BMC Genomics最新文献

{"title":"Mutual suppression between mutations in the Dictyostelium Greenbeard pathway restores wild-type development.","authors":"Mariko Katoh-Kurasawa, Lena Trnovec, Peter Lehmann, Blaž Zupan, Gad Shaulsky","doi":"10.1186/s12864-025-11745-0","DOIUrl":"10.1186/s12864-025-11745-0","url":null,"abstract":"<p><strong>Background: </strong>The Dictyostelium greenbeard pathway is mediated by two polymorphic transmembrane proteins, the TgrC1 ligand and the TgrB1 receptor. These proteins mediate allorecognition, altruism, and the developmental transition to multicellularity. A genetic suppressor screen revealed activating mutations in tgrB1 and inactivating mutations in rapgapB, a regulator of the GTPase protein RapA. Inactivation of either tgrB1, tgrC1, or rapgapB leads to developmental defects, but the respective double-mutant strains rapgapB^-tgrB1^- and rapgapB^-tgrC1^- develop well and produce spores. This mutual suppression could result from inducing an alternative pathway or from restoring wild-type development, but morphological analyses alone could not resolve this question.</p><p><strong>Results: </strong>Here, we show that the mutual suppression between rapgapB^- and tgrB1^- restores wild-type development. We also analyzed an activated tgrB1 allele in the wild-type background and found evidence for interactions between the wild-type and the activated alleles. Using RNA-sequencing analyses, we compared the transcriptomes of the wild type to those of several mutant strains and found that the single-gene mutations attenuated transcriptome progression over developmental time, whereas the double-gene mutation strain rapgapB^-tgrB1^- and the activated tgrB1 mutation exhibited near wild-type transcriptomes. Our findings suggest that tgrB1, tgrC1, and rapgapB are involved in a pathway in which rapgapB negatively regulates tgrB1 and tgrC1 expression, whereas tgrB1 and tgrC1 positively regulate rapgapB expression.</p><p><strong>Conclusions: </strong>These findings suggest that the Dictyostelium greenbeard pathway interfaces with the central RapGAPB-RapA regulatory pathway, providing molecular insight into a mutual suppression mechanism in which two deleterious mutations restore wild-type behavior.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"563"},"PeriodicalIF":3.5,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12142906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233017","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":"Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.","authors":"Kevin Green, Benjamin Krajacich, Kelly Wiseman, Peter T Mains, Samantha Robertson, Sophie Billings, Marina McCowin, Mitch Sudkamp, Ching Shing Lo, Bryan R Lajoie, Semyon Kruglyak, Shawn Levy, Junhua Zhao","doi":"10.1186/s12864-025-11741-4","DOIUrl":"10.1186/s12864-025-11741-4","url":null,"abstract":"<p><p>Human whole-genome sequencing (hWGS) provides comprehensive genomic information that can help guide research in disease prevention and treatment. Recent advancements in sequencing technology have improved sequencing quality and further reduced sequencing costs on bench-top sized instruments, making whole-genome sequencing an accessible technology for broader use. Here, we demonstrate the feasibility of a large WGS project using a benchtop sequencer in a small laboratory setting, on a scale previously reserved for production-scale machines. In this project, 807 samples were prepared and sequenced across 313 flow cells, with high sequencing quality at a median %Q30 of 96.6% and a median %Q40 of 89.31%. To screen library quality and maximize sample yield, we utilized 48-plex sample pre-pool 'QC' runs to provide > 1 × coverage per sample prior to sample pooling and full-depth sequencing, providing valuable sample-level insights prior to full-depth sequencing. With this strategy, we consistently achieved > 30 × human whole genome sequencing of three-plex sample trios with standard settings. To demonstrate additional flexibility present in the platform, we explored two different use cases 1) large insert sizes (1kb +) library to achieve superior genome coverage; 2) proof of concept rapid WGS sequencing to minimize sample to answer turnaround time for time-critical sequencing applications. Sequencing of a 2 × 100 > 30 × human WGS can be achieved in < 12 h and subsequent file generation in < 1 additional hour. This study provides a cost-effective and flexible real-world demonstration of achieving both high quality hWGS sequencing and instrument flexibility without the need for complex batching schemes or factory-sized sequencers.