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Transcriptomic analysis reveals differentially expressed genes associated with meat quality in Chinese Dagu chicken and AA+ broiler roosters. 转录组分析揭示了与中国大谷鸡和 AA+ 肉用公鸡肉质相关的差异表达基因。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-26 DOI: 10.1186/s12864-024-10927-6
Hongyan Zhu, Xiaohan Li, Jie Wang, Haoming Wang, Song Zhao, Yumin Tian, Yuhong Su

Background: With the improvement of living standards, the quality of chicken has become a significant concern. Chinese Dagu Chicken (dual-purpose type) and Arbor Acres plus broiler (AA+ broiler) (meat-type) were selected as the research subjects in this study, the meat quality of the breast and leg muscles were measured. However, the molecular mechanism(s) underlying regulation of muscle development are not yet fully elucidated. Therefore, finding molecular markers or major genes that regulate muscle quality has become a crucial breakthrough in chicken breeding. Unraveling the molecular mechanism behind meat traits in chicken and other domestic fowl is facilitated by identifying the key genes associated with these developmental events. Here, a comparative transcriptomic analysis of chicken meat was conducted on breast muscles (BM) and leg muscles (LM) in AA+ broilers (AA) and Dagu chicken (DG) to explore the differences in their meat traits employing RNA-seq.

Results: Twelve cDNA libraries of BM and LM from AA and DG were constructed from four experimental groups, yielding 14,464 genes. Among them, Dagu chicken breast muscles (DGB) vs AA+ broilers breast muscles (AAB) showed 415 upregulated genes and 449 downregulated genes, Dagu chicken leg muscles (DGL) vs AA+ broilers leg muscles (AAL) exhibited 237 upregulated genes and 278 downregulated genes, DGL vs DGB demonstrated 391 upregulated genes and 594 downregulated genes, and AAL vs AAB displayed 122 upregulated genes and 154 downregulated genes. 13 genes, including nine upregulated genes (COX5A, COX7C, NDUFV1, UQCRFS1, UQCR11, BRT-1, FGF14, TMOD1, MYOZ2) and four downregulated genes (MYBPC3, MYO7B, MTMR7, and TNNC1), were found to be associated with the oxidative phosphorylation signaling pathway. Further analysis revealed that the differentially expressed genes (DEGs) from muscle were enriched in various pathways, such as metabolic pathways, oxidative phosphorylation, carbon metabolism, glycolysis, extracellular matrix-receptor interaction, biosynthesis of amino acids, focal adhesion, vascular smooth muscle contraction, and cardiac muscle contraction, all of which are involved in muscle development and metabolism. This study also measured the meat quality of the breast and leg muscles from the two breeds, which demonstrated superior overall meat quality in Chinese Dagu Chicken compared to the AA+ broiler.

Conclusions: Our findings show that the meat quality of dual-purpose breeds (Chinese Dagu chicken) is higher than meat-type (AA+ broiler), which may be related to the DEGs regulating muscle development and metabolism. Our findings also provide transcriptomic insights for a comparative analysis of molecular mechanisms underlying muscle development between the two breeds, and have practical implications for the improvement of chicken breeding practices.

