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The promotion of liver vitamin metabolism is of great significance for laying hens during fasting. 对蛋鸡禁食期间肝脏维生素代谢的促进具有重要意义。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11730-7
Jun Zhang, Zhixuan Luo, Mengyan Zhang, Yujie Gong, Yadong Tian, Ruili Han, Donghua Li, Yujie Guo, Xiangtao Kang, Yawei Yang, Zhuanjian Li, Ruirui Jiang
{"title":"The promotion of liver vitamin metabolism is of great significance for laying hens during fasting.","authors":"Jun Zhang, Zhixuan Luo, Mengyan Zhang, Yujie Gong, Yadong Tian, Ruili Han, Donghua Li, Yujie Guo, Xiangtao Kang, Yawei Yang, Zhuanjian Li, Ruirui Jiang","doi":"10.1186/s12864-025-11730-7","DOIUrl":"10.1186/s12864-025-11730-7","url":null,"abstract":"<p><strong>Background: </strong>Induced molt is an effective measure to reduce the introduction cost, cope with the continuous rise of feed cost, and realize the prolonged rearing of laying hens as well. Vitamins are beneficial to the antioxidant capacity and reproductive performance of laying hens, however, studies on vitamin metabolism during fasting are rarely reported.</p><p><strong>Results: </strong>We analyzed the association between cecal metabolome and liver transcriptome of laying hens during molt. The results showed that 3009 differences genes (FDR < 0.05), among which there were 62 differential genes related to vitamin metabolism. Eight core genes (ALDH1A1, CYP1A1, CYP1A4, AOX2P, AOX1, CYP3A7, BCAT1, CYP26B1) were obtained by protein network interaction (PPI). These genes were mainly enriched in Metabolic pathways, Retinol metabolism, Folate biosynthesis, One carbon pool by Folate, and Chemical carcinogenesis. After association analysis between these genes and cecal metabolites, a total of 176 differential metabolites were obtained. Among them, the metabolites with higher connectivity were Bifemelane, L-valine, Butyryl Fentanyl-D5 and Rimcazole.</p><p><strong>Conclusion: </strong>During fasting, vitamin A and vitamin E stored in the liver of laying hens are released in large quantities with the oxidative decomposition of lipids in the liver during fasting, which accelerates the metabolism of vitamin A in the liver. Folate and biotin may participate in the physiological remodeling of laying hens through epigenetic regulation. In addition, through association analysis, we constructed a data platform for vitamin metabolism-related pathway genes and cecal metabolites, laying a foundation for future research. However, whether the relationship between gene expression in the liver and metabolites in the cecum is bidirectional or unidirectional is still unclear and needs to be further studied.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"603"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538420","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}
引用次数: 0
Brassinosteroid-mediated carotenoid regulation enhances chilling tolerance in pepper. 油菜素内酯介导的类胡萝卜素调节增强辣椒的抗寒性。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11820-6
Jie Li, Jian Li, Jianghong Luo, Juan Li, Hamza Sohail, Keyan Zhu, Ping Yang
{"title":"Brassinosteroid-mediated carotenoid regulation enhances chilling tolerance in pepper.","authors":"Jie Li, Jian Li, Jianghong Luo, Juan Li, Hamza Sohail, Keyan Zhu, Ping Yang","doi":"10.1186/s12864-025-11820-6","DOIUrl":"10.1186/s12864-025-11820-6","url":null,"abstract":"<p><strong>Background: </strong>Low temperature stress severely limits the growth and development of pepper (Capsicum annuum L.). Brassinolides (BRs) and carotenoids play key roles in alleviating low-temperature stress. At present, the research on the regulatory relationship between BRs and carotenoids remains rather limited. In this study, CaBZR1 (Brassinazole-Resistant 1), a key transcription factor of BR signaling pathway, and CaLCYB (Lycopene β-Cyclase), a carotenoid synthesis gene, were silenced using virus-induced gene silencing (VIGS) technology. The role of BR-mediated carotenoid regulation of cold tolerance was explored.</p><p><strong>Results: </strong>The results showed that after silencing CaBZR1 and CaLCYB respectively, the carotenoid content, the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), as well as the chlorophyll fluorescence parameter (Fv/Fm) all decreased significantly. The levels of superoxide anion (O₂⁻), hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) increased significantly, leading to oxidative damage to membrane lipids. The expressions of cold-responsive genes such as CaFbox1 (F-box protein 1), CaMBF1 (Multiprotein Bridging Factor 1) and CaNAC3 (NAC domain containing protein 3) were significantly reduced. Exogenous spraying of EBR alleviated the damage in CaBZR1 and CaLCYB-silenced plants under low-temperature stress.