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"559"},"PeriodicalIF":3.5,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214810","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":"Comparative study on the mechanism of yellow petal formation in Paphiopedilum armeniacum: an integrated transcriptomic and metabolomic analysis of three Paphiopedilum species.","authors":"Yaqin Ye, Yanting Chang, Yanjun Ma, Yayun Deng, Wenbo Zhang, Tiankui Chu, Hanchen Tian, Baokun Yan, Pengda Zhao, Zehui Jiang, Tao Hu","doi":"10.1186/s12864-025-11648-0","DOIUrl":"10.1186/s12864-025-11648-0","url":null,"abstract":"<p><strong>Backgrounds: </strong>Paphiopedilum orchids, particularly the Chinese endemic Paphiopedilum armeniacum, are prized for their commercial and ornamental value, with the latter serving as a vital breeding resource owing to its distinctive yellow petals. However, the molecular mechanisms underlying yellow petal formation remain unclear.</p><p><strong>Results: </strong>This work employed an integrated transcriptomic and metabolomic comparative analysis of P. armeniacum and two lighter-colored Paphiopedilum species (The sepals and petals are white.) to identify carotenoid-related differentially expressed genes and metabolites before and after blooming in all three species. Metabolomic analysis revealed a marked increase in six differential metabolites, including zeaxanthin, precorrin 2, and β-D-gentiobiosyl crocetin, in P. armeniacum, highlighting their critical role in yellow petal formation. Transcriptomic comparison identified 40 DEGs (including D27, GDSL-like, CYP97B3, LUT1, and PSY) linked to yellow pigmentation, most of which were consistently upregulated in P. armeniacum before and after blooming Integrative metabolomic and transcriptomic analyses demonstrated significant correlations between these genes and metabolites, suggesting their role in regulating carotenoid synthesis and accumulation in yellow petal formation. Furthermore, qRT-PCR elucidates the expression levels of candidate genes, identifying RPL13AD as the optimal reference gene across these three orchid species.</p><p><strong>Conclusions: </strong>These works elucidate the expression patterns and regulatory roles of carotenoid-related genes in metabolic pathways during P. armeniacum blooming, providing new insights into the molecular mechanisms of carotenoid-mediated plant coloration.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"560"},"PeriodicalIF":3.5,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224205","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 transcriptomic and metabolomic analyses reveal tissue-specific accumulation and expression patterns of monoterpene glycosides, gallaglycosides, and flavonoids in Paeonia Lactiflora Pall.","authors":"Pan Xu, Jinghui Li, Cuiting Chen, Jing Chen, Meiping Yang, Huimin Deng, Xuechun Jiang, Kelang Lou, Xiaojun Wu, Rubing Chen, Yijuan Hu, Weiqing Liang, Jinbao Pu","doi":"10.1186/s12864-025-11750-3","DOIUrl":"10.1186/s12864-025-11750-3","url":null,"abstract":"<p><strong>Background: </strong>Paeonia lactiflora Pall. (PL) is widely recognized for its ornamental, edible, and medicinal properties. Its principle bioactive constituents include monoterpene glycosides (MGs), gallaglycosides (GGs), and flavonoids. However, the metabolic and molecular basis underlying their biosynthesis in PL remain poorly understood. In this study, an integrated non-targeted metabolomics and transcriptomics approach was employed to investigate the metabolic profiles and gene expression patterns in four distinct PL tissues.</p><p><strong>Results: </strong>Metabolomic and transcriptome profiling revealed tissue-specific patterns of metabolite accumulation and gene expression. KEGG enrichment analysis of differentially expressed metabolites (DEMs) showed that secondary metabolites biosynthesis and transport processes play vital roles in the tissue-specific accumulation of bioactive constituents. A total of 19 DEMs and 90 differentially expressed genes (DEGs) associated with MGs, 10 DEMs and 14 DEGs associated with GGs, and 205 DEMs and 67 DEGs associated with flavonoids were identified. Roots, the primary medicinal tissue, exhibited substantial accumulation of eight MGs, two GGs, and 18 flavonoids, as well as elevated expression levels of 16, two and nine structural genes, respectively. Nine CYP450 s and two UGTs associated with MGs, and 14 UGTs associated with flavonoids, were identified as new candidate genes through phylogenetic and expression analyses. CYP71E1, CYP71 AN24.1, CYP71 AU50.2, and UGT91 A1.1 for MGs biosynthesis, and UGT71 K1.4, UGT89B2, UGT73 C25, and UGT71 K1.2 for flavonoids biosynthesis were prioritized through correlation analysis. WGCNA revealed that turquoise, green, and blue modules were significantly correlated with MGs and flavonoids biosynthesis, identifying 24 hub genes for MGs and 18 for flavonoids. The overlap of phylogenetic, expression, correlation and WGCNA analyses identified CYP71 AN24.1 and UGT91 A1.1 as putative MGs biosynthetic genes, and UGT89B2 as a flavonoid-related gene. Protein structure prediction and similarity analysis further supported their functional conservation with known terpenoid-modifying enzymes and flavonoid-specific glycosyltransferases, respectively.