Molecular Genetics and Genomics最新文献

{"title":"Prevalence and molecular spectrum of thalassemia in infertile population among different ethnic groups in Hainan Province, China.","authors":"Yongle Zhang, Jinyu Kang, Wenye Sun, Fei Sun, Ge Gao, Junhong Chen, Qi Li, Qiuling Jie, Yanlin Ma","doi":"10.1007/s00438-025-02234-w","DOIUrl":"https://doi.org/10.1007/s00438-025-02234-w","url":null,"abstract":"<p><p>Hainan is an area with high prevalence of thalassemia and complex genetic background. There are few studies on the prevalence and genotype of thalassemia in different ethnic groups of infertility patients in Hainan province. The aim of our study was to explore the prevalence and genotype of thalassemia among infertile individuals in Hainan Province. Thalassemia genotypes were determined using gap-PCR and PCR-RBD in 13,856 infertile individuals in our study. Among them, 3458 (24.96%) were diagnosed as thalassemia carriers. In Li ethnic group, 649 (75.12%) were diagnosed as thalassemia carriers, which significantly higher than Han (21.62%) and other ethnicities (22.09%). As the molecular spectrum of thalassemia, the most common α-thalassemia genotype among Han and other ethnicities was -α^3.7/αα, while among Li ethnic group was -α^4.2/αα. For β-thalassemia, the most common genotype among Han and Li ethnic groups was β^41-42 M/βN, while both β^41-42 M/βN and β^17M/βN were common genotype in other ethnic groups. In αβ-complex thalassemia, the most common genotype among the Han ethnic group was -α^3.7/αα & β^41-42 M /βN, followed by -α^4.2/αα & β^41-42 M /βN in the Li ethnic group, and αα^WS/αα & β^41-42 M /βN and -α^4.2/αα & β^41-42 M /β^17M were common in other ethnic groups. Compare with reproductive age population, the infertile population in our study exhibits a notably higher prevalence of α-thalassemia carriers, particularly those with the silent type. This study reveals the genetic epidemiology of thalassemia in the region, providing a scientific basis for targeted health interventions, screening programs, and genetic counseling for infertile population in Hainan Province.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"29"},"PeriodicalIF":2.3,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trio-WES and functional validation reveals a novel splice site variant of SLC26A3 in a case with congenital chloride diarrhea and a systematic review of SLC26A3 mutations in China.","authors":"Ruixue Zhang, Hongping Li, Rong Qiang, XinRu Gao, Jinzhen Guo, Guoqiang Chen, Qin Nan, Limei Zhong, Lin Wang","doi":"10.1007/s00438-025-02233-x","DOIUrl":"https://doi.org/10.1007/s00438-025-02233-x","url":null,"abstract":"<p><p>Congenital chloride diarrhea (CCD) is an autosomal recessive disease, characterized by watery diarrhea, hypochloremia and metabolic alkalosis. It is associated with defects in solute carrier family 26 member 3 (SLC26A3) which acts as Na⁺-independent Cl^-/HCO₃^- exchanger. Early diagnosis allows planning of perinatal care and timely treatment to improve the prognosis of CCD. However, only few cases were diagnosed in the fetus period, while most of CCD cases were diagnosed after birth without timely diagnosis and treatment. This study was conducted to verify the disease-causing gene by prenatal genetic and functional tests for assisting prenatal diagnosis of a fetus with suspected CCD and reviewed the mutation spectrum of Chinese CCD patients for the first time. Here, we reported a suspected CCD fetus with signs of polyhydramnios and intestinal dilatation by prenatal ultrasound. Subsequent prenatal Trio-whole-exome sequencing identified a novel homozygous mutation (c.383-5A > G) of SLC26A3, which was classified as uncertain significance (VUS). Mini-Gene Splicing Assay confirmed the effect of VUS variant on abnormal splicing of SLC26A3, increasing pathogenicity evidence, and determining the prenatal diagnosis and subsequent treatment of CCD. Literature review of 18 CCD cases showed that t c.270_271insAA (p.G91Kfs*3) was the most frequent mutation in China. In conclusion, our study found the novel c.383-5A > G mutation of SLC26A3 as the pathogenic cause in the proband, which expanded the mutation spectrum of SLC26A3. There also highlights the importance of integrative genetic and functional tests that provide a reference for prenatal diagnosis of suspected CCD to access postnatal management in a timely manner.