背景:随着人们生活水平的提高,鸡肉的品质已成为人们关注的焦点。本研究选取了中国大谷鸡(两用型)和大树加肉鸡(AA+肉鸡)(肉用型)作为研究对象,测定了胸肌和腿部肌肉的肉质。然而,肌肉发育的分子调控机制尚未完全阐明。因此,寻找调控肌肉质量的分子标记或主要基因已成为鸡育种的关键突破口。通过鉴定与这些发育事件相关的关键基因,有助于揭示鸡和其他家禽肉质性状背后的分子机制。在此,我们利用 RNA-seq 对 AA+ 肉鸡(AA)和大谷鸡(DG)的胸肌(BM)和腿部肌肉(LM)进行了鸡肉转录组学比较分析,以探讨它们肉质性状的差异:从4个实验组中构建了12个AA和DG胸肌和腿肌的cDNA文库,共获得14 464个基因。其中,大古鸡胸肌(DGB)与AA+肉鸡胸肌(AAB)相比,上调基因415个,下调基因449个;大古鸡腿肉(DGL)与AA+肉鸡腿肉(AAL)相比,上调基因237个,下调基因278个;DGL与DGB相比,上调基因391个,下调基因594个;AAL与AAB相比,上调基因122个,下调基因154个。研究发现,13 个基因与氧化磷酸化信号通路有关,其中包括 9 个上调基因(COX5A、COX7C、NDUFV1、UQCRFS1、UQCR11、BRT-1、FGF14、TMOD1 和 MYOZ2)和 4 个下调基因(MYBPC3、MYO7B、MTMR7 和 TNNC1)。进一步分析发现,肌肉中的差异表达基因(DEGs)富集在不同的通路中,如代谢通路、氧化磷酸化、碳代谢、糖酵解、细胞外基质与受体相互作用、氨基酸的生物合成、病灶粘附、血管平滑肌收缩和心肌收缩等,所有这些通路都参与了肌肉的发育和代谢。本研究还测定了两个品种的胸肌和腿部肌肉的肉质,结果表明中国大谷鸡的整体肉质优于 AA+ 肉鸡:我们的研究结果表明,两用鸡(中国大谷鸡)的肉质高于肉用型鸡(AA+肉鸡),这可能与调节肌肉发育和代谢的 DEGs 有关。我们的研究结果还为比较分析两个品种肌肉发育的分子机制提供了转录组学见解,对改进鸡育种实践具有实际意义。
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引用次数: 0
snRNA-seq of adipose tissues reveals the potential cellular and molecular mechanisms of cold and disease resistance in Mongolian cattle. 脂肪组织的 snRNA 序列分析揭示了蒙古牛抗寒和抗病的潜在细胞和分子机制。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-25 DOI: 10.1186/s12864-024-10913-y
Zhiduan Chi, Qiong Jia, Haoyu Yang, Hongrui Ren, Congli Jin, Jinxin He, Nile Wuri, Ze Sui, Junzhen Zhang, Bayier Mengke, Lixian Zhu, Ge Qiqi, Sarengaowa Aierqing, Ji Wuli, Dong Ai, Ruiwen Fan, Muren Herrid

Background: Mongolian cattle are local breeds in northern China with excellent adaptability to harsh environmental conditions. Adipose tissues play essential roles in tolerance to cold and disease, but the associated cellular and molecular mechanisms are unclear.

Methods: Single-nucleus RNA sequencing (snRNA-seq) was performed on the adipose tissues from the subcutaneous (SAT), greater omentum (OAT) and perirenal (PAT) of 3 healthy cattle. The adipogenic trajectory was analyzed, and the functional roles of gene of interest were verified in vitro.

Results: There were different cell subpopulations in adipose tissues. The lipid-deposition adipocytes identified by the PTGER3 marker exhibited outstanding characteristics in SAT. In PAT and OAT, aldosterone was expressed to provide clues for the differential brown adipocytes. Among the DEGs by comparing OAT with SAT and PAT with OAT, C3 was significantly expressed in most of the cell populations in SAT. G0S2, LIPE, LPIN1, PTGER3 and RGCC took part in the adipogenic trajectory from preadipocyte commitment to mature adipocytes. S100A4 expression affected Ca2+ signaling and the expression of UCP1 ~ 3, FABP4 and PTGER3.

Conclusion: The cell heterogeneity and genes expressed in adipose tissues of Mongolian cattle not only determine the endocrine and energy storage, but contribute to adapt to cold and disease resistance.

