BMC Genomics最新文献

{"title":"Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.","authors":"Xu Wang, Ming Yan, Shanshan Cui, Fang Li, Qingqing Zhao, Qingnan Wang, Bin Jiang, Yixin Huang, Yang Sun, Xiangdong Kong","doi":"10.1186/s12864-025-11662-2","DOIUrl":"10.1186/s12864-025-11662-2","url":null,"abstract":"<p><p>Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"495"},"PeriodicalIF":3.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085524","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 analyses of CYP450 genes in Chrysanthemum indicum.","authors":"Yuyuan Chen, Tongjun Zhou, Jian Zhong, Yuxian Xu, Peng Zhang, Xiaoyu Yue, Hua Zhang, Ming Sun, Xuehao Fu","doi":"10.1186/s12864-025-11664-0","DOIUrl":"10.1186/s12864-025-11664-0","url":null,"abstract":"<p><strong>Background: </strong>The cytochrome P450 superfamily comprises a large group of enzymes crucial for the biosynthesis and metabolism of diverse endogenous and exogenous secondary metabolites in plants. Chrysanthemum, an ornamental genus with considerable medicinal value, is one of the most economically important floricultural crops in the world. The characteristics and functions of CYP450 genes in Chrysanthemum species, however, remain largely unknown.</p><p><strong>Results: </strong>In this study, we identified 371 CYP450 genes in the Chrysanthemum indicum genome, and categorized them into 8 clans and 44 families through phylogenetic analysis. Gene duplication analysis revealed 111 genes in 47 tandem duplicated clusters and 28 genes in 15 syntenic blocks, suggesting that extensive duplication events may account for the rapid expansion of CiCYP450 superfamily. Additionally, extensive variations in gene structure, motif composition, and cis-regulatory element likely enhance the functional diversity of CiCYP450 proteins. Volatile metabolomic analysis detected a total of 53 distinct volatile organic compounds across the leaves, stems, and roots of C. indicum, with 19 and 16 compounds being exclusive to leaves and stems, respectively. Transcriptomic analysis identified 248 expressed CiCYP450 genes, with 31, 40, and 88 specifically or preferentially expressed in leaves, stems, and roots, respectively. Further correlation analyses between gene expression levels and compound contents highlighted 36 candidate CiCYP450 genes potentially responsible for the biosynthesis of 47 volatile organic compounds.</p><p><strong>Conclusions: </strong>The genome-wide analyses of cytochrome P450 superfamily offers essential genomic resources for functional studies of CiCYP450 genes, and is significant for the molecular breeding of Chrysanthemum.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"494"},"PeriodicalIF":3.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075650","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":"Genomic changes of Lassa virus associated with mammalian host adaptation.","authors":"Linda Easterbrook, Xiaofeng Dong, Jack Smith, Susan Fotheringham, Sarah Kempster, Catherine Hartley, Tessa Prince, Victoria Graham, Emma Kennedy, Stephen Findlay-Wilson, Lucy Crossley, Roger Hewson, Neil Almond, Julian A Hiscox, Stuart Dowall","doi":"10.1186/s12864-025-11666-y","DOIUrl":"10.1186/s12864-025-11666-y","url":null,"abstract":"<p><strong>Background: </strong>Lassa virus (LASV) causes a severe haemorrhagic fever in humans, with estimates of 100,000 to 300,000 infections annually in endemic regions and accounting for around 5000 deaths. The natural reservoir is the Mastomys rat, but through zoonotic transmissions humans are accidental hosts. Regular outbreaks continue to exert pressures on public health systems, with its ability to cause nosocomial infections posing risks to healthcare workers. It is a concern that larger outbreaks and introduction of LASV to new territories will intensify, including risk of adaptation to new mammalian host reservoirs.</p><p><strong>Results: </strong>To evaluate genetic changes in LASV during adaptation to a new host, a guinea pig model of infection was utilised. Initial infection with LASV stocks cultured from cell culture resulted in only mild or subclinical disease. To study the susceptibility in naïve animals, the virus was serially passaged which increased clinical signs during disease progression ultimately resulting in severe disease. An RNAseq and consensus mapping approach was undertaken to evaluate nucleotide changes in LASV genome from each animal at each passage.</p><p><strong>Conclusions: </strong>During adaptation to guinea pigs, no significant new mutations occurred. Instead, a selection pressure on two genes of the L segment was observed resulting in their increased frequency in the genome population during passaging.