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"28"},"PeriodicalIF":2.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of Indian waxy and non-waxy maize germplasm for genetic differentiation through SNP genotyping.","authors":"Sreya Venadan, Abhijit Kumar Das, Shubhank Dixit, Arushi Arora, Bhupender Kumar, Firoz Hossain, Saurav Saha, Sujay Rakshit","doi":"10.1007/s00438-024-02222-6","DOIUrl":"https://doi.org/10.1007/s00438-024-02222-6","url":null,"abstract":"<p><p>Waxy maize characterized by high amylopectin content resulting from a recessive wx1 gene, is important for both dietary and industrial applications, yet it suffers from low yields and limited breeding options. This study aims to develop a thorough understanding of the underlying genetics for successful hybridization experiments in waxy maize and the identification of potential cross combinations to derive high-yielding waxy maize hybrids in India. Here, we evaluated the kernel starch composition, yield-related traits, molecular diversity, kinship, LD, population structure, and selection signatures in a panel of 11 waxy and 37 non-waxy maize genotypes. The starch content in the panel ranged from 57.85 to 66.96%, while the amylopectin ranged from 70.65% to 96.32%. A significant positive correlation between kernel starch and amylopectin (0.39**) was identified suggesting the potential for simultaneous improvement of both these traits. The 48 maize lines were genotyped with 24,477 highly polymorphic single nucleotide polymorphisms (SNPs). Seventy-eight per cent of the pair-wise relative kinship values were less than or equal to 0, indicating minimal redundancy in the genomic composition of the inbred lines. The range of genetic distance among the pairs of waxy lines was 0.190 to 0.231 as compared to 0.076-0.264 in the non-waxy genotypes suggesting a greater genetic variation among the non-waxy genotypes. The mean LD value across the genome was 0.44. Two to four groups were identified using the model-based population structure, phylogenetic analysis and principal component analysis with no clear pattern of clustering based on the type of corn. Pairwise comparisons using the SNP dataset between waxy and non-waxy maize detected 27 loci under positive selection. The information generated in this study will be useful in the diversification of Indian waxy maize lines and the development of superior waxy maize hybrids.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"27"},"PeriodicalIF":2.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome analysis of Bacillus velezensis HF-14,109 with potential for broad-spectrum antimicrobial activity and high enzyme-producing ability from common carp (Cyprinus carpio L.).","authors":"Jianxin Zhang, Jingyu Wu, Yongyan Chen, Xiuxiu Li, Yiran Jia, Xiaotong Zhang, Xulu Chang, Junchang Feng, Xiaolin Meng","doi":"10.1007/s00438-025-02229-7","DOIUrl":"https://doi.org/10.1007/s00438-025-02229-7","url":null,"abstract":"<p><p>Bacillus velezensis (B. velezensis) HF-14,109 is an aerobic Gram-positive bacterium isolated from the gut of healthy carp (Cyprinus carpio L.). Here, we sequenced and annotated the genome of HF-14,109, identified and classified its enzyme-producing genes and secondary metabolite biosynthesis gene clusters (BGCs), and verified the inhibitory effects on pathogenic bacteria in vitro. Results suggested that HF-14,109 had a circular 4,214,172 bp genome that contains 4,392 predicted genes with an average length and GC content of 851.56 bp and 46.94%, respectively. A total of 210 non-coding RNAs, 8 CRISPR sequences, and 152 tandem repeats were predicted. Based on a CAZy database analysis, HF-14,109 contains 93 genes encoding enzymes for carbohydrate-related processes, 38 of which were glycoside hydrolase genes and divided into 20 families. Based on enzyme predictions, HF-14,109 had the capability to hydrolyze high molecular carbohydrates such as starch, disaccharides such as lactose and sucrose, and non-starch polysaccharides such as β-glucan, mannan, fructan and xylan. Twelve BGCs for producting secondary metabolites were identified by antiSMASH analysis, 5 of which were predicted to encode polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs), indicating that HF-14,109 could produce multiple secondary metabolites. The genome of HF-14,109 contained numerous genes encoding glycoside hydrolases and BGCs for producting secondary metabolites. Besides, the HF-14,109 could inhibit pathogenic bacteria such as E. tarda, A. hydrophila, S. aurenus, and E. coli in vitro. In conclusion, our results demonstrate that HF-14,109 has the effects of hydrolyzing non-starch polysaccharides and inhibiting pathogenic bacteria, which lays a solid foundation for elucidating its antibacterial and enzyme-producing mechanisms, and is expected to be developed as a probiotic for aquaculture feed in the future.