背景:蒙古牛是中国北方的地方品种,对恶劣的环境条件具有极强的适应性。脂肪组织在耐寒和抗病方面发挥着重要作用,但相关的细胞和分子机制尚不清楚:方法:对 3 头健康牛的皮下(SAT)、大网膜(OAT)和肾周(PAT)脂肪组织进行了单核 RNA 测序(snRNA-seq)。分析了脂肪形成的轨迹,并在体外验证了相关基因的功能作用:结果:脂肪组织中有不同的细胞亚群。结果:脂肪组织中存在不同的细胞亚群。在 SAT 中,通过 PTGER3 标记鉴定的脂质沉积脂肪细胞表现出突出的特征。在 PAT 和 OAT 中,醛固酮的表达为棕色脂肪细胞的差异提供了线索。通过比较 OAT 与 SAT 和 PAT 与 OAT 的 DEGs,发现 C3 在 SAT 的大多数细胞群中都有显著表达。G0S2、LIPE、LPIN1、PTGER3和RGCC参与了前脂肪细胞到成熟脂肪细胞的成脂过程。S100A4 的表达影响了 Ca2+ 信号转导以及 UCP1 ~ 3、FABP4 和 PTGER3 的表达:结论:蒙古牛脂肪组织的细胞异质性和基因表达不仅决定了其内分泌和能量储存,而且有助于适应寒冷和抗病。
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引用次数: 0
Identification of the optimal reference genes for atrial fibrillation model established by iPSC-derived atrial myocytes. 为由 iPSC 衍生的心房肌细胞建立的心房颤动模型鉴定最佳参考基因。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-25 DOI: 10.1186/s12864-024-10922-x
Lei Li, Zijuan Zhao, Zihao Liu, Yuquan Tang, Tan Yang, Nailin Gong, Bing Liao, Yang Long, Yongmei Nie, Fengxu Yu

Background: Atrial fibrillation (AF) stands as a prevalent and detrimental arrhythmic disorder, characterized by intricate pathophysiological mechanisms. The availability of reliable and reproducible AF models is pivotal in unraveling the underlying mechanisms of this complex condition. Unfortunately, the researchers are still confronted with the absence of consistent in vitro AF models, hindering progress in this crucial area of research.

Methods: Human induced pluripotent stem cells derived atrial myocytes (hiPSC-AMs) were generated based on the GiWi methods and were verified by whole-cell patch clamp, immunofluorescent staining, and flow cytometry. Then hiPSC-AMs were employed to establish the AF model by HS. Whole-cell patch clamp technique and calcium imaging were used to identify the AF model. The stability of 29 reference genes was evaluated using delta-Ct, GeNorm, NormFinder, and BestKeeper algorithms; RESULTS: HiPSC-AMs displayed atrial myocyte action potentials and expressed the atrial-specific protein MLC-2 A and NR2F2, about 70% of the cardiomyocytes were MLC-2 A positive. After HS, hiPSC-AMs showed a significant increase in beating frequency, a shortened action potential duration, and increased calcium transient frequency. Of the 29 candidate genes, the top five most stably ranked genes were ABL1, RPL37A, POP4, RPL30, and EIF2B1. After normalization using ABL1, KCNJ2 was significantly upregulated in the AF model; Conclusions: In the hiPSC-AMs AF model established by HS, ABL1 provides greater normalization efficiency than commonly used GAPDH.

背景:心房颤动(房颤)是一种普遍存在的有害心律失常疾病,其病理生理机制错综复杂。可靠且可重复的心房颤动模型对于揭示这一复杂疾病的内在机制至关重要。方法:根据 GiWi 方法生成人诱导多能干细胞衍生心房肌细胞(hiPSC-AMs),并通过全细胞膜片钳、免疫荧光染色和流式细胞术进行验证。利用全细胞膜片钳技术和钙成像技术鉴定房颤模型。结果:HiPSC-AMs显示心房肌细胞动作电位并表达心房特异性蛋白MLC-2 A和NR2F2,约70%的心肌细胞为MLC-2 A阳性。HS 后,hiPSC-AMs 的跳动频率显著增加,动作电位持续时间缩短,钙离子瞬态频率增加。在 29 个候选基因中,排名最稳定的前五个基因是 ABL1、RPL37A、POP4、RPL30 和 EIF2B1。在使用 ABL1 进行归一化后,KCNJ2 在房颤模型中显著上调;结论:在 hiPSC-AMs 中,KCNJ2 在房颤模型中显著上调:在 HS 建立的 hiPSC-AMs AF 模型中,ABL1 比常用的 GAPDH 具有更高的归一化效率。
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引用次数: 0
Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak. 尼泊尔登革热病毒监测首次获得 2022 年疫情分离物的现场全基因组序列。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s12864-024-10879-x
Rajindra Napit, Annie Elong Ngono, Kathie A Mihindukulasuriya, Aunji Pradhan, Binod Khadka, Smita Shrestha, Lindsay Droit, Anne Paredes, Lata Karki, Rabindra Khatiwada, Mamata Tamang, Bimal Sharma Chalise, Manisha Rawal, Bimalesh Kumar Jha, David Wang, Scott A Handley, Sujan Shresta, Krishna Das Manandhar

