BMC Genomics最新文献

{"title":"Transcriptomic analysis reveals the growth of Populus Schneideri in different light qualities.","authors":"Xiaolin Zhang, Rong Xu, Cai Wang, Shaojie Ma, Yulan Xu, Dan Zong","doi":"10.1186/s12864-025-11951-w","DOIUrl":"10.1186/s12864-025-11951-w","url":null,"abstract":"<p><strong>Background: </strong>Light plays a key role in plant growth, development and response to adversity. Plants perceive different wavelengths of light in the environment through various photoreceptors and regulate plant growth and development through light signaling. Nevertheless, it remains unknown how high-altitude plants adapt to different light conditions. To elucidate the molecular mechanisms of high-altitude plants responding to light quality, this research compared the transcriptome of P. schneideri cuttings under blue and green film treatments.</p><p><strong>Results: </strong>Blue film treatment significantly promoted the height growth of P. schneideri, while green film treatment inhibited it, and both treatments significantly suppressed stem thickness growth. Transcriptomic analysis revealed that blue film treatment induced a significantly higher number of differentially expressed genes (DEGs) compared to green film treatment, with multiple transcription factor families (such as WRKY, NAC, bHLH, MIKC, and MYB) down-regulated across various treatments. DEGs were primarily enriched in the hormone signaling pathway, where blue film treatment significantly up-regulated the expression of CRY1, HY5 and ARF8 genes, while down-regulating GH3.1, Aux/IAA14 and Aux/IAA16. In contrast, green film treatment exhibited the opposite regulatory pattern.</p><p><strong>Conclusion: </strong>These results imply that P. schneideri may benefit from blue film treatment in terms of growth and development, which may be helpful for further research into the introduction and cultivation of P. schneideri and other popular species in high-altitude regions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"871"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190860","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 of two rice cultivars highlights the role of auxin- and JA-responsive genes under heat stress.","authors":"Fan Deng, Zixuan Dang, Xue Gong, Chi Zhang, Gengwei Wu, Song Yan, Lanlan Wang, Dali Zeng, Hua Wang","doi":"10.1186/s12864-025-12079-7","DOIUrl":"10.1186/s12864-025-12079-7","url":null,"abstract":"<p><p>Elevated temperatures pose a significant threat to rice crops, necessitating the elucidation of the regulatory mechanisms underlying the response of rice to heat stress. Such comprehension is vital for the cultivation of rice cultivars that can withstand high temperatures, thereby enhancing secure and sustainable food production. In this study, we discovered a rice near-isogenic line, S49, in the Sasanishiki (Sa) genetic background that is resistant to heat stress. Compared with the heat-susceptible cultivar Sa, S49 demonstrated superior growth under heat stress conditions of 43 ℃ for three days. Through a comparative analysis of plant hormones and transcriptomes between these two lines, we observed that S49 presented relatively high levels of indole-3-acetic acid (IAA) and relatively low levels of jasmonic acids (JAs) under heat stress for 24 h, which was consistent with our transcriptome analysis. The findings revealed that under heat stress, the JA and IAA pathways exhibit distinct regulatory patterns between Sa and S49, suggesting that these two signaling pathways may independently mediate different stress resistance strategies. These results shed new light on the mechanisms of high-temperature tolerance in rice and lay the groundwork for future genetic research into this tolerance.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"863"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190871","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":"SoMaCX: a complex generative genome modeling framework.","authors":"Timothy James Becker","doi":"10.1186/s12864-025-12023-9","DOIUrl":"10.1186/s12864-025-12023-9","url":null,"abstract":"<p><strong>Background: </strong>Somatic structural variations (SVs) are commonly observed in cancer tissue, but remain challenging to discover with short and long read sequencing due to tumor heterogeneity and other technical sequencing factors. Only SVs with a sufficient fraction of reads spanning the event will be detectable, while issues like chromothripsis increase the complexity and resulting interpretation significantly. Because structural variation is difficult to measure and reproduce in vivo, it is logical to make use of simulation frameworks to determine realistic system limitations. Our generative modeling approach called soMaCX uses distributions from data to empower simulations that approach real data.