BMC Genomics最新文献

{"title":"M6A methyltransferase METTL3 promotes glucose metabolism hub gene expression and induces metabolic dysfunction-associated steatotic liver disease (MASLD).","authors":"Shuowen Wang, Ziying Xu, Zijun Wang, Xiaoyu Yi, Jianxin Wu","doi":"10.1186/s12864-025-11377-4","DOIUrl":"10.1186/s12864-025-11377-4","url":null,"abstract":"<p><strong>Background: </strong>N6-methyladenosine (m6A) RNA modification plays a crucial role in various biological events and is implicated in various metabolic-related diseases. However, its role in MASLD remains unclear. This study aims to investigate the impact of METTL3 on MASLD through multi-omics analysis, with a focus on exploring its potential mechanisms of action.</p><p><strong>Methods: </strong>An MASLD mouse model was established by feeding C57BL/6J mice a high-fat diet for 12 weeks. A METTL3 stable overexpression AML12 cell model was also constructed via lentiviral transfection. Subsequent transcriptomic and proteomic analyses, as well as integrated analysis between different omics datasets, were conducted.</p><p><strong>Results: </strong>METTL3 expression was significantly increased in the MASLD mouse model. Through our transcriptomic and proteomic analyses, we identified 848 genes with significant inconsistencies between the transcriptomic and proteomic datasets. GO/ KEGG enrichment analyses identified terms that may be involved in post-transcriptional modifications, particularly METTL3-mediated m6A modification. Subsequently, through integrated proteomic analysis of the METTL3-overexpressed AML12 cell model and the MASLD mouse model, we selected the top 20 co-upregulated and co-downregulated GO/ KEGG terms as the main biological processes influenced by METTL3 during MASLD. By intersecting with pathways obtained from previous integrated analyses, we identified GO/ KEGG terms affected by METTL3-induced m6A modification. Protein-protein interaction analysis of proteins involved in these pathways highlighted GAPDH and TPI1 as two key hub genes.</p><p><strong>Conclusions: </strong>During MASLD, METTL3 regulates the glycolytic pathway through m6A modification, influencing the occurrence and development of the disease via the key hub genes GAPDH and TPI1. These findings expand our understanding of MASLD and provide strong evidence for potential therapeutic targets and drug development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"188"},"PeriodicalIF":3.5,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490453","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 QTL mapping with transcriptome analysis mined candidate genes of growth stages in castor (Ricinus communis L.).","authors":"Guanrong Huang, Jiannong Lu, Xuegui Yin, Liuqin Zhang, Haihong Lin, Xiaoxiao Zhang, Chaoyu Liu, Jinying Zuo","doi":"10.1186/s12864-025-11348-9","DOIUrl":"10.1186/s12864-025-11348-9","url":null,"abstract":"<p><strong>Background: </strong>The growth stages largely determine the crop yield, while little is known about their genetic mechanisms in castor. In this study, the QTL mapping and candidate gene mining of growth stages were conducted using populations F₂ and BC₁, combining with differential expression analysis and weighted gene co-expression network analysis (WGCNA). The traits studied included the emergence date (ED), the budding date of primary spike (PSBD), the flowering date of primary spike (PSFD), the maturation date of primary spike (PSMD), and the maturation date of primary branch spike (PBSMD).</p><p><strong>Results: </strong>A total of 20 QTLs conferring four traits (ED, PSBD, PSFD and PBSMD) were identified in the F₂ population, with a phenotypic variation explained (PVE) of single QTL ranged from 0.24 to 25.46%. Five QTLs underlying PSMD and PBSMD were identified in the BC₁ population, with a PVE of single QTL ranged from 4.74 to 10.82%. To our surprise, almost all the identified QTLs were clustered within two marker intervals, the RCM1769-RCM1838 on linkage group 6 and RCM950-RCM917 on linkage group 3. Subsequently, 473 open reading frames (ORFs) were searched out within these two clusters and 110 differentially expressed genes (DEGs) were screened out from these ORFs by the comparative transcriptome clean data (a total of 140.86 G) at the budding date, the initial flowering date and the full flowering date between parental racemes. With these DEGs, five distinct gene co-expression modules were generated using WGCNA. Showing significant differential expression between parents, four candidate genes (LOC8261128, LOC8278994, LOC8281165 and LOC8259049) in module MEturquoise, were recognized and were annotated as RcSYN3, RcNTT, RcGG3 and RcSAUR76 respectively. This finding implies their potential role in regulating the growth stages of castor.</p><p><strong>Conclusion: </strong>In this study, numerous QTLs conferring growth stages were detected and four candidate genes were mined, which need to be functionally validated. The results provided a new insight into the genetic structure of ED, PSBD, PSFD, PSMD and PBSMD, offered the candidate genes and molecular markers for their improvement as well in castor.