Background: The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies.

Methods and results: During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018.

Conclusion: These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.

背景:登革热病毒的 4 种血清型(DENV1-4)可分别导致潜在的致命登革热疾病,并且正在从热带和亚热带地区向温带地区蔓延。尼泊尔是这一全球现象的一个缩影,已经达到了这些严峻的基准。为了更好地了解登革热病毒的传播动态和向新地区的传播,我们选择在尼泊尔研究登革热,并以此建立管理未来更大规模研究所需的现场基础设施:在2022年登革热流行季节,我们在加德满都一家医院招募了384名出现登革热样症状的患者;79%的研究参与者有登革热病毒感染活动或近期感染(NS1抗原和IgM)。为了确定循环血清型,我们通过 RT-PCR 对 50 名 NS1+ 参与者的血清进行了筛查,确定了 DENV1、2 和 3,其中 DENV1 和 3 为隐性感染。我们还利用新的现场能力,首次在尼泊尔对 DENV 进行了全基因组测序。测序分析表明,DENV1和3基因组与2019年印度报告的序列聚类,DENV2基因组与2018年中国报告的序列聚类:这些发现凸显了 DENV 从邻国向地域扩张的趋势,确定了中国和印度可能是尼泊尔 2022 年 DENV 病例的来源国,并证明了建设现场能力以更快速地对流行的 DENV 进行基因组监测的可行性。这些正在进行的工作有望为 DENV 药物和疫苗的开发和部署提供实时信息,从而保护尼泊尔及其他地区的人口。
{"title":"Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak.","authors":"Rajindra Napit, Annie Elong Ngono, Kathie A Mihindukulasuriya, Aunji Pradhan, Binod Khadka, Smita Shrestha, Lindsay Droit, Anne Paredes, Lata Karki, Rabindra Khatiwada, Mamata Tamang, Bimal Sharma Chalise, Manisha Rawal, Bimalesh Kumar Jha, David Wang, Scott A Handley, Sujan Shresta, Krishna Das Manandhar","doi":"10.1186/s12864-024-10879-x","DOIUrl":"10.1186/s12864-024-10879-x","url":null,"abstract":"<p><strong>Background: </strong>The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies.</p><p><strong>Methods and results: </strong>During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1<sup>+</sup> participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018.</p><p><strong>Conclusion: </strong>These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494711","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
Exploring the longitudinal expression dynamics of midguts in adult female Amblyomma americanum ticks. 探索成年雌性美洲大蜱中肠的纵向表达动态。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s12864-024-10905-y
Stephen Lu, Lucas C de Sousa-Paula, Jose M C Ribeiro, Lucas Tirloni

Background: Female ticks remain attached to their host for multiple days to complete a blood meal. This prolonged feeding period is accompanied by a significant increase in the tick's size and body weight, paralleled by noteworthy changes to the tick midgut. While the midgut is recognized for its established role in blood storage and processing, its importance extends to playing a crucial role in the acquisition, survival, and proliferation of pathogens. Despite this, our overall understanding of tick midgut biology is limited.

Results: Our transcriptome analysis identified 15,599 putative DNA coding sequences (CDS), which were classified into 26 functional groups. Dimensional and differential expression analyses revealed four primary transcriptional profiles corresponding to unfed, slow-feeding, transitory (from slow- to rapid-feeding), and rapid-feeding stages. Additionally, comparing the current dataset with previously deposited transcriptome from other tick species allowed the identification of commonly expressed transcripts across different feeding stages.