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"489"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075719","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":"Assembly and analysis of the complete mitochondrial genome of an endemic Camellia species of China, Camellia tachangensis.","authors":"Dongzhen Jiang, Lei Zhou, Zhaohui Ran, Xu Xiao, Xuehang Yang, Zhi Li","doi":"10.1186/s12864-025-11673-z","DOIUrl":"10.1186/s12864-025-11673-z","url":null,"abstract":"<p><strong>Background: </strong>Camellia tachangensis F. C. Zhang is an endemic Camellia species of the junction of Yunnan, Guizhou and Guangxi Provinces in China. It is characterized by a primitive five-chambered ovary morphology and serves as the botanical source of the renowned \"Pu'an Red Tea\". Unfortunately, the populations of the species have declined due to the destruction of their habitats by human activities. The lack of mitochondrial genomic resources has hindered research into molecular breeding and phylogenetic evolution of C. tachangensis.</p><p><strong>Result: </strong>In this study, we had sequenced, assembled, and annotated the mitochondrial genome of C. tachangensis to reveal its genetic characteristics and phylogenetic relation with other Camellia species. The assembly result indicated that the mitochondrial genome sequence of C. tachangensis was 746,931 bp (GC content = 45.86%). It consisted of one multibranched sequence (Chr1) and one circular sequence (Chr2), with Chr1 capable of producing 7 substructures. The comparative analysis of the mitochondrial and chloroplast DNA of C. tachangensis revealed 23 pairs of chloroplast homologous fragments, with 10 fully preserved tRNA genes within them. Interspecies comparison of Ka/Ks ratios revealed that mutations in mitochondrial protein-coding genes (PCGs) of C. tachangensis were predominantly shaped by purifying selection throughout its evolution (Ka/Ks < 1). The mitochondrial CDS-based phylogenetic tree indicated that within the Camellia lineage, C. tachangensis was phylogenetically independent of the species of sections Oleifera, Camellia, Heterogenea, and Chrysantha. However, it also did not support the clustering of C. tachangensis with certain variants of C. sinensis, due to the extremely low support (BS = 22, PP = 0.41). Meanwhile, the chloroplast PCG-based phylogenetic analysis revealed that C. tachangensis formed a strongly supported basal clade (BS = 100, PP = 1.00), alongside C. makuanica (NC_087766), C. taliensis (NC_022264), and C. gymnogyna (NC_039626).</p><p><strong>Conclusions: </strong>Our study deciphered the mitochondrial genome and its multibranched structure of C. tachangensis. These findings not only enhanced our comprehension of the complexity and diversity of mitochondrial genome structures in Camellia species, but also established a foundational genetic data framework for future research on molecular breeding programs and phylogenetic relationship involving C. tachangensis and its related species.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"490"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075679","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":"Outside your shell: exploring genetic variation in two congeneric marine snails across a latitude and temperature gradient.","authors":"D M Wuitchik, J E Fifer, A K Huzar, J A Pechenik, L H Uricchio, S W Davies","doi":"10.1186/s12864-025-11603-z","DOIUrl":"10.1186/s12864-025-11603-z","url":null,"abstract":"<p><p>Intertidal organisms withstand extreme temperature fluctuations, and theirability to cope with this variation may affect their distributions across the seascape. Genetic variation and local environments likely interact to determine variation in thermal performances across intertidal species' ranges, so characterizing the relationship between temperature variation and population structure is key to understanding the biology of marine invertebrates. Here, we use 2bRAD-sequencing to examine population genetic structure in two congeneric intertidal marine gastropods (Crepidula fornicata, C. plana), sampled from locations along a natural temperature gradient on the Northeast shores of the United States. These two species share similar life histories, yet C. plana exhibits a narrower distribution than C. fornicata. Our results demonstrate that both species show patterns of genetic divergence consistent with isolation by distance, though this pattern was only significant in C. fornicata. Both putatively selected and neutral loci displayed significant spatial structuring in C. fornicata; however, only putatively selected loci showed significant clustering in C. plana. When exploring whether temperature differences explained genetic differentiation, we found that 9-12% of genetic differentiation was explained by temperature variation in each species even when controlling for latitude and neutral population structure. Our results suggest that temperature shapes adaptive variation across the seascape in both Crepidula species and encourages further research to differentiate our results from models of neutral evolutionary drift.