</p><p><strong>Conclusions: </strong>These results emphasize that carotenoids and BRs enhance cold resistance in pepper by enhancing antioxidant enzyme activities, scavenging reactive oxygen species (ROS) and transcriptional responses. This study provides new insights into the interactions between BR signaling and carotenoid metabolism under low-temperature stress and offers a potential strategy for improving low-temperature tolerance in crops.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"601"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538302","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}
引用次数: 0
Novel insights into the Leishmania infantum transcriptome diversity of protein-coding and non-coding sequences in both stages of parasite development using nanopore direct RNA sequencing. 利用纳米孔直接RNA测序对寄生虫发育两个阶段的蛋白质编码和非编码序列的婴儿利什曼原虫转录组多样性进行了新的见解。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11767-8
Jean-Guillaume Emond-Rheault, Gabriel Reis Ferreira, Camille Lavoie-Ouellet, Martin A Smith, Barbara Papadopoulou
{"title":"Novel insights into the Leishmania infantum transcriptome diversity of protein-coding and non-coding sequences in both stages of parasite development using nanopore direct RNA sequencing.","authors":"Jean-Guillaume Emond-Rheault, Gabriel Reis Ferreira, Camille Lavoie-Ouellet, Martin A Smith, Barbara Papadopoulou","doi":"10.1186/s12864-025-11767-8","DOIUrl":"10.1186/s12864-025-11767-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"573"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538403","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}
引用次数: 0
Oral exposure to PET microplastics induces the pancreatic immune response and oxidative stress in immature pigs. 未成熟猪口服暴露于PET微塑料诱导胰腺免疫反应和氧化应激。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11760-1
Karol Mierzejewski, Aleksandra Kurzyńska, Monika Golubska, Ismena Gałęcka, Jarosław Całka, Iwona Bogacka
{"title":"Oral exposure to PET microplastics induces the pancreatic immune response and oxidative stress in immature pigs.","authors":"Karol Mierzejewski, Aleksandra Kurzyńska, Monika Golubska, Ismena Gałęcka, Jarosław Całka, Iwona Bogacka","doi":"10.1186/s12864-025-11760-1","DOIUrl":"10.1186/s12864-025-11760-1","url":null,"abstract":"<p><p>Microplastics are a widespread environmental hazard and their impact on human health has become a growing concern in last years. Recently, the potential role of microplastics in the development of various diseases, including diabetes, has been highlighted. Therefore, the aim of this study was to investigate the effects of PET microplastics on the pancreas using immature pigs as a model organism. We analyzed the global transcriptomic profile of the pancreas by RNA-Seq in piglets treated with either a low (0.1 g/day) or a high dose (1 g/day) of PET microplastics for 4 weeks. The analysis revealed a dose-dependent effect of PET microplastics on gene expression. A low dose changed the expression of one gene, while a high dose affected the expression of 86 genes. The differentially expressed genes, including immune cell markers, cytokines and chemokines, may activate the immune system in the pancreas in a way that is characteristic of the pathogenesis of diabetes. In addition, PET microplastics induced oxidative stress in the pancreas. These above imply that oral exposure to PET microplastics could be a new risk factor for the development of diabetes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"578"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538405","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}
引用次数: 0
An insight into the draft genome of the Oriental rat flea, Xenopsylla cheopis, together with its Wolbachia endosymbiont. 对东方鼠蚤,非洲鼠蚤及其沃尔巴克氏体内共生体基因组草图的洞察。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11759-8
Stephen Lu, David M Bland, Eric Dahlstrom, Neelam Redekar, Melina G Guizzo, Kent Barbian, B Joseph Hinnebusch, José M C Ribeiro