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"26"},"PeriodicalIF":2.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome characterisation of three mycorrhizal helper bacterial strains isolated from a polycyclic aromatic hydrocarbon polluted site.","authors":"Klaudia Peczyk, Piotr Siupka, Franco Magurno, Monika Malicka, Zofia Piotrowska-Seget","doi":"10.1007/s00438-025-02232-y","DOIUrl":"https://doi.org/10.1007/s00438-025-02232-y","url":null,"abstract":"<p><p>The study aimed to explore the genetic and functional potential of mycorrhizal helper bacteria (MHB) strains isolated from polluted soil, focusing on their ability to enhance plant growth and ameliorate the adverse effects of polycyclic aromatic hydrocarbons (PAHs). We sequenced the genomes of three MHB strains isolated from soil contaminated with PAHs and phenol. Moreover, experiments were carried out to check if these bacteria have ability to stimulate the growth of arbuscular mycorrhizal fungi (AMF) and promote plant development. Phylogenomic analysis identified the strains as belonging to the Streptomyces, Pantoea, and Bacillus genera, all exhibiting high tolerance to hydrocarbons. Genome mining revealed genes encoding enzymes for the degradation of aromatic compounds, alongside biosynthetic gene clusters for secondary metabolites such as siderophores and antibiotics. Laboratory experiments confirmed that the studied MHB strains enhance AMF development and spore production while exhibiting plant growth-promoting mechanisms such as siderophore and ammonia production, phosphate solubilization, and cellulolytic enzyme synthesis. These findings highlight the potential application of MHB in microbial-assisted remediation of hydrocarbon-contaminated soils through the tripartite plant-MHB-AMF system.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"24"},"PeriodicalIF":2.3,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel urease gene structure of Sporosarcina pasteurii with double operons.","authors":"Di Pei, Zhiming Liu, Biru Hu","doi":"10.1007/s00438-025-02236-8","DOIUrl":"https://doi.org/10.1007/s00438-025-02236-8","url":null,"abstract":"<p><p>Microbially induced calcium carbonate precipitation (MICP) had emerged as an important biomineralization process with wide-ranging applications in construction, environmental remediation, and space exploration. Sporosarcina pasteurii (S. pasteurii) was a key bacterium in MICP due to its efficient urease activity, yet the regulation of its urease genes remains poorly understood, limiting its practical applications. This study aimed to elucidate the structure and expression regulation mechanism of urease genes in S. pasteurii to enhance its mineralization potential. We compared the growth and urease gene expression of S. pasteurii under three different culture conditions using transcriptome sequencing. Operon, Transcription Start Site (TSS) and Transcription Termination Site (TTS) were predicted based on the distribution of reads on the genome using Rockhopper online analysis software. The 700 bp sequence upstream of the TTS was extracted and promoter prediction was performed by Time-Delay Neural Network (TDNN) method. Finally, we verified the prediction results by RT-PCR. Our results revealed, for the first time, a double operon structure of S. pasteurii urease, with operon 1 containing ureA, ureB, ureC, ureE, and ureF genes, and operon 2 containing ureG and ureD genes. This discovery provides crucial insights into the regulation of urease expression in S. pasteurii, paving the way for more efficient and controllable mineralization applications. The findings of this study not only advanced our understanding of urease gene regulation but also opened new avenues for optimizing S. pasteurii-based biomineralization technologies.