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"486"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075784","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 molecular characterization of the MAPK family members in sand pear (Pyrus pyrifolia).","authors":"Yue Xu, Huiying Wang, Haiyan Shi","doi":"10.1186/s12864-025-11672-0","DOIUrl":"10.1186/s12864-025-11672-0","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;'Whangkeumbae', a highly regarded variety of sand pear, is celebrated in the market for its distinctive and superior flavor. However, the rapid production of ethylene after harvest significantly shortens its shelf life, becoming a major limiting factor for enhancing its commercial value. Mitogen-activated protein kinases (MAPKs) are a highly conserved family of transferases in eukaryotes. Although the importance of this family has been extensively studied in other plants, the precise composition and functional mechanisms of MAPK members in sand pear remain elusive. A genome-wide identification and molecular characterization of the MAPK gene family were conducted in Pyrus pyrifolia. This comprehensive analysis aimed to elucidate the genomic distribution, evolutionary relationships, and potential biological roles of MAPK genes in fruit senescence.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Four PpMAPKs were identified from our transcriptome data of sand pear, and 22 PpMAPK proteins were identified from the sand pear genome. Specifically, the transcriptomic PpMAPK3-L (GenBank accession number: PP992971), PpMAPK7-L (GenBank accession number: PP992972), PpMAPK10-L (GenBank accession number: PP992973), and PpMAPK16-L (GenBank accession number: PP992974) exhibited sequence homology values of 99.19%, 100%, 94.51%, and 95.75%, respectively, with their corresponding genomic counterparts (EVM0007944.1, EVM0004426.1, EVM0023771.1, EVM0027166.1). These findings indicate that the integrated analysis of transcriptomic and genomic data provides critical genetic insights into the MAPK genes in sand pear, culminating in the identification of a total of 25 PpMAPK genes in this species. Further phylogenetic analysis classified these genes into four subfamilies (A, B, C, and D), with subfamilies A and B each comprising six members, subfamily C with four members, and subfamily D with nine members. The potential functional differences among the gene members of each subfamily provide valuable clues for future research into MAPK signaling pathways. Further analysis by qRT-PCR revealed that the expression of four PpMAPK genes was positively correlated with fruit senescence in Pyrus pyrifolia. Additionally, interaction analysis revealed a significant interaction between PpMAPK3-L and PpbZIP2, which coordinatively regulate the senescence traits of fruits in sand pear through their joint influence during the senescence process.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The results of this study suggest that PpMAPK3-L, PpMAPK7-L, PpMAPK10-L, and PpMAPK16-L are likely to play pivotal roles in the maturation and senescence of sand pear fruit. Specifically, the interaction between PpMAPK3-L and PpbZIP2 could play a key role in the regulation of fruit senescence, indicating that the MAPK signaling pathway may modulate the fruit's physiological state through interactions with transcription factors. This finding offers significant insights for further investigation in","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"485"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075655","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 enhancer-gene regulatory maps of liver reveal novel regulatory mechanisms underlying NAFLD pathogenesis.","authors":"Ruofan Li, Kaiyan Su, Tianzhun Wu, Li Xu, Wenyu Song, Dandan Sun, Tao Zeng, Jinzhang Chen, Haibei Xin, Yuanfeng Li, Mengya Zang, Minggen Hu","doi":"10.1186/s12864-025-11668-w","DOIUrl":"10.1186/s12864-025-11668-w","url":null,"abstract":"<p><strong>Introduction: </strong>Non-alcoholic fatty liver disease (NAFLD) represents the most widespread liver disease globally, ranging from non-alcoholic fatty liver (NAFL) and steatohepatitis (NASH) to fibrosis/cirrhosis, with potential progression to hepatocellular carcinoma (HCC). Genome-wide association studies (GWASs) have identified several single nucleotide polymorphisms (SNPs) associated with NAFLD. However, numerous GWAS signals associated with NAFLD locate in non-coding regions, posing a challenge for interpreting their functional annotation.