</p><p><strong>Results: </strong>Our generative framework includes mechanisms for biological conservation in the germline as well as tissue composition in the somatic along with regional distribution controls and complex SV generation that is not available in other systems. The output of this system is FASTA format which can then be used as input to any downstream read simulator making Illumina, PacBio, 10X genomics, Oxford-Nanopore and Bionano FASTQ data files which are further processed to become standard BAM files for SV calling.</p><p><strong>Conclusions: </strong>The soMaCX framework provides superior generative modeling-based performance when compared to other simulation frameworks with respect to real data. Our open-source method introduces an important conceptual element to simulation by utilizing biological relevant regions (genes and regulatory elements) as the distribution controls along with the biological modulation of known pathways (end-joining) leading to more detailed and realistic simulated genomes. By designing a generative method to explore the most difficult genomic conditions, we provide a means to measure germline variation calling performance and to calibrate the results for rare variants needed in the clinical setting. We provide a python 3 implementation at: https://github.com/timothyjamesbecker/somacx .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"853"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190855","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":"Functional studies on methylation of the promoter region of the NR2E1 gene regulating adipocytes in beef cattle.","authors":"Lan Feng, Xue Bai, Yuan Liu, Hongen Chu, Na Rina, Fen Li, Bei Cai, Dawei Wei, Runjun Yang, Lupei Zhang, Yun Ma","doi":"10.1186/s12864-025-11886-2","DOIUrl":"10.1186/s12864-025-11886-2","url":null,"abstract":"<p><strong>Background: </strong>Methylation plays a pivotal role in the modulation of gene expression, with the occurrence of promoter and exon 1 methylation typically resulting in transcriptional repression. Lipid deposition constitutes a complex economic trait, with a multitude of genes participating in the regulatory cascade that shapes meat quality attributes. Nonetheless, the available data on genetic markers for meat quality and the corresponding functional genes remains scarce, posing significant challenges to the selection of superior breeds and the development of novel strains in beef cattle breeding programs.</p><p><strong>Results: </strong>In the present investigation, we evaluated the methylation profile of the NR2E1 gene within the promoter CpG islands across three distinct breeds of beef cattle, and elucidated its regulatory role in modulating the proliferation, differentiation, and apoptosis of adipocytes specifically in the Guyuan cattle breed. Subsequently, the functional validation of the NR2E1 gene was conducted in the predipocyte of Guyuan cattle. The results revealed an inverse correlation between the methylation level assessments and the RNA-seq data. Specifically, the mean methylation levels in 10 CpG islands situated within the promoter region of the NR2E1 gene were observed to be highest in Wagyu cattle, with Guyuan cattle exhibiting the subsequent highest levels, and the lowest in Chinese Simmental cattle. This methylation pattern exhibited a negative correlation with the RNA-seq outcomes. The interference with the NR2E1 gene repressed the proliferation and differentiation of bovine adipocytes by down-regulating the expression of both proliferation-associated genes and differentiation-related genes. Moreover, it potentially facilitated apoptosis in bovine adipocytes through up-regulating the pro-apoptotic gene BAD and down-regulating the apoptosis suppressor gene BCL2. Further downstream pathway analysis revealed that interference with the NR2E1 gene activated the AKT pathway, whereas its over expression led to the inhibition of this pathway.</p><p><strong>Conclusions: </strong>In the present investigation, we conducted methylation sequencing of the CpG island within the promoter region of the NR2E1 in three breeds of beef cattle, followed by a comprehensive co-analysis with transcriptome data. We further explored the influence of the NR2E1 on the proliferation, differentiation, apoptosis, and downstream signaling pathways in bovine adipocytes. The findings of this research serve as a foundational reference for advancing the molecular understanding of NR2E1 regulation in the context of bovine adipocyte biology.