{"title":"An insight into the draft genome of the Oriental rat flea, Xenopsylla cheopis, together with its Wolbachia endosymbiont.","authors":"Stephen Lu, David M Bland, Eric Dahlstrom, Neelam Redekar, Melina G Guizzo, Kent Barbian, B Joseph Hinnebusch, José M C Ribeiro","doi":"10.1186/s12864-025-11759-8","DOIUrl":"10.1186/s12864-025-11759-8","url":null,"abstract":"<p><strong>Background: </strong>The Oriental rat flea, Xenopsylla cheopis, is a main vector of plague caused by the bacterium Yersinia pestis. Transcriptomic analysis of this insect and the interaction between Yersinia and the flea digestive tract have been the subject of several studies. However, to develop more refined studies on this vector in the future, we sequence and describe a draft genome of the rat flea Xenopsylla cheopis, discuss the physiological implications of its genetic features, and compare them with the only other sequenced member of the Siphonaptera, the cat flea, Ctenocephalides felis.</p><p><strong>Results: </strong>Sequencing data from both long and short reads were assembled into 7,694 contigs, from which 95,638 putative coding sequences (CDSs) were extracted and functionally annotated, providing insights into various aspects of flea physiology. This includes the identification of putative salivary proteins, such as acid phosphatases and FS-H/I, associated with blood acquisition; classification of multiple serine peptidases likely representing the primary digestive enzymes of X.cheopis; and the identification of all enzymes involved in heme biosynthesis, as well as heme oxygenases and unique heme-binding proteins potentially involved in heme detoxification. Comparison of detoxification-related genes-namely those in the cytochrome P450, carboxylesterase, and glutathione S-transferase families-with homologs from the cat flea (C. felis) revealed the presence of a platelet-activating factor (PAF) acetyl hydrolase that appears to be unique to rat fleas, cat fleas, and human head and body lice, but is absent in other blood-feeding arthropods. Additionally, we identified key components of immune-related pathways known from other arthropods, including the Toll, IMD, and JAK/STAT pathways. Finally, a contig encoding a novel bacterium was discovered within the assembled flea genome. Phylogenetic analysis of the Wolbachia endosymbiont in X. cheopis suggests it is closely related to the Wolbachia strain found in Drosophila melanogaster.</p><p><strong>Conclusions: </strong>The disclosure of the X. cheopis genome, together with its Wolbachia symbiont, should advance research on the biology of this vector.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"621"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538296","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}
引用次数: 0
Genome assembly and annotation of Babesia rossi, a protozoan parasite for canine babesiosis. 犬巴贝斯虫病原生寄生虫巴贝斯虫的基因组组装与注释。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11495-z
Neelam Redekar, Xu Wang, Luis Neves, Steven Brooks, Justin Lack, Andrew Leisewitz, Hans Ackerman
{"title":"Genome assembly and annotation of Babesia rossi, a protozoan parasite for canine babesiosis.","authors":"Neelam Redekar, Xu Wang, Luis Neves, Steven Brooks, Justin Lack, Andrew Leisewitz, Hans Ackerman","doi":"10.1186/s12864-025-11495-z","DOIUrl":"10.1186/s12864-025-11495-z","url":null,"abstract":"<p><strong>Background: </strong>Apicomplexan parasite, Babesia rossi, is an Ixodid tick-transmitted pathogen that causes the most severe form of canine babesiosis disease. Compared to other Babesia pathogens of dogs, B. rossi exhibits unique pathophysiology, virulence, and a responsiveness to drugs that differs from the small Babesia parasites.</p><p><strong>Results: </strong>Here we report the first near-complete chromosome-level assembly of Babesia rossi strain PMB - isolated from a sick dog from Pietermaritzburg, South Africa. Assembly with long-read HiFi data yielded 21.06 Mbp genome size, spanning across five gene-dense chromosome-level scaffolds, a single apicoplast scaffold, and a remaining 54 unplaced low gene density scaffolds with 1.32 Mb N50 and 96.6% BUSCO Apicomplexan completeness. The genome annotation identified a total of 3,098 protein-coding genes, 71 tRNA, and 16 rRNA genes. The mitochondrial genome (6.4 Kbp) was also identified. Genome assemblies of two additional field isolates of B. rossi were also reported. Comparative genomic analyses revealed four syntenic genomic inversions and multiple polymorphisms across three B. rossi isolates, although SNP and indel density was higher within the gene desserts of the genomes. Despite these differences, three B. rossi isolates' genome assemblies showed 99% conserved orthologous gene sets. About 76% of protein-coding genes of Babesia rossi isolate PMB were shared with four other Babesia species.</p><p><strong>Conclusion: </strong>This report provides valuable genomic information that is crucial to comprehend B. rossi evolution, virulence, and potential drug targets for canine babesiosis.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"579"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538312","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}