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"25"},"PeriodicalIF":2.3,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"P2RX1 in neutrophils mediates JAK/STAT signaling pathway to regulate malignant phenotype of gastric Cancer cells.","authors":"Yan Zhang, Fenglin Zhang, Zhi Liu, Min Li, Ge Wu, Hui Li","doi":"10.1007/s00438-025-02227-9","DOIUrl":"https://doi.org/10.1007/s00438-025-02227-9","url":null,"abstract":"<p><p>Gastric cancer is one of the most frequent malignancies and a serious concern in the global public health realm. Neutrophils, the most numerous myeloid cells in human blood, are emerging as significant regulatory variables in cancer. This study examines the molecular processes behind the link between gastric cancer's malignant character and neutrophils in the disease. This study aims to reveal the role of P2RX1 in neutrophils in gastric cancer and investigate its effects on the migration, invasion, and apoptosis of gastric cancer cells, with the hope of providing new targets and strategies for the treatment of gastric cancer. P2RX1 expression levels in gastric cancer samples were examined using The Cancer Genome Atlas-Stomach adenocarcinoma (TCGA-STAD). The signal pathways enriched by P2RX1-related differential gene expression were examined using GSEA. P2RX1 mRNA levels were examined using qPCR. Jak/Stat signaling pathway-related proteins and P2RX1 expression levels were subjected to western blot analysis. The apoptotic rate, migration, invasion, and cell viability were evaluated using flow cytometry, Transwell, and CCK-8 tests. Immunohistochemistry was used to detect the expression of P2RX1 in tumor tissues. Neutrophils and P2RX1 were both underexpressed in gastric cancer. In gastric cancer neutrophils, overexpression of P2RX1 increased cancer cell apoptosis while suppressing migration, invasion, and viability of the cells. Jak/Stat signaling pathway was connected to production of neutrophil P2RX1, and P2RX1 overexpression could trigger the pathway in vivo and in vitro. By activating its own Jak/Stat signaling pathway, overexpression of P2RX1 in gastric cancer neutrophils improved neutrophil survival, which in turn suppressed the migration, invasion, and viability of gastric cancer cells and raised their apoptosis rate. This suggests that P2RX1 may play a significant anti-tumor role in the tumor microenvironment of gastric cancer, indicating its value as a potential therapeutic target.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"23"},"PeriodicalIF":2.3,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing tiny millets through genome editing: current status and future prospects.","authors":"Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn","doi":"10.1007/s00438-025-02231-z","DOIUrl":"https://doi.org/10.1007/s00438-025-02231-z","url":null,"abstract":"<p><p>This study aims to address the critical need for genetic improvement of small millets, which are vital yet underutilized cereal crops cultivated in semi-arid regions of Africa and Asia. Given their high nutritional value and climate resilience, small millets hold significant potential for food security and sustainable agriculture in arid regions. However, traditional breeding methods have proven to be time-consuming and inefficient in enhancing desirable traits. This study highlights the transformative potential of genome editing technologies, particularly the CRISPR/Cas9 system, in accelerating the development of improved small millet varieties. The findings presented in this paper detail recent advancements in using CRISPR/Cas for enhancing resistance to biotic stresses, including bacterial, viral, and fungal pathogens. Additionally, we explore how genome editing can be applied to improve abiotic stress tolerance, addressing challenges such as drought, cold, heat, and herbicides in small millets. We discuss the existing challenges faced by breeders, including issues related to ploidy levels, off-target effects, and limitations in organelle genome modification. The review also suggests potential strategies for overcoming these bottlenecks, aiming to develop stress-resistant super cultivars. Overall, this paper provides an overview of the current state of genome editing research in small millets while identifying future opportunities to enhance key traits for nutrient enrichment and climate resilience, ultimately paving the way for advancements in these crucial crops.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"22"},"PeriodicalIF":2.