</p><p><strong>Conclusions: </strong>These findings identified CYP71 AN24.1, UGT91 A1.1, and UGT89B2 as novel genes involved in MGs and flavonoids biosynthesis. The study provides a valuable theoretical foundation for future metabolic engineering aimed at optimizing the biosynthetic pathways of these primary active constituents in PL.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"561"},"PeriodicalIF":3.5,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224206","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":"Transcriptomic analysis reveals genetic factors underlying impaired symbiotic nitrogen fixation in lines derived from crosses between cultivated peanut (Arachis hypogaea L.) and its wild ancestors.","authors":"Darius Tchoutang Nzepang, Maïmouna Cissoko, Djamel Gully, Valérie Hocher, Jean-François Rami, Saliou Fall, Daniel Fonceka, Sergio Svistoonoff","doi":"10.1186/s12864-025-11739-y","DOIUrl":"10.1186/s12864-025-11739-y","url":null,"abstract":"<p><strong>Background: </strong>Symbiotic nitrogen fixation (SNF) is a complex process regulated by numerous genes extensively studied in legumes that undergo intracellular infection, such as Lotus japonicus, Medicago truncatula, and Glycine max. However, the molecular and genetic mechanisms of SNF in legumes that rely on the intercellular infection pathway, such as peanut (Arachis hypogaea L.), remain poorly understood. In a previous study, we identified two chromosome segment substitution lines (CSSLs), 12CS_051 and 12CS_044, each contains a wild segment on homeologous regions of chromosomes A02 and B02 respectively, that are severely impaired in nitrogen fixation. In this study, we have compared the transcriptomes of those lines with that of their recurrent parent, Fleur11, in roots inoculated with the effective Bradyrhizobium vignae strain ISRA400 to identify candidate genes associated with the reduced nitrogen fixation observed in these CSSLs.</p><p><strong>Results: </strong>A comparative analysis of the transcriptome profiles of the CSSLs and Fleur11 revealed significant changes in the expression of genes involved in plant immune signaling and key symbiotic genes, such as NIN, EFD, FEN1 or SNF-related transporters. These results align with the phenotypic differences observed during the symbiotic process in the CSSLs. When focusing on each QTL region, we found that only the orthologs of the symbiotic gene FEN1, which is responsible for the failure in the enlargement of infected cells in L. japonicus, exhibited a lack of expression in the two CSSLs compared to Fleur11. FEN1 encodes a homocitrate synthase that is essential for the nitrogenase activity. We hypothesize that changes in the expression of FEN1 could affect the nitrogenase activity, potentially leading to the unfair SNF observed in these lines.</p><p><strong>Conclusions: </strong>In this study, we analyzed the expression profiles of two ineffective nitrogen-fixing chromosome segment substitution lines and identified FEN1 as a suitable candidate gene involved in peanut symbiosis. This research provides valuable insights into understanding and improving SNF in peanut.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"556"},"PeriodicalIF":3.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214812","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":"Transcriptome analysis identifies CCR7 and cell adhesion molecules as mediators of B cell migration to the bursa of Fabricius during chicken embryonic development.","authors":"Milena Brunner, Catarina L C T Cavaleiro, Tom V L Berghof, Theresa von Heyl, Mohanned Naif Alhussien, Christine Wurmser, Daniel Elleder, Benjamin Schusser","doi":"10.1186/s12864-025-11749-w","DOIUrl":"10.1186/s12864-025-11749-w","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"555"},"PeriodicalIF":3.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214811","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 scalable distributed pipeline for reference-free variants calling.","authors":"Lorenzo Di Rocco, Umberto Ferraro Petrillo","doi":"10.1186/s12864-025-11722-7","DOIUrl":"10.1186/s12864-025-11722-7","url":null,"abstract":"<p><strong>Background: </strong>Precision medicine pipelines typically begin with variant calling to identify disease-related mutations for optimal treatment selection. Reference-free approaches assess variations in the genetic profiles of distinct individuals through the utilization of a De Bruijn graph. However, the timely analysis of large-scale sequencing data may be beyond the capabilities of single workstations, requiring alternative computational approaches.