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"178"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476222","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":"Physiological and transcriptomic analyses revealed the alleviating effects of exogenous Ca²⁺ and NO compound treatment on high salt stress in Reaumuria soongorica.","authors":"Zehua Liu, Hanghang Liu, Bingbing Tan, Xidui Wang, Peifang Chong","doi":"10.1186/s12864-025-11355-w","DOIUrl":"10.1186/s12864-025-11355-w","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Soil salinization represents the most prevalent abiotic stress, severely impacting a severe impact on plant growth and crop yield. Consequently, delving into the mechanism through which exogenous substances enhance plant salt tolerance holds significant importance for the stabilization and augmentation of crop yield.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;In this study, within the context of salt stress, the seedlings of R. soongorica were subjected to exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO treatments. The aim was to comprehensively explore the alleviation effects of exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO on the high salt stress endured by R. soongorica from the perspectives of physiology and transcriptomics. The experimental results demonstrated that the combined treatment of exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO increased the relative water content and free water content of R. soongorica seedlings during salt stress conditions. Simultaneously, it induced a reduction in the leaf sap concentration, leaf water potential, water saturation deficit, and the ratio of bound water to free water. These modifications effectively regulated water metabolism and mitigated physiological drought induced by salt stress. In addition, the concurrent treatment of exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO could diminish Na&lt;sup&gt;+&lt;/sup&gt; and Cl&lt;sup&gt;-&lt;/sup&gt; levels in R. soongorica seedlings under salt stress. At the same time, it was effective in elevating the contents of K&lt;sup&gt;+&lt;/sup&gt; and Ca&lt;sup&gt;2+&lt;/sup&gt;, thereby facilitating the adjustment of the ion equilibrium. As a result, this treatment served to relieve the ion toxicity precipitated by salt stress, which is crucial for maintaining the physiological homeostasis and viability of the seedlings. Transcriptional analysis revealed that 65 differentially expressed genes (DEGs) were observable at three distinct stress time points in the context of high salt stress. Additionally, 154 DEGs were detected at three stress time points during the combined treatment. KEGG enrichment analysis revealed that phenylpropanoids biosynthesis, plant hormone signal transduction, MAPK signalling pathway, brassinosteroid biosynthesis and zeatin biosynthesis were significantly enriched under high salt stress and exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO compound treatment. Furthermore, WGCNA uncovered that multiple genes, including ADK, SBT, F-box protein, MYB, ZIP, PAL, METTL, and LRR, were implicated in the adaptive and mitigating mechanisms associated with the combined treatment of exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO in modulating high salt stress within R. soongorica seedlings.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The outcomes of this study are highly conducive to disclosing the mechanism through which the combined treatment of exogenous Ca&lt;sup&gt;2+&lt;/sup&gt; and NO ameliorates the salt tolerance of R. soongorica from both physiological and transcriptional aspects. It also paves a solid theoretical groundwork for the employment of biotechnology in the breed","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"179"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11847379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476235","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":"Anthocyanin metabolites and related regulatory genes analysis in leaves of Acer Pseudosieboldianum mutant during different periods of color change.","authors":"Zi-Han Gong, Shu-Han Chen, Xin-Yu Li, Wei-Wei Lv, Ming-Rui Li, Xin-Mei Jin, Yu-Fu Gao, Li-Ping Rong","doi":"10.1186/s12864-025-11378-3","DOIUrl":"10.1186/s12864-025-11378-3","url":null,"abstract":"<p><strong>Background: </strong>Acer pseudosieboldianum (Pax) Komarov, is a colorful leaf species belonging to the family Aceraceae, mainly distributed in Northeast China, Russia, and northern Korea. The leaves of Acer pseudosieboldianum are green in spring and summer, and turning red in autumn, which is of high ornamental value. In previous study, a mutant maple was selected with alternating red-green leaf color in spring and summer. However, the reason for the color mutation was not clear. Therefore, UPLC /LC-MS and RNA-seq were used to analyze the anthocyanin components and related differentially expressed genes in the spring leaf color changes of A. pseudosieboldianum mutant, which can provide broader insights into the complex coloration process of leaf color.