</p><p><strong>Results: </strong>In this study, we utilized the Activity-by-Contact (ABC) model to construct the enhancer-gene maps of liver by integrating epigenomic data from 15 liver tissues and cell lines. We constructed the most comprehensive genome-wide regulatory maps of the liver, identifying 543,486 enhancer-gene connections, including 267,857 enhancers and 16,872 target genes. Enrichment analyses revealed that the ABC SNPs are significantly enriched in active chromatin regions and active chromatin state. By combining the ABC regulatory maps and NAFLD GWAS data, we systematically identified ABC SNPs associated with NAFLD risk. Through the functional annotations, such as pathway enrichment and drug-gene interaction analyses, we identified 6 genes (GGT1, ACTG1, SPP1, EPHA2, PROZ and SHMT1) as candidate NAFLD genes, with SHMT1 previously reported. Among the SNPs connected to the candidate genes, the ABC SNP rs2017869 (odds ratio [OR] for the C allele = 1.10, 95% CI = 1.04-1.16, P = 5.97 × 10^- 4) had the highest ABC score. According to the ABC maps, rs2017869 links to GGT1, and several drugs targeting this gene, such as liothyronine, showed potential benefits to patients with NAFLD. Furthermore, we identified that another novel gene, EPHA2, may play a crucial role in NAFLD by regulating the GGT levels.</p><p><strong>Conclusions: </strong>Our study provides the most comprehensive ABC regulatory maps of the liver to date. This resource offers a valuable reference for identifying regulatory variants and prioritizing susceptibility genes of liver diseases, such as NAFLD.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"493"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075711","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":"Mutagenic impact of picric acid on chloroplast genome and a selection of biological attributes of Brassica napus L. (Brassicaceae).","authors":"Ishtiaq Ahmad, Barkat Ullah, Zahir Muhammad, Dikhnah Alshehri, Muhammad Nauman Khan, Alevcan Kaplan, Majid Iqbal, Laila A Al-Shuraym, Uthman Balgith Algopishi, Sadeq K Alhag, Meshari A Alsuwat, Diriba Dereje Olana, Muhammad Ammar Javed, Sarah Abdul Razak","doi":"10.1186/s12864-025-11565-2","DOIUrl":"10.1186/s12864-025-11565-2","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The present study was conducted to investigate the possible mutagenic effects of picric acid on the chloroplast genome and certain biological properties of Brassica napus L. under field conditions. The experimental design for this study was a randomized complete block trial, based on 3 factors (dose, duration of priming, and three oilseed rape (cultivars). The seeds of oilseed rape cultivars (Abasin- 95, Dur e Nifa, and Nifa Gold) were exposed to five doses (0 mM, 5 mM, 10 mM, 15 mM, and 20 mM) of picric acid for different soaking times (3 h, 6 h, and 9 h) and the data on agromorphological characteristics were recorded. Control and test samples were collected and compared for genomic chloroplast studies. The results confirmed the inhibitory effect of picric acid on days to emergence, completion of germination, and percent emergence. Seeds treated with a dose of 20 mM delayed seedling emergence (6.15) compared to other treatments. In addition, the differences between seeds primed for 3 h (6.07), and 6 h (5.89) were also highly significant. Similarly, the effects of 0 mM (7.52), 5 mM (8.26) and 10 mM (8.11) doses on germination time were not significant. Comparison of the mean values with respect to germination showed that picric acid led to a reduction in the percentage emergence of the oilseed rape seedlings. A significant increase in leaf size was observed in the Nifa Gold cultivar (10.27). On the other hand, the differences in leaf size between the cultivars Dur e Nifa (9.51) and Abasin-95 (9.20) were not significant. The inhibitory effect of picric acid on the number of leaves could be due to the fact that the meristematic cells are damaged by the mutagen, leading to a reduction in the number of leaves. The Nifa Gold cultivar showed the highest value for plant height (17.53), and the highest number of siliqua (14.69) compared to other genotypes. The number of siliqua confirms that Nifa Gold is best adapted to picric acid in contrast to the other genotypes. However, the differences between the Abasin-95 cultivar (0.068) and the Nifa Gold cultivar (0.062) in terms of seed weight were not significant. The dose of 15 mM (37.72) showed the highest moisture content, followed by 10 mM (37.08), 0 mM (33.87), 5 mM (33.11) and 20 mM (32.73). The chloroplast genome of plants grown from picric acid-treated seeds was mutated. Therefore, annotation of the genome was not possible. Numerous single nucleotide substitutions (187) were detected between the control and test samples. In addition, 43 additions/deletions were observed. The present study suggests that picric acid has a mutagenic effect, which is confirmed by numerous mutations in chloroplast samples. Subsequently, the doses have stimulating effects on plant height and seed weight. Furthermore, priming can improve the emergence and certain biological characteristics of B. napus. In the present study, all parameters were investigated and the significant response of the selected genotypes was