Conclusion: Our findings provide a detailed temporal resolution of numerous metabolic pathways in the midgut of A. americanum adult females throughout the feeding process, highlighting the dynamic transcriptional regulation of the tick's midgut as feeding progresses. Furthermore, we identified conserved transcripts across three different tick species that exhibit similar expression patterns. This knowledge not only enhances our understanding of the physiological processes within the tick midgut but also opens up potential avenues for developing control methods that target multiple tick species.

背景:雌性蜱会在宿主身上停留多日,以完成一次血食。伴随着这一漫长的进食期,蜱的体型和体重会显著增加,同时蜱的中肠也会发生显著变化。虽然中肠在血液储存和处理方面的作用已得到公认,但它在病原体的获取、存活和增殖方面也发挥着至关重要的作用。尽管如此,我们对蜱中肠生物学的总体了解仍然有限:我们的转录组分析确定了 15,599 个假定 DNA 编码序列 (CDS),并将其分为 26 个功能组。维度和差异表达分析揭示了四种主要的转录谱,分别对应未进食、慢速进食、过渡阶段(从慢速进食到快速进食)和快速进食阶段。此外,将目前的数据集与以前保存的其他蜱物种的转录组进行比较,可以确定不同摄食阶段的常见表达转录本:我们的研究结果提供了雌性成年蜱中肠在整个摄食过程中许多代谢途径的详细时间分辨率,突出了蜱中肠在摄食过程中的动态转录调控。此外,我们还发现了三个不同蜱物种中表现出相似表达模式的保守转录本。这些知识不仅加深了我们对蜱中肠生理过程的了解,还为开发针对多种蜱的控制方法开辟了潜在的途径。
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引用次数: 0
Genome-wide analysis of the SWEET gene family and its response to powdery mildew and leaf spot infection in the common oat (Avena sativa L.). SWEET 基因家族及其对普通燕麦(Avena sativa L.)白粉病和叶斑病感染的响应的全基因组分析。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s12864-024-10933-8
Yuanbo Pan, Kuiju Niu, Peiqin Miao, Guiqin Zhao, Yuehua Zhang, Zeliang Ju, Jikuan Chai, Juanjuan Yang, Xiaoning Cui, Ran Zhang

The nutritional quality and yield of oats (Avena sativa) are often compromised by plant diseases such as red leaf, powdery mildew, and leaf spot. Sugars Will Eventually be Exported Transporters (SWEETs) are newly identified sugar transporters involved in regulating plant growth and stress responses. However, the roles of SWEET genes in biotic stress responses remain uncharacterized in oats. In this study, 13 AsSWEET genes were identified across nine chromosomes of the oat genome, all of which were predicted to contain seven transmembrane regions. Phylogenetic analysis revealed four clades of AsSWEET proteins, with high homology to SWEET proteins in the Poaceae family. Collinearity analysis demonstrated strong relationships between oat and Zea mays SWEETs. Using subcellular localization prediction tools, AsSWEET proteins were predicted to localize to the plasma membrane. Promoter analysis revealed cis-acting elements associated with light response, growth, and stress regulation. Six AsSWEET proteins were predicted to interact in a network centered on AsSWEET1a and AsSWEET11. Gene expression analysis of two oat varieties, 'ForagePlus' and 'Molasses', indicated significant expression differences in several AsSWEET genes following infection with powdery mildew or leaf spot, including AsSWEET1a, AsSWEET1b, AsSWEET2b, AsSWEET3a, AsSWEET11, and AsSWEET16. These SWEET genes are potential candidates for disease resistance in oats. This study provides a foundation for understanding the regulatory mechanisms of AsSWEET genes, particularly in response to powdery mildew and leaf spot, and offers insights for enhancing oat molecular breeding.