</p><p><strong>Results: </strong>The results showed that the mutant leaves contained a total of 50 anthocyanin metabolites. In all differential metabolites of anthocyanins, Cyanidin-3,5-O-diglucoside, Cyanidin-3-O-glucoside, Cyanidin-3-O-sambubioside not only had higher content, but also showed significant changes at different stages. Especially, the consistent high content of anthocyanins in Cyanidin-3-O-glucoside, which are the main pigments for leaf color. In addition, 11,522 genes were found to be significantly differentially with 5,477 genes up-regulated, and 6,045 genes down-regulated. We identified relevant information for differentially expressed genes (DEGs) associated with leaf color, including 20 structural genes involved in anthocyanin biosynthesis, 12 transcription factors, and eight genes related to anthocyanin transport.</p><p><strong>Conclusions: </strong>Among all anthocyanins of A. pseudosieboldianum mutant leaf, Cyanidin-3-O-glucoside remained high in all three stages of leaves, which is main substances for the leaf color. Additionally, 20 structure gene, 12 transcription factors and some genes associated with anthocyanin synthesis and transport were screened and there was a complex metabolic network in mutant leaves. This study provided a basis for resource innovation and landscaping applications of Acer plants by analyzing the anthocyanin metabolites and expression of DEGs in the leaf coloring process.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"182"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11847387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476220","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":"Pan-WD40ome analysis of 26 diverse inbred lines reveals the structural and functional diversity of WD40 proteins in maize.","authors":"Shenghui Ji, Pengfei Yin, Tao Li, Xiaoxia Du, Wenkang Chen, Renyu Zhang, Xiaohong Yang, Xuan Zhang","doi":"10.1186/s12864-025-11342-1","DOIUrl":"10.1186/s12864-025-11342-1","url":null,"abstract":"<p><strong>Background: </strong>The WD40 repeat proteins are crucial components of eukaryotic genomes and contribute to a wide array of plant developmental processes and environmental interactions. However, the true extent of intraspecific WD40 diversity in plants is unclear.</p><p><strong>Results: </strong>We defined a nearly complete species-wide pan-WD40ome in maize based on the published genome sequences of 26 nested association mapping (NAM) population founders. The pan-WD40ome largely saturated with inclusion of approximately 20 inbred lines, with about 95% of the pan-WD40ome being present in at least two founders. The architectural diversity of the WD40 domains, additional domains, and consequent spatial protein structures suggested the functional diversity of the maize pan-WD40ome. This finding was supported by significant associations between 87 WD40 genes and 19 agronomic, 3 kernel-quality, and 3 biotic-stress traits, as well as the multiple molecular pathways through which the trait-associated WD40 genes were predicted to function. In addition, WD40 genes exhibited abundant genomic variations among the NAM founders. Sequence analysis indicated that gene duplications and gene translocations caused by Helitron transposons may play important roles in the amplification of WD40 genes during the evolution of the maize WD40 gene family.</p><p><strong>Conclusions: </strong>In summary, this study provides a comprehensive framework for understanding the structural and functional diversity of the pan-WD40ome in maize and other agronomically important species with complex genomes, as well as excellent candidate genes/alleles for maize genetic improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"181"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11847395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476234","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 analysis of the UBA2 gene family in wheat (Triticum aestivum L.).","authors":"Juan Li, Chunge Cui, Fengying Han, Jin Liu","doi":"10.1186/s12864-025-11352-z","DOIUrl":"10.1186/s12864-025-11352-z","url":null,"abstract":"<p><strong>Background: </strong>RNA-binding proteins (RBPs) participate in multiple aspects of RNA metabolism, which in turn regulates gene expression, thereby involving in organism growth and development. The UBA2 family, one of the subfamilies of RBPs, has been identified in several plant species. However, few researches have been performed to investigate the role of UBA2 in wheat (Triticum aestivum).