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"864"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190770","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":"Identification of sugar transporter MrSTP20 responding to high-salt stress and hexoses induction in apple rootstock (Malus robusta Rehd).","authors":"Yu-Lei Yan, Tian-Le Shi, Jia Zhou, Yu-Zhang Yang, Meng-Xia Zhang, Xing-Liang Li, Jun-Ke Zhang","doi":"10.1186/s12864-025-12062-2","DOIUrl":"10.1186/s12864-025-12062-2","url":null,"abstract":"<p><strong>Background: </strong>Sugar distribution regulation, especially in the roots, is an important pathway for plants to cope with abiotic stress. Sugar transport proteins (STPs) mediate the transmembrane transport of hexoses such as glucose and fructose; however, the molecular mechanism underlying the response to salt stress remains unclear.</p><p><strong>Results: </strong>Here, we identified 22 STP genes in apple (Malus domestica) using genome-wide screening. Under salt stress, 17 genes were detected in the roots of the apple rootstock Malus robusta Rehd; of them, MrSTP3, MrSTP7, MrSTP14, and MrSTP20 showed stronger positive responses to salt stress. Under exogenous sugar induction, MrSTP7, MrSTP17, and MrSTP20 were significantly upregulated for all three hexoses (glucose, fructose, and mannose), one sugar alcohol (mannitol), and sucrose. MrSTP20 exhibited the strongest response to high salt, glucose, and fructose concentrations. Furthermore, we found that MrSTP20 has a conserved STP domain and is expressed in Arabidopsis protoplasts localized to the plasma membrane, supporting its function in transporting hexoses from the extracellular space into the cells. Association analysis showed that MrSTP20 synergized with the salt-responsive glycosyltransferase gene (UGT71), pentatriocopeptide repeat protein (PPR), cytochrome c oxidase synthesis (HCC1), and S-phase kinase-associated protein 1 (SKP1) at the gene expression level.</p><p><strong>Conclusions: </strong>These findings suggest that MrSTP20 transports hexoses from the extracellular space into cells, positively involving in salt stress tolerance and sugar transport regulation, thereby providing new insights into the salt tolerance mechanism in apple trees.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"860"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190849","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":"Quantitative proteomic analysis of Arabidopsis thaliana with different levels of phospholipid:diacylglycerol acyltransferase1 expression.","authors":"Artur Piróg, Sylwia Klińska-Bąchor, Bartosz Głąb, Sara Kędzierska, Katarzyna Jasieniecka-Gazarkiewicz, Antoni Banaś, Sachin Kote","doi":"10.1186/s12864-025-12041-7","DOIUrl":"10.1186/s12864-025-12041-7","url":null,"abstract":"<p><strong>Background: </strong>Phospholipid:diacylglycerol acyltransferase1 (PDAT1) enzyme is known to play an important role in lipid metabolism. Initially, it was suggested that the construction of PDAT1 overexpressors may result in plant varieties with increased oil content. Contrary to those expectations, Arabidopsis thaliana lines overexpressing AtPDAT1 did not exhibit an increased accumulation of the triacylglycerol pool. However, the overexpressing lines exhibited accelerated growth rate, increased seed yield, and when subjected to cold treatments, they had greater thermotolerance, whereas knock-out line were more susceptible than the wild-type.</p><p><strong>Result: </strong>In this work, we have performed a comparative proteomic analysis among wild-type, AtPDAT1-overexpressing and knock-out lines of Arabidopsis thaliana. For overexpressor lines we have observed significant changes in protein profiles related to processes that may partially explain increased plant vitality. Among others, we noticed elevated levels of subsequent groups of proteins: plastoglobule structural components and associated enzymes, proteins involved in photoprotection and in autophagy. The overexpressor lines were also characterized by upregulated level of proteins involved in abiotic stress responses, whereas the level of the proteins involved in biotic stress responses was downregulated. The opposite results were detected for the knock-out line.