燕麦(Avena sativa)的营养质量和产量经常受到红叶病、白粉病和叶斑病等植物病害的影响。糖类终将出口转运体(SWEETs)是新发现的糖类转运体,参与调节植物生长和胁迫反应。然而,燕麦中的 SWEET 基因在生物胁迫响应中的作用仍未得到表征。本研究在燕麦基因组的九条染色体上鉴定了 13 个 AsSWEET 基因,预测所有这些基因都包含七个跨膜区。系统进化分析表明,AsSWEET 蛋白有四个支系,与 Poaceae 家族中的 SWEET 蛋白同源性很高。共线性分析表明燕麦和玉米的 SWEET 蛋白之间存在密切关系。利用亚细胞定位预测工具,AsSWEET 蛋白被预测定位在质膜上。启动子分析揭示了与光反应、生长和胁迫调控相关的顺式作用元件。预测有六个 AsSWEET 蛋白在以 AsSWEET1a 和 AsSWEET11 为中心的网络中相互作用。对两个燕麦品种 "ForagePlus "和 "Molasses "的基因表达分析表明,在感染白粉病或叶斑病后,几个 AsSWEET 基因的表达存在显著差异,包括 AsSWEET1a、AsSWEET1b、AsSWEET2b、AsSWEET3a、AsSWEET11 和 AsSWEET16。这些 SWEET 基因是燕麦抗病性的潜在候选基因。这项研究为了解 AsSWEET 基因的调控机制(尤其是对白粉病和叶斑病的响应)奠定了基础,并为提高燕麦分子育种水平提供了启示。
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引用次数: 0
Identification and validation of qRT-PCR reference genes for analyzing grape infection with gray mold. 鉴定和验证用于分析葡萄灰霉病感染的 qRT-PCR 参考基因。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s12864-024-10889-9
Lina Tan, Lijuan Lu, Wen Sun, Xinyuan Zhang, Yanglin Liu, Yan Xiang, Hanwei Yan

Background: Grapes are highly valued for their nutritional and economic benefits, and have been widely studied for their biological attributes such as fruit development, quality formation, and stress resistance. One significant threat to grape quality is gray mold, caused by Botrytis cinerea, which can infect the flowers, fruits, leaves, and stems. The quantitative real-time PCR (qRT-PCR), known for its high sensitivity and quantitative accuracy, is an essential tool for analyzing gene expression related to the pathogenesis of gray mold, thereby providing deeper insights into the disease.

Result: In this study, we aim to identify stable internal reference genes crucial for accurate gene expression analysis via qRT-PCR. Utilizing transcriptome data from grapes under various disease stresses, we identified twelve candidate reference genes with consistently high expression levels. The stability of these genes was assessed through delta-CT, geNorm, NormFinder, BestKeeper, and RefFinder analyses after establishing the cycling thresholds (Ct) in different grape varieties treated with Botrytis cinerea.

Conclusions: Our findings reveal that VIT-17s0000g02750 and VIT-06s0004g04280 exhibit stable expression and are suitable as new reference genes. This foundational work supports further research into the molecular mechanisms of grape biological processes.

背景:葡萄因其营养和经济效益而备受重视,人们对其生物学特性(如果实发育、品质形成和抗逆性)进行了广泛研究。灰霉病是葡萄质量的一个重要威胁,由灰葡萄孢菌(Botrytis cinerea)引起,可感染花、果实、叶片和茎。定量实时 PCR(qRT-PCR)以其高灵敏度和定量准确性而著称,是分析与灰霉病发病机制相关的基因表达的重要工具,从而为深入了解该疾病提供了依据:在这项研究中,我们旨在确定对通过 qRT-PCR 精确分析基因表达至关重要的稳定内部参考基因。利用各种病害胁迫下葡萄的转录组数据,我们确定了 12 个具有持续高表达水平的候选参考基因。在确定了不同葡萄品种在灰霉病下的循环阈值(Ct)后,我们通过 delta-CT、geNorm、NormFinder、BestKeeper 和 RefFinder 分析评估了这些基因的稳定性:我们的研究结果表明,VIT-17s0000g02750 和 VIT-06s0004g04280 表现出稳定的表达,适合作为新的参考基因。这项基础性工作为进一步研究葡萄生物过程的分子机制提供了支持。
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引用次数: 0
Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae. 蓼科植物细胞器基因组大小变化和细胞内 DNA 转移的因素。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1186/s12864-024-10914-x
Yi Xiong, Xiong Lei, Yanli Xiong, Yingjie Liu, Zhixiao Dong, Junming Zhao, Qingqing Yu, Xiao Ma

The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.