</p><p><strong>Results: </strong>In this study, we identified eleven TaUBA2s and divided them into three groups according to their domain characteristics. Phylogenetic analysis was conducted to forecast functional similarities among Arabidopsis, rice, maize and wheat UBA2 genes. Members within the same subfamily of TaUBA2 are relatively conserved in terms of protein structure, motifs, and gene structure. Chromosomal location and synteny analysis suggested that the segmental duplication events played important roles during TaUBA2s evolution. The cis-acting element analysis showed that TaUBA2s were involved in hormone response, development, light response, metabolism, and response to environmental stress. Furthermore, TaUBA2C contains two RNA recognition motifs (RRMs), and the first RRM is responsible for the nuclear speckle formation of TaUBA2C, whereas the two RRMs are necessary for its biological function.</p><p><strong>Conclusions: </strong>Taken together, our study provides a comprehensive analysis of the TaUBA2 family in wheat and lays the foundation for the future functional investigations of TaUBA2s in wheat growth, development and stress responses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"180"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11847341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476221","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 interna rootlets of the rhizocephalan Parasacculina sinensis reveals potential mechanisms of parasite host control.","authors":"Wenjie Li, Yiheng Feng, Haocheng Liu, Niklas Dreyer, Yue Him Wong","doi":"10.1186/s12864-025-11315-4","DOIUrl":"10.1186/s12864-025-11315-4","url":null,"abstract":"<p><strong>Background: </strong>The endoparasitic rhizocephalan Parasacculina sinensis has a radically simplified morphology and primarily infests decapods crustaceans. Rhizocephalan barnacles usually absorb nutrients from the host through a complex rootlet system (the interna), and also change the morphology, physiology and behavior of their hosts. However, little is known about the transcriptomic landscape, ultrastructural details and gene expression of the interna rootlets in the group. In this study, we investigated the structural and molecular signatures of the interna of P. sinensis by using detailed histological staining and transcriptomic analyses.</p><p><strong>Results: </strong>The interconnected F-actin nodal network, lipid droplets, and nucleus of interna rootlets were visualized using fluorescence straining. We successfully obtained a clean transcriptome of P. sinensis and conducted functional analyses of interna embedded within host hepatopancreas, claw muscle, and eyestalk. The gene ontology (GO) terms related to translation, metabolic process, biosynthetic process, cellular process were highly expressed in the top 10% transcripts from the interna. The GO category of shared differential expression of genes (DEGs) among internae was related to embryonic development. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway neuroactive ligand-receptor interaction and the GO term neurotransmitter transporter activity were identified in the shared DEGs among internae. The interna entangled within host hepatopancreas, eyestalk and claw muscle fibers had similarities and differences in the functional biology. Additionally, the interna specific candidate genes probably involved in host immune, lipid metabolism, molting and growth were identified.</p><p><strong>Conclusions: </strong>Our study demonstrates an in-depth function of interna rootlets of P. sinensis and reveals potential mechanisms of parasite host control. This study provides novel information to further investigate the evolutionary drivers of parasitism in barnacles.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"177"},"PeriodicalIF":3.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476236","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":"Improving genomic prediction of vitamin C content in spinach using GWAS-derived markers.","authors":"Jana Jeevan Rameneni, A S M Faridul Islam, Carlos A Avila, Ainong Shi","doi":"10.1186/s12864-025-11343-0","DOIUrl":"10.1186/s12864-025-11343-0","url":null,"abstract":"<p><p>Vitamin C (VC), also known as ascorbic acid and ascorbate, is a water-soluble antioxidant in plants that promotes skin health and immune function in humans. Spinach (Spinacia oleracea L.) is a leafy green widely consumed for its health benefits. Recent reports have shown that nutritional content, including VC, can be improved in spinach. However, due to its complex inheritance, new selection methods are needed to improve selection for cultivar development. In this study, single nucleotide polymorphism (SNP) markers identified by genome-wide association (GWAS) were used for genomic prediction (GP) to improve prediction accuracy (PA) for VC content in spinach. A set of 147,977 SNPs generated from whole genome resequencing was used for GWAS in a panel of 347 spinach genotypes by six GWAS models. Sixty-two SNP markers distributed on all six spinach chromosomes were associated with VC content. PA for the selection of VC content was estimated with fourteen random SNP sets across seven GP models. The results indicated that the PA can be > 40% after using 1,000 or more SNPs in six of the seven models tested; using GWAS-derived significant SNP markers PA increases to a high r-value up to 0.7 when using 62 associated SNP markers in Bayes ridge regression (BRR) model. Upon validation, identified accessions with high VC and high PA genomic selection model can be used in spinach breeding programs to develop high VC content cultivars.