引用次数: 0
NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis. NuclampFISH能够基于核RNA表达进行细胞分选,用于染色质分析。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11818-0
Yifang Liu, Yuchen Qiu, Keqing Nian, Sara H Rouhanifard
{"title":"NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis.","authors":"Yifang Liu, Yuchen Qiu, Keqing Nian, Sara H Rouhanifard","doi":"10.1186/s12864-025-11818-0","DOIUrl":"10.1186/s12864-025-11818-0","url":null,"abstract":"<p><strong>Background: </strong>Transcriptional bursts are periods when RNA polymerase interacts with a DNA locus, leading to active gene transcription. This bursting activity can vary across individual cells, and analyzing the differences in transcription sites can help identify key drivers of gene expression for a specific target RNA. Scaffolding methods based on fluorescence in situ hybridization (FISH) have been widely used to amplify the fluorescent signal of RNAs and sort cells based on RNA expression levels. Examples include click-amplifying FISH (clampFISH) and hybridization chain reaction (HCR). However, these methods are limited in their ability to target and amplify transcription sites, due to the long probes' hindered accessibility through cellular compartment membranes and crosslinked proteins. Thus, sorting based on transcriptional bursting has not been achieved. Additionally, the required formaldehyde fixation interferes with downstream analysis of chromatin and protein-binding interactions.</p><p><strong>Results: </strong>To address these challenges, we developed a platform, nuclear clampFISH (nuclampFISH) that integrates click-amplified FISH with reversible crosslinkers and allows access to the nucleus. We demonstrate that with optimized parameters and by eliminating the cytosol and cell membrane, this method enables the amplification of fluorescent signal for RNAs using a reversible crosslinker, enabling the sorting of cells based on nuclear RNA expression and is compatible with downstream biochemical analysis including chromatin conformation assays. We applied this assay to demonstrate that transcriptionally active cells have more accessible chromatin for a respective gene.</p><p><strong>Conclusions: </strong>This new method enables the sorting of cells based on transcriptional bursts. This method combines the specificity of a single-cell assay for detecting transcription sites with the throughput of flow cytometry to enable bulk assays such as chromatin conformation or other biochemical assays. Notably, the tools developed are highly accessible and do not require specialized computation or equipment.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"624"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538404","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}
引用次数: 0
Single-cell transcriptome of mouse hippocampus identifies neural precursor-like cells, and reveals IL15Rα knock out-mediated neuron remodeling. 小鼠海马单细胞转录组鉴定神经前体样细胞,揭示IL15Rα敲除介导的神经元重构。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11785-6
Yanting Luo, Yadan Nie, Xuemei Huang, Haixia Wang, Zuoli Sun, Jian Yang, Yi He
{"title":"Single-cell transcriptome of mouse hippocampus identifies neural precursor-like cells, and reveals IL15Rα knock out-mediated neuron remodeling.","authors":"Yanting Luo, Yadan Nie, Xuemei Huang, Haixia Wang, Zuoli Sun, Jian Yang, Yi He","doi":"10.1186/s12864-025-11785-6","DOIUrl":"10.1186/s12864-025-11785-6","url":null,"abstract":"<p><strong>Background: </strong>IL15Rα is highly expressed in brain tissues, especially in hippocampus. IL15Rα knock-out induces the behavior, physiological and molecular changes in mice similar to the phenotype of psychiatric disorders.</p><p><strong>Results: </strong>To study how IL15Rα knock-out affects cellular function of the hippocampus in adult mice, we produced 64,399 single-cell transcriptomes from WT and KO mice and identified precursor-like neuron (PLN), a type of neural cells exhibiting precursor-like attributes, as well as four variant glial cell types. PLN displayed top-ranked functional changes despite barely changing in cell counts, along with high abundance of ribosomal genes, heavy energy consumption, quiescent cell-cell communication, intensive distribution in developmental stages, and a widespread yet moderate distribution across adult brain regions. We proposed PLN is in an intermediate and unprepared state, reserved for regulating inhibitory neuron fitness and exerting excitatory-inhibitory balance. We developed \"polarization score\" to evaluate the degree of cell aggregation and found its relation to transcription redundancy.</p><p><strong>Conclusions: </strong>In summary, we demonstrate the precursor-like attributes of PLN and its potential as a regulatory fulcrum for adjusting brain's excitatory-inhibitory balance and robustness in IL15Rα-KO mice.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"598"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538418","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}