</p><p><strong>Conclusion: </strong>These results reveal a wide range of proteomic changes that reflect cellular alterations - some of which are supported by previous physiological and biochemical studies - induced by the genetic manipulation of a single gene encoding an enzyme directly involved in lipid metabolism. The results suggest a significant role of AtPDAT1 in plants responses to both biotic and abiotic stresses, highlighting its potential as a target for further research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"846"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190830","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 closed-loop method for precise genome size estimation using HiFi reads.","authors":"Jianfeng Xing, Jiangshan Hao, Chaorong Tang, Shangqian Xie, Kaiye Liu","doi":"10.1186/s12864-025-12031-9","DOIUrl":"10.1186/s12864-025-12031-9","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"878"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coupled transcriptome and proteome analysis of L3 and L4 developmental stages of Anisakis simplex s. s.: insights into target genes under glucose influence.","authors":"Iwona Polak, Robert Stryiński, Mateusz Maździarz, Lukasz Paukszto, Mónica Carrera, Iwona Bogacka, Elżbieta Łopieńska-Biernat","doi":"10.1186/s12864-025-12068-w","DOIUrl":"10.1186/s12864-025-12068-w","url":null,"abstract":"<p><p>Anisakis simplex is a cosmopolitan parasitic nematode of marine organisms with a complex life cycle. Consuming fish infected with its larvae poses a health risk, as the parasites can penetrate gastrointestinal mucosa, damage stomach and intestinal walls, and trigger allergic reactions. The resulting disease is known as anisakiasis. The European Food Safety Authority (EFSA) classifies A. simplex as a biohazard. Most of its developmental stages (L3, L4, and adults) occur under anaerobic conditions, and larvae derive energy mainly from saccharides. However, the effect of glucose on L3 and L4 larvae-stages pathogenic to humans-has not been described. This study aimed to identify genes and pathways involved in glucose (10 mg/mL) response through transcriptomic and proteomic analyses of L3 and L4 larvae. Differentially expressed genes (DEGs), long non-coding RNAs (DELs), and differentially regulated proteins (DRPs) were identified. DEGs were involved in cuticle structure, lyase activity, and metabolic processes. Comparing L3 CTR and L4 CTR (control) to glucose-treated samples revealed 1,969 DEGs; 259 overlapped between L4 GLU vs. L3 GLU, (glucose-treated) with 11 showing reversed expression. Additionally, 84 DELs were identified in L3 GLU vs. control, 40 in L4 GLU vs. control, and 163 between glucose-treated L4 and L3. Larval and glucose-specific alternative splicing events were also analyzed. Proteomic analysis revealed 35 DRPs-5 more abundant in L4, 30 in L3. The data reveal that developmental stage exerts a more substantial influence than glucose exposure on gene and protein expression profiles. However, glucose still modulates several pathways related to translation, cytoskeletal remodeling, extracellular matrix (ECM) reorganization, and energy metabolism.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"866"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191069","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":"Evolutionary and functional diversification of the DOG gene family in wheat (Triticum aestivum L.) and their roles in seed dormancy.","authors":"Yongjing Ni, Can Guo, Xiuyin Zhang, Mengjin Ma, Xuemin Liu, Yanping Li, Shaoying Lian, Junchang Li, Yumei Jiang, Jishan Niu, Lei Li","doi":"10.1186/s12864-025-12071-1","DOIUrl":"10.1186/s12864-025-12071-1","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"861"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190733","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":"Identification of key genes for fish adaptation to freshwater and seawater based on attention mechanism.","authors":"Songping Qian, Youjie Zhao, Fangrong Liu, Lei Liu, Qingyang Zhou, Shunrong Zhang, Yong Cao","doi":"10.1186/s12864-025-12089-5","DOIUrl":"10.1186/s12864-025-12089-5","url":null,"abstract":"<p><p>The evolutionary divergence of freshwater and marine fish reflects their adaptation to distinct ecological environments, with differences evident in their morphological traits, physiological functions, and genomic structures. Traditional molecular methods often fail to uncover the intricate regulatory relationships among genes under environmental stress. This study proposes the weighted attention gene analysis (WAGA) model, a novel approach that integrates natural language processing (NLP) for protein-coding gene feature representation with deep learning and self-attention (SA) mechanisms. WAGA effectively identifies key genes associated with sensory functions, osmoregulation, and growth and development on the basis of attention weights. The experimental results highlight its effectiveness in revealing genes crucial for ecological adaptation and evolution. This approach is essential for elucidating the mechanisms of ecological adaptability and evolutionary processes, while also offering novel insights and tools to support targeted breeding in aquaculture and fish genomics research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"875"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190865","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}