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"171"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472074","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 reveal gene regulation mechanisms of the barnacle Chthamalus challengeri for microhabitat adaption in the intertidal zone.","authors":"HaoYuan Li, MengMeng Huang, ZhiBin Gan, XinZheng Li","doi":"10.1186/s12864-025-11357-8","DOIUrl":"10.1186/s12864-025-11357-8","url":null,"abstract":"<p><strong>Background: </strong>Microhabitat environmental factors (e.g., temperature, oxygen concentration, nutrients, osmotic stress, and topography) are critical to the survival of intertidal organisms. Understanding how transcription responses are regulated in relation to intertidal microhabitat variation has important implications for studying adaptive evolution in these organisms. The barnacle Chthamalus challengeri, which survives in the intertidal zone and is subjected to periodic tidal changes, serves as an ideal species for detecting adaptive evolution in intertidal organisms.</p><p><strong>Results: </strong>In this study, we designed a series of in situ tidal conditions for C. challengeri and sequenced their transcriptome collected from various microhabitats. We aimed to detect the genetic adaptation mechanisms of barnacles responding to the microhabitat changes in the intertidal zone based on comparative transcriptomics. Our results indicated that different intertidal microhabitats significantly affected the gene expression models of C. challengeri, particularly for genes related to physiological and biochemical functions. Specifically, the expression of genes such as CYP450, HSP70, CYTB, and COX1 was significantly increased under low tide (air-exposed conditions), while genes like CNGA3, AK, and CP52 showed significantly increased expression under high tide (seawater-immersed conditions).</p><p><strong>Conclusion: </strong>The results suggest that C. challengeri relies on cytochrome p450 enzymes to enhance oxidative capacity, counts on heat shock proteins and cell phagocytosis to resist microhabitat changes in response to different tidal conditions, and produces a hypoxic stress response to regulate energy metabolism and body temperature changes upon entering into seawater. This study provides genetic resources and clues for investigating the adaptation mechanisms of intertidal barnacles and identifies different gene expression models for C. challengeri responding to various microhabitats.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"176"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472080","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 of the AAAP gene family and expression analysis under tissue-specific expression in five legumes.","authors":"Naiyu Chen, Shulei Wang, Yajie Yin, Guoling Ren, Yiting Zhang, Lina Qu, Lei Ling","doi":"10.1186/s12864-025-11224-6","DOIUrl":"10.1186/s12864-025-11224-6","url":null,"abstract":"<p><p>Amino acid/auxin permease (AAAP) is a transcription factor with a highly conserved amino acid region that regulates physiological processes and development in many plants and responds to various abiotic stresses. In this study, a genome-wide analysis of five legumes (Phaseolus vulgaris, Medicago truncatula, Lotus japonicus, Glycine max, and Cicer arietinum) identified 74, 106, 87, 147, and 70 AAAP genes, respectively. In addition, chromosomal localisation, phylogenesis, conserved motifs, gene structure, and gene replication analyses were performed on AAAP genes. The results showed that legume AAAP gene branches from the same evolutionary system had similar protein structures. In addition, by analysing the transcriptome data, we determined that the expression levels of AAAP differed in each tissue. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to investigate the expression patterns of AAAP under tissue-specific conditions. These results show that AAAP genes play crucial regulatory roles in tissue-specific gene expression. This study provides a basis for further exploration of the biological functions of the AAAP gene family in legumes. AAAP plays an important role in the growth and development of the five legumes. In particular, tissue-specific expression analysis provides a scientific basis for the development of agricultural production of these five legumes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"173"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472070","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}