</p><p><strong>Results: </strong>We introduce the first-known distributed pipeline for detecting isolated SNPs (Single Nucleotide Polymorphisms), by leveraging the computational resources of multiple machines in parallel. Our pipeline efficiently analyzes large datasets thanks to the usage of a distributed De Bruijn graph representation. Furthermore, we introduce a cluster-driven algorithm to partition the De Bruijn graph across multiple independent machines according to the inner structure of the sequences under analysis, thus further improving the scalability of our pipeline.</p><p><strong>Conclusions: </strong>The results of our experiments, conducted on real-world datasets, show the good performance of our pipeline in terms of efficiency, output quality and scalability. Moreover, the reported results also confirm that the adoption of a specialized partitioning algorithm for the distributed representation of the De Bruijn graph leads to a relevant performance speed-up compared to using standard partitioning techniques.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 Suppl 1","pages":"557"},"PeriodicalIF":3.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214813","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":"Chromosome-level genome assembly and anticoagulant protein annotation of the buffalo leech Hirudinaria bpling (Hirudinea: Hirudinidae).","authors":"Muhammad Salabat Khan, Christian Müller, Baozhen Zhou","doi":"10.1186/s12864-025-11690-y","DOIUrl":"10.1186/s12864-025-11690-y","url":null,"abstract":"<p><p>This study aimed to obtain and analyze the chromosome-level genome assembly of Hirudinaria bpling, a species vital for aquatic ecosystem health and medical research. Understanding its genomic information is crucial for advancing its medical applications and elucidating its ecological role. We assembled the genome of H. bpling using a combination of PacBio HiFi long reads, Illumina sequencing, and Hi-C chromosome conformation capture techniques. This approach allowed us to achieve a high-resolution genome assembly with detailed chromosomal organization. The final genome assembly of H. bpling is 144.08 Mb, with an N50 size of 11.27 Mb, anchored onto thirteen pseudo-chromosomes. BUSCO analysis indicated a genome completeness of 96.20%. We annotated a total of 20,126 protein-coding genes and identified 18.80% repetitive elements within the genome. Phylogenetic analysis included nine other leech species, positioning H. bpling as a sister taxon to Hirudo manillensis. A comparative analysis focused on the identification of putative anticoagulant proteins (e.g. Hirudin, Antistasin, Hirustasin, Therostasin, Bdellastasin, Guamerin/Piguamerin, Gelin, Bplins, Saratin, Eglin C, Bdellin B-3, LDTI, Hyaluronidase, Destabilase, Apyrase, Leech carboxypeptidase inhibitor, Gamma-glutamyl transpeptidase, Lefaxin, Progranulin), identifying conserved regions and evolutionary relationships among these proteins across different leech species. As a medically significant species, H. bpling offers promising opportunities for research into anticoagulant therapies. This study provides a comprehensive genomic and phylogenetic analysis of H. bpling, offering new insights into leech genomics and the evolution of anticoagulant genes. The findings enhance our understanding of the genetic and evolutionary mechanisms underlying anticoagulant production in leeches.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"558"},"PeriodicalIF":3.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214840","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":"Comparative transcriptomic and proteomic analyses of hypoxia response in wild and cultivated tomato roots.","authors":"Zhihan Zhang, Yabing Hou, Hao Yin, Song Lu, Daliang Liu, Lin Cheng, Houlin Yu, Tao Li, Yiyong Zhao","doi":"10.1186/s12864-025-11653-3","DOIUrl":"10.1186/s12864-025-11653-3","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Hypoxia significantly impairs tomato productivity and yield. Although cultivated tomato varieties (Solanum lycopersicum) are generally sensitive to low-oxygen conditions, their wild relatives (Solanum habrochaites) display substantially lower sensitivity. To elucidate the molecular mechanisms underlying these contrasting phenotypes, as well as the impact of positive selection and protein-protein interactions of differentially expressed genes (DEGs) and proteins (DEPs), we conducted transcriptomic and proteomic analyses of root samples from a wild tomato accession, T178 (S. habrochaites), and a cultivated tomato variety, Fenzhenzhu (S. lycopersicum, FZZ).