利用完整的细胞器基因组,包括叶绿体和线粒体基因组,是研究生物进化和基因转移的一种强有力的分子方法。然而,蓼科是一个重要的科,有许多食用、药用和观赏物种,目前仅对三个物种的线粒体基因组进行了测序和分析。在本研究中,我们展示了两种重要的藏药用植物--大叶女贞(Bistorta viviparum)和大叶女贞(B. macrophyllum)的线粒体和叶绿体基因组。所有细胞器基因组都组装成一个环状结构,包含一组共同的 32 个蛋白质编码基因(PCGs)。在叶绿体基因组中,一些基因(如 rps2 和 ndhF)具有较高的核苷酸多态性(Pi),而在线粒体基因组中,cox1、mttB 和 rps12 则显示出明显的 Pi 值。此外,我们的分析表明,蓼科植物的大多数叶绿体基因和线粒体 PCGs 都处于净化选择过程中。然而,在某些蓼科植物中,包括叶绿体基因 psaJ 和线粒体基因 ccmFc、atp8 和 nad4 在内的少数基因表现出了正选择,表现为 Ka/Ks 比值大于 1。结构变异分析揭示了五个蓼科植物线粒体基因组之间的大量差异,其中在 Reynoutria japonica 和 Fallopia aubertii 之间观察到的大规模反转尤为显著。此外,对叶绿体基因组和线粒体基因组同源序列的分析表明,在所有五个蓼科植物中,rps7 已从叶绿体转移到线粒体基因组。最后,构建了B. viviparum和B. macrophyllum的生态位模型,表明年平均温度和海拔高度是影响这两个物种分布的主要气候因素。虽然目前大叶榕树的分布范围明显比小叶榕树广,但预测表明这两个物种的最佳生长范围在未来都将扩大,大叶榕树有可能超过小叶榕树。这项研究不仅为蓼科植物的质粒基因组数据库做出了贡献,还为这些植物的适应性进化提供了理论依据。
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引用次数: 0
A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species. 冰山一角:基因组调查显示 Garuga Roxb.
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1186/s12864-024-10917-8
Dongbo Zhu, Rui Rao, Yu Du, Chunmin Mao, Rong Chen, Liangliang Yue

BACKGROUND : Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation of the genus. RESULTS: This study utilized genome survey of G. forrestii generated approximately 54.56 GB of sequence data, with approximately 112 × coverage. K-mer analysis indicated a genome size of approximately 0.48 GB, smaller than 0.52GB estimated by flow cytometry. The heterozygosity is of about 0.54%, and a repeat rate of around 51.54%. All the shotgun data were assembled into 339,729 scaffolds, with an N50 of 17,344 bp. The average content of guanine and cytosine was approximately 35.16%. A total of 330,999 SSRs were detected, with mononucleotide repeats being the most abundant at 70.16%, followed by dinucleotide repeats at 20.40%. We conducted a preliminary ploidy assessment using Smudgeplot and observed a clear bimodal distribution in G. forrestii at 1/2 relative coverage depth and total coverage depth (2n), suggesting a potential diploid genome structure. A pseudo chromosome of G. forrestii and a gemone of Boswellia sacra were used as reference genome to perform a primer population resequencing analysis within three Garuga species. Principal component analysis (PCA) indicated three distinct groups, but genome wide phylogenetics represented conflicting both between the dataset of different reference genomes and between maternal and nuclear genome. CONCLUSION: In summary, the genome of G. forrestii is small, and the phylogenetic relationships within the Garuga genus are complex. The genetic data presented in this study holds significant value for comprehensive whole-genome analyses, the evaluation of population genetic diversity, investigations into adaptive evolution, the advancement of artificial breeding efforts, and the support of species conservation and restoration initiatives. Ultimately, this research contributes to reinforcing the conservation and management of natural ecosystems, promoting biodiversity conservation, and advancing sustainable development.