引用次数: 0
Dynamic transcriptome landscape of oat grain development. 燕麦籽粒发育的动态转录组景观。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11827-z
Ting Wang, Bing Han
{"title":"Dynamic transcriptome landscape of oat grain development.","authors":"Ting Wang, Bing Han","doi":"10.1186/s12864-025-11827-z","DOIUrl":"10.1186/s12864-025-11827-z","url":null,"abstract":"<p><strong>Background: </strong>Oats are widely consumed throughout the world because of their nutritive value, with their yield and quality being associated with the developmental process of grain development. However, the underlying molecular mechanisms of the transcriptional dynamics of this process have not yet been fully elucidated. In this study, RNA-seq was performed to investigate the transcriptional dynamics and identify the key genes involved in the development of the oat grain at four different developmental stages.</p><p><strong>Results: </strong>A total of 33,197 differentially expressed genes (DEGs), including 1,308 differentially expressed transcription factors (TFs) were identified, 398 DEGs associated with plant hormone signal transduction and 107 DEGs associated with starch and sucrose metabolism. The main concern of this study was to include those genes associated with hormone signaling, and the sucrose and starch metabolism pathways.</p><p><strong>Conclusions: </strong>The results of this study provide valuable insights into the genetic resources affecting the molecular mechanism underlying the development of the oat grain, as well as establishing a strong theoretical foundation for its improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"616"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538284","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}
引用次数: 0
Genome-wide survey of the HMA gene family in wheat (Triticum aestivum L.) and its potential role in cadmium stress. 小麦HMA基因家族的全基因组研究及其在镉胁迫中的潜在作用。
IF 3.5 2区 生物学
BMC Genomics Pub Date : 2025-07-01 DOI: 10.1186/s12864-025-11746-z
Leilei Shao, Xuyu Guo, Yang Wang, Tianzhen Lei, Yijie Wan, Lingjian Ma, Na Niu
{"title":"Genome-wide survey of the HMA gene family in wheat (Triticum aestivum L.) and its potential role in cadmium stress.","authors":"Leilei Shao, Xuyu Guo, Yang Wang, Tianzhen Lei, Yijie Wan, Lingjian Ma, Na Niu","doi":"10.1186/s12864-025-11746-z","DOIUrl":"10.1186/s12864-025-11746-z","url":null,"abstract":"<p><p>Cadmium has been accumulating in the agricultural and ecological environment in recent years due to the release of industrial pollutants. Due to its high solubility, slow degradability and high toxicity, it is highly susceptible to occurring in agricultural fields. The presence of cadmium at low concentrations is harmful to plants. Heavy metal ATPases (HMAs) are proteins that can detoxify high concentrations of heavy metals through vacuole compartmentalization or exocytosis pathways. They have been extensively studied in plants. However, the cadmium transport function of HMAs in wheat has not been explored. In this study, a comprehensive and systematic investigation of HMA gene family members in wheat was conducted. A total of 28 putative TaHMAs were identified. Phylogenetically, these 28 putative TaHMAs were divided into two subgroups: Cu/Ag and Zn/Co/Cd/Pb. The gene structures and conserved motifs were consistent within the same branch and diverse in different branches. The TaHMA gene family is closely related to rice, B. distachyon and A. tauschii. GO analysis results suggest that TaHMAs may be involved in cation transport and membrane components. Protein interaction analysis results suggest that TaHMAs may interact with TaSOD to activate the SOD defense mechanism in wheat. Expression patterns exhibited tissue specificity. Finally, the expression patterns of TaHMAs were validated in the roots and leaves of wheat plants under cadmium stress. Our findings will be valuable for functional studies and applications of HMA gene family members in wheat.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"619"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538385","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}
引用次数: 0
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