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Compared with cultivated seedlings, wild tomato seedlings exhibited markedly reduced sensitivity to hypoxia, as demonstrated by lower growth inhibition and higher membership function values under low-oxygen conditions. In T178, 2,351 DEGs were identified (1,238 upregulated and 1,113 downregulated), whereas in FZZ, 2,931 DEGs were detected (1,326 upregulated and 1,605 downregulated). Heatmap clustering and functional enrichment analysis revealed significant differences in transcriptional regulation between T178 and FZZ under hypoxia. Specifically, among the unique DEGs in T178, genes related to carbohydrate metabolism were significantly upregulated, whereas genes associated with single-organism metabolic processes were downregulated. In contrast, among the unique DEGs in FZZ, genes related to DNA-templated transcription were significantly upregulated, whereas genes associated with protein phosphorylation were downregulated. Proteomic analysis identified 544 and 493 DEPs in T178 and FZZ, respectively, with T178 DEPs predominantly linked to metabolic flexibility and antioxidant responses, whereas both sets were enriched in similar metabolic pathways. Further positive selection analyses emphasized the adaptive evolution of hypoxic responses in wild and cultivated tomatoes, exemplified by T178, which harbors 1,289 positively selected genes linked to carbon metabolism and energy homeostasis, underscoring its adaptation to low-oxygen environments. Moreover, protein-protein interaction (PPI) network analyses revealed distinct adaptive strategies in T178 and FZZ. By analyzing the gene and protein networks of FZZ and T178 under hypoxic conditions, we inferred that T178 enhances hypoxia adaptation by forming more independent small modules and multilevel regulatory networks, whereas FZZ relies on a few large modules with limited functional diversity, resulting in weaker hypoxia tolerance.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Our results demonstrated that the molecular response mechanisms to hypoxia differ substantially between wild and cultivated tomatoes, with wild tomatoes showing more distinctive and effective adaptations. The differentially regulated genes identified in this study represent promising targets for future research and breeding e","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"552"},"PeriodicalIF":3.5,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207615","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":"Integrating SNP data to reveal the adaptive selection features of goat populations in extreme environments.","authors":"Wannian Wang, Ke Cai, Mengdan Fan, Zhixu Pang, Yangyang Pan, Lifen Cheng, Liying Qiao, Ruizhen Wang, Wenzhong Liu, Jianhua Liu","doi":"10.1186/s12864-025-11743-2","DOIUrl":"10.1186/s12864-025-11743-2","url":null,"abstract":"<p><p>The frequent occurrence of extreme climate events globally has elevated the requirements for environmental adaptability in livestock and poultry. Some goat populations have shown strong adaptability in specific extreme environments, and their genomes often leave genetic traces of adaptive evolution. This study integrated global goat single nucleotide polymorphism (SNP) chip data and raster data of 11 environmental variables. We retained 162 native goat populations and analyzed the environmental data of their regions. We detected 23 candidate genes related to environmental adaptation using selection signal analysis and genome-environment association analysis. After that, we screened out goat populations in extreme environments based on environmental data. Then, we used three selection signal analysis methods (F_ST, XPEHH and θπ methods) to detect the genomes of these goat populations. In four different extreme environments (high elevation, hot, cold, and arid), 91, 43, 21, and 115 candidate genes were identified, respectively. Combined with studies related to environmental adaptation, we found that genes such as GULP1, GPC5, GPC6, and PDE4D may play important roles in the adaptation of goats to extreme environments. This study provides new insights into the adaptive mechanism of goats in extreme environments and provides an important theoretical basis for goat breed improvement and stress resistance breeding. At the same time, these findings also provide a reference for the study of the adaptability of other livestock in extreme environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"553"},"PeriodicalIF":3.5,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207617","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}