背景:石蒜属(Garuga Roxb.)是中国西南部和东南亚其他热带地区的特有种,由于热带森林的消失和土地利用的变化,该属面临灭绝的危险。对石蒜属植物进行基因组调查有助于加深对该属植物的了解和保护。结果:该研究利用 G. forrestii 的基因组调查生成了约 54.56 GB 的序列数据,覆盖率约为 112 ×。K-mer 分析表明基因组大小约为 0.48GB,小于流式细胞仪估计的 0.52GB。杂合度约为 0.54%,重复率约为 51.54%。所有霰弹枪数据被组装成 339 729 个支架,N50 为 17 344 bp。鸟嘌呤和胞嘧啶的平均含量约为 35.16%。共检测到 330,999 个 SSR,其中单核苷酸重复序列最多,占 70.16%,其次是双核苷酸重复序列,占 20.40%。我们利用 Smudgeplot 进行了初步倍性评估,在相对覆盖深度和总覆盖深度(2n)均为 1/2 的情况下,观察到 G. forrestii 存在明显的双峰分布,表明其基因组结构可能为二倍体。以G. forrestii的一条假染色体和Boswellia sacra的一条gemone作为参考基因组,对三个Garuga物种进行了引物群体重测序分析。主成分分析(PCA)显示有三个不同的群体,但不同参考基因组数据集之间以及母基因组与核基因组之间的全基因组系统发育存在冲突。结论:总之,G. forrestii 的基因组很小,Garuga 属内部的系统发育关系很复杂。本研究提供的遗传数据对于全基因组综合分析、种群遗传多样性评估、适应性进化研究、人工育种工作的推进以及物种保护和恢复计划的支持具有重要价值。最终,这项研究有助于加强自然生态系统的保护和管理,促进生物多样性保护,推动可持续发展。
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引用次数: 0
Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean. 绿豆幼苗生长和发育过程中 CAMTA 基因的全基因组鉴定及其对光和钙信号的表达依赖性。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1186/s12864-024-10893-z
Adhityo Wicaksono, Teerapong Buaboocha

Background: Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant.

Results: Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression.

Conclusions: The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.

背景:钙调蛋白结合转录激活因子(CAMTA)由一组转录因子组成,在 Ca2+ 信号通路中发挥重要作用,通过与其他转录因子的相互作用以及与特定基因启动子区域的结合,介导各种分子反应。绿豆(Vigna radiata)是亚洲最常消费的商品之一。迄今为止,CAMTA 蛋白尚未在这种重要的作物植物中得到表征:结果:确定了 8 个 VrCAMTA 同源异源基因,发现它们分布在 11 条染色体中的 5 条上。这些蛋白具有带双向 NLS 信号的 CG-1 DNA 结合结构域、ankyrin 结构域、CaM 结合 IQ motifs 和 CaM 结合结构域(CaMBD)。VrCAMTA 基因上游 2 kb 区域含有脱落酸反应元件(ABRE)和乙烯反应元件(ERE)的序列基序,以及 bZIP 和 bHLH 结构域转录因子的结合位点。对公共储存库中的 RNA-seq 数据进行分析后发现,VrCAMTA 基因的表达无处不在,其中 VrCAMTA1 在幼苗叶片中的表达水平最高,而 VrCAMTA8 的表达水平最低,这与对第一片真叶进行的 RT-qPCR 分析结果一致。出叶后第 4 天,所有 VrCAMTA 基因都上调,其中 VrCAMTA1 上调程度最高。在第 4 天的黑暗条件下,大多数 VrCAMTA 基因都没有上调,只有 VrCAMTA7 基因上调程度较低,而 VrCAMTA8 基因的表达在光照和黑暗条件下没有差异。在叶片萌发后的不同时间,用钙离子体处理可提高光照和/或黑暗条件下的 VrCAMTA 表达,这表明钙信号转导参与了光照诱导的 VrCAMTA 基因表达上调:结论:几乎所有 VrCAMTA 基因的表达都依赖于光信号和钙信号,这表明它们在绿豆生长发育的早期阶段可能起着不同的作用,但很可能是互补的。
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