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mapping and transfer of sheath blight resistance QTLs from PAU-shb8  to cultivated rice PR-121.","authors":"Sheezana Rasool, Ankita Babbar, Saundarya Kumari, Safoora Javed, Jagjeet Singh Lore, Rupinder Kaur, Navjot Sidhu, Yogesh Vikal, Kuldeep Singh, Kumari Neelam","doi":"10.1007/s00438-024-02220-8","DOIUrl":"https://doi.org/10.1007/s00438-024-02220-8","url":null,"abstract":"<p><p>Sheath blight, caused by Rhizoctonia solani, severely affects rice, causing 20-69% yield losses in tropical and temperate regions. Key challenges include the pathogen's broad host range, persistent sclerotia, climate change, and the reliance on semi-dwarf varieties. The disease's complex inheritance and lack of highly resistant cultivars hinder management, making resistant variety breeding a sustainable solution. This study mapped sheath blight resistance Quantitative trait locus (QTLs) from PAU-shb8, a moderately resistant rice line. This line exhibited moderate resistance with a disease score of 3 (RLH < 20%), whereas susceptible rice cultivar PR121 scored 9 (RLH > 60%). Screening of 1160 plants from BC₁F₅ and BC₁F₆ populations revealed 50.34% as moderately resistant, 37.76% moderately susceptible, and 11.88% susceptible. (QTL) mapping using 4622 SNP markers identified 20 QTLs across eight traits, with significant loci on chromosomes 2, 4, 6, 8, 9, 10, 11, and 12. Chromosome 12 harbored a cluster of QTLs associated with multiple traits, including RLH, lesion height, and disease score, while chromosome 8 exhibited a major QTL for RLH with a LOD score of 9.8 and 9.2% phenotypic variance. Genomic analysis pinpointed candidate genes related to resistance, such as leucine-rich repeat proteins and calcium/calmodulin-dependent protein kinases. Promising genotypes 7168, 7183, and 7152 demonstrated moderate resistance, combining key QTLs for RLH, disease severity, and lesion height with favorable agronomic traits. These backcross inbred lines are pivotal for breeding sheath blight-resistant rice varieties and for the expansion of resistance gene pool of sheath blight.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"21"},"PeriodicalIF":2.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome analysis of Bacillus velezensis exploring the probiotic potential and plant growth promotion traits of strains isolated from fish intestines.","authors":"Evelise Bach, Ana Carolina Ritter, Rafaela Diogo Silveira, Mariah Ávila de Souza, Luciane Maria Pereira Passaglia, Juliane Elisa Welke, Adriano Brandelli","doi":"10.1007/s00438-025-02230-0","DOIUrl":"https://doi.org/10.1007/s00438-025-02230-0","url":null,"abstract":"<p><p>New Bacillus velezensis strains with impressive antimicrobial activities are being continuously described. Here we performed genomic comparisons of five B. velezensis strains isolated from Amazonian fish intestines with other 266 genomes from the RefSeq database through a pangenome approach. We aimed to analyze the commonalities and specificities of each strain within this clade to explore their potential as probiotics and for promoting plant growth (PGP). High-quality draft genome sequences were obtained for strains P7 and P11, with genome metrics confirming their identification as B. velezensis. The evaluation of 271 B. velezensis genome sequences revealed an open pangenome composed of 14,918 homologs, while 16% of them represented the core genome. Therefore, the majority of genes belonged to the accessory variable genome, with many strains harboring numerous unique genes, including the Amazonian strain P45. This strain also stood out as carrying the potential to produce many hydrolytic enzymes and PGP traits. Genome mining of all five Amazonian strains annotated secondary metabolites with unknown identifications. The evaluated probiotic genes are mostly conserved in all B. velezensis strains. Moreover, the investigation of the mobilome, resistome, and virulence factors showed that these strains can be considered safe for probiotic and agricultural applications, corroborating our previous studies. This data will be useful to improve our understanding and biotechnological exploration of these strains and other B. velezensis as well.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"20"},"PeriodicalIF":2.3,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}