conf","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"491"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075659","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 whole genome analysis of the wild-type and attenuated orf virus reveals that ORF022 facilitates viral replication.","authors":"Tian Jing, Yunpeng Wang, Yukun Bu, Xi Chen, Shutong Feng, Wenbo Liu, Zhannur Niyazbekova, Dekun Chen, Xiaolong Gao, Wentao Ma","doi":"10.1186/s12864-025-11663-1","DOIUrl":"10.1186/s12864-025-11663-1","url":null,"abstract":"<p><strong>Background: </strong>Contagious ecthyma is an acute infectious zoonosis caused by orf virus (ORFV). Live-attenuated ORFV vaccines have played a crucial role in preventing contagious ecthyma for decades. However, these vaccines often fail to induce long-lasting immunity. In recent years, numerous ORFV genome sequences have been published, yet genomic data for attenuated strains remain limited. Furthermore, no comprehensive whole-genome-based single nucleotide polymorphisms (SNPs) analysis has been conducted to compare ORFV wild-type and attenuated strains.</p><p><strong>Results: </strong>In this study, we performed whole-genome sequencing of ORFV wild-type and attenuated strains from Shaanxi Province. We identified two ORFV strains with genomes shorter than 130 kb, which are closely related to the SC1 attenuated strain from Sichuan Province. Additionally, we noticed that 24 genes in the attenuated strain had SNPs, with the highest number of mutations occurring in the ORF022 gene. The function of the ORF022 gene has not been previously reported. Through in vitro experiments, we demonstrated that overexpression of ORF022 enhances ORFV replication in cells. The RNA-sequencing analysis revealed that ORF022 modulates host inflammation-related signaling pathways, as evidenced by the suppression of TNF, IL-17, and Toll-like receptor signaling pathways.</p><p><strong>Conclusions: </strong>Our findings suggest that the ORF022 in ORFV wild-type strain inhibits the host inflammatory response, reduces the immune response to ORFV, and facilitates viral replication. SNP events in attenuated strains (aFX0910) are one of the reasons for its attenuation. Investigations into the genomic sequences of attenuated viruses and the functional impact of mutated genes provide valuable insights into the mechanisms underlying ORFV attenuation and offer a foundation for the development of more effective ORFV vaccines.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"488"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075731","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":"In-silico analysis of deleterious non-synonymous SNPs in the human AVPR1a gene linked to autism.","authors":"Md Delowar Kobir Jibon, Md Asadul Islam, Md Eram Hosen, Md Omar Faruqe, Rashed Zaman, Uzzal Kumar Acharjee, Biswanath Sikdar, Yewulsew Kebede Tiruneh, Md Khalekuzzaman, Motasim Jawi, Magdi E A Zaki","doi":"10.1186/s12864-025-11655-1","DOIUrl":"10.1186/s12864-025-11655-1","url":null,"abstract":"<p><p>Single nucleotide polymorphisms are the most prevalent type of DNA variation occurring at a single nucleotide within the genomic sequence. The AVPR1a gene exhibits genetic polymorphism and is linked to neurological and developmental problems, including autism spectrum disorder. Due to the difficulties of studying all non-synonymous single nucleotide polymorphisms (nsSNPs) of the AVPR1a gene in the general population, our goal is to use a computational approach to identify the most detrimental nsSNPs of the AVPR1a gene. We employed several bioinformatics tools, such as SNPnexus, PROVEAN, PANTHER, PhD-SNP, SNP & GO, and I-Mutant2.0, to detect the 23 most detrimental mutants (R85H, D202N, E54G, H92P, D148Y, C203G, V297M, D148V, S182N, Q108L, R149C, G212V, M145T, G212S, Y140S, F207V, Q108H, W219G, R284W, L93F, P156R, F136C, P107L). Later, we used other bioinformatics tools to perform domain and conservation analysis. We analyzed the consequences of high‑risk nsSNPs on active sites, post-translational modification (PTM) sites, and their functional effects on protein stability. 3D modeling, structure validation, protein-ligand binding affinity prediction, and Protein-protein docking were conducted to verify the presence of five significant substitutions (R284W, Y140S, P107L, R149C, and F207V) and explore the modifications induced due to these mutants. These non-synonymous single nucleotide polymorphisms can potentially be the focus of future investigations into various illnesses caused by AVPR1a malfunction. Employing in-silico methodologies to evaluate AVPR1a gene variants will facilitate the coordination of extensive investigations and the formulation of specific therapeutic approaches for diseases associated with these variations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"492"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075696","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}