistance profiles of clinical Klebsiella pneumoniae species complex isolates from a tertiary hospital in Wenzhou, China (2019-2021).","authors":"Weiyan Jiang, Yanhui Chen, Meimei Lai, Yongan Ji, Suzhen Lin, Jiao Shao, Xiaojian Chen","doi":"10.1186/s12864-025-11509-w","DOIUrl":"10.1186/s12864-025-11509-w","url":null,"abstract":"<p><strong>Background: </strong>The main issue of the Klebsiella pneumoniae species complex (KpSC) research in clinical settings is the accurate identification and differentiation of the closely related species within this complex. Moreover, the emergence and spread of carbapenem-resistant K. pneumoniae (CRKP) represent a significant public health threat due to limited treatment options and high mortality rates. Understanding the genetic basis of resistance and virulence is crucial for developing effective infection control strategies. In this work, the genomic epidemiology and antimicrobial resistance profile of KpSC isolates from Wenzhou, China, was investigated to fully understand the implications of the KpSC in clinical settings.</p><p><strong>Methods: </strong>We conducted a comprehensive analysis of 156 clinical KpSC isolates collected from a tertiary hospital in China over a three-year period (2019-2021). Antimicrobial susceptibility testing was performed according to CLSI standards. Whole-genome sequencing (WGS) and subsequent bioinformatic analyses were conducted to identify resistance genes, plasmid types, and virulence factors. Phylogenetic relationships were determined using maximum-likelihood analysis.</p><p><strong>Results: </strong>All CRKP isolates exhibited high levels of resistance to carbapenems, cephalosporins, and aminoglycosides. The most prevalent carbapenemase genes were bla_KPC-2 (100%), with significant associations between bla_KPC-2 and ST11. Phylogenetic analysis revealed considerable genetic diversity, with over 50 sequence types (STs) present. A subset of isolates harbored both resistance and hypervirulence genes, including rmpA, rmpA2, and siderophore systems, which were associated with potential higher pathogenesis.</p><p><strong>Conclusion: </strong>This study provides novel insights into the molecular epidemiology of KpSC in Wenzhou, China, highlighting the coexistence of antimicrobial resistance and virulence factors in clinical isolates. The findings underscore the importance of continuous genomic surveillance and targeted therapeutic strategies to combat KpSC infections. Our research fills critical gaps in the current understanding of KpSC epidemiology in China and offers valuable data for global comparative studies, contributing to the development of effective infection control measures. Genomic surveillance in China thus provides crucial insights for local risk mapping and informs necessary adaptions for implementation of control strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"318"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751010","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":"Genome-wide identification and expression pattern analysis of the cinnamoyl-CoA reductase gene family in flax (Linum usitatissimum L.).","authors":"Xixia Song, Dandan Liu, Yubo Yao, Lili Tang, Lili Cheng, Lie Yang, Zhongjuan Jiang, Qinghua Kang, Si Chen, Jiarong Ru, Lili Zhang, Guangwen Wu, Hongmei Yuan","doi":"10.1186/s12864-025-11481-5","DOIUrl":"10.1186/s12864-025-11481-5","url":null,"abstract":"<p><strong>Background: </strong>Cinnamoyl-CoA reductase (CCR) is the first important and committed enzyme in the monolignol synthesis branch of the lignin biosynthesis (LB) pathway, catalyzing the conversion of cinnamoyl-CoAs to cinnamaldehydes and is crucial for the growth of Linum usitatissimum (flax), an important fiber crop. However, little information is available about CCR in flax (Linum usitatissimum L.).</p><p><strong>Results: </strong>In this study, we conducted a genome-wide analysis of the CCR gene family and identified a total of 22 CCR genes. The 22 CCR genes were distributed across 9 chromosomes, designated LuCCR1-LuCCR22. Multiple sequence alignment and conserved motif analyses revealed that LuCCR7/13/15/20 harbor completely conserved NADP-specific, NAD(P)-binding, and CCR signature motifs. Furthermore, each of these LuCCRs is encoded by 5 exons separated by 4 introns, a characteristic feature of functional CCRs. Phylogenetic analysis grouped LuCCRs into two clades, with LuCCR7/13/15/20 clustering with functional CCRs involved in LB in dicotyledonous plants. RNA-seq analysis indicated that LuCCR13/20 genes are highly expressed throughout all flax developmental stages, particularly in lignified tissues such as roots and stems, with increased expression during stem maturation. These findings suggest that LuCCR13/20 play crucial roles in the biosynthesis process of flax lignin. Additionally, LuCCR2/5/10/18 were upregulated under various types of abiotic stress, highlighting their potential roles in flax defense-related processes.</p><p><strong>Conclusions: </strong>This study systematically analyzes the CCR gene family (CCRGF) of flax (Linum usitatissimum L.) at the genomic level for the first time, so as to select the whole members of the CCRGF of flax and to ascertain their potential roles in lignin synthesis. Therefore, in future work, we can target genetic modification of LuCCR13/20 to optimize the content of flax lignin. As such, this research establishes a theoretical foundation for studying LuCCR gene functions and offers a new perspective for cultivating low-lignin flax varieties.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"315"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751017","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-sequence analysis of Bacillus subtilis strain KC14-1 with broad-spectrum antifungal activity.","authors":"Xiaowei Li, Yahan Chen, Shunyi Yang, Yi Zhou, Chengde Yang","doi":"10.1186/s12864-025-11227-3","DOIUrl":"10.1186/s12864-025-11227-3","url":null,"abstract":"<p><strong>Background: </strong>Bacillus is used as a biological control agent in agricultural production. The main mechanisms responsible for its biocontrol activity encompass the generation of various antifungal active substances during life activities, competition, antagonism with pathogens, promotion of growth, and induction of plant resistance, enhancing the inhibition of pathogenic fungi. Bacillus has high biological control potential and has become a research hotspot.</p><p><strong>Results: </strong>It was found that strain KC14-1 had significant inhibitory effects on Fusarium fujikuroi, Rhizoclonia solani, Alternaria solani, Fusarium oxysporum, and Valsa mali. Based on morphological observations, physiological and biochemical determinations, and 16 S rRNA, gyrA, and gyrB gene sequencing, strain KC14-1 was identified as Bacillus subtilis. Whole genome sequencing results showed that the genome of strain KC14-1 was composed of a ring chromosome 3,908,079 bp in size, with a GC content of 43.82% and 3,895 coding genes. Anti-SMASH predicted that the genome of strain KC14-1 contained nine gene clusters that synthesised antibacterial substances. The homology between fengycin, bacillibactin, pulcherriminic acid, subtilosin A, and bacilysin was 100%.</p><p><strong>Conclusion: </strong>The biocontrol potential of Bacillus subtilis KC14-1 was determined through whole-genome analysis. Our study provides a solid foundation for developing and utilising this strain.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"319"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750517","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}