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Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns. Ophioglossum vulgatum 的全长转录组分析:实验确定的叶绿体基因簇对表达和进化模式的影响。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-21 DOI: 10.1007/s11103-024-01423-2
Jing Hao, Yingyi Liang, Jingyao Ping, Ting Wang, Yingjuan Su
{"title":"Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns.","authors":"Jing Hao, Yingyi Liang, Jingyao Ping, Ting Wang, Yingjuan Su","doi":"10.1007/s11103-024-01423-2","DOIUrl":"10.1007/s11103-024-01423-2","url":null,"abstract":"<p><p>Genes with similar or related functions in chloroplasts are often arranged in close proximity, forming clusters on chromosomes. These clusters are transcribed coordinated to facilitate the expression of genes with specific function. Our previous study revealed a significant negative correlation between the chloroplast gene expression level of the rare medicinal fern Ophioglossum vulgatum and its evolutionary rates as well as selection pressure. Therefore, in this study, we employed a combination of SMRT and Illumina sequencing technology to analyze the full-length transcriptome sequencing of O. vulgatum for the first time. In particular, we experimentally identified gene clusters based on transcriptome data and investigated the effects of chloroplast gene clustering on expression and evolutionary patterns. The results revealed that the total sequenced data volume of the full-length transcriptome of O. vulgatum amounted to 71,950,652,163 bp, and 110 chloroplast genes received transcript coverage. Nine different types of gene clusters were experimentally identified in their transcripts. The chloroplast cluster genes may cause a decrease in non-synonymous substitution rate and selection pressure, as well as a reduction in transversion rate, transition rate, and their ratio. While expression levels of chloroplast cluster genes in leaf, sporangium, and stem would be relatively elevated. The Mann-Whitney U test indicated statistically significant in the selection pressure, sporangia and leaves groups (P < 0.05). We have contributed novel full-length transcriptome data resources for ferns, presenting new evidence on the effects of chloroplast gene clustering on expression land evolutionary patterns, and offering new theoretical support for transgenic research through gene clustering.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Overexpression of transcription factor FaMYB63 enhances salt tolerance by directly binding to the SOS1 promoter in Arabidopsis thaliana. 拟南芥转录因子 FaMYB63 通过直接与 SOS1 启动子结合而提高耐盐性。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-21 DOI: 10.1007/s11103-024-01431-2
Shuaishuai Wang, Rongyi Jiang, Jian Feng, Haodong Zou, Xiaohuan Han, Xingbin Xie, Guanghui Zheng, Congbing Fang, Jing Zhao
{"title":"Overexpression of transcription factor FaMYB63 enhances salt tolerance by directly binding to the SOS1 promoter in Arabidopsis thaliana.","authors":"Shuaishuai Wang, Rongyi Jiang, Jian Feng, Haodong Zou, Xiaohuan Han, Xingbin Xie, Guanghui Zheng, Congbing Fang, Jing Zhao","doi":"10.1007/s11103-024-01431-2","DOIUrl":"10.1007/s11103-024-01431-2","url":null,"abstract":"<p><p>Salinity is a pivotal abiotic stress factor with far-reaching consequences on global crop growth, yield, and quality and which includes strawberries. R2R3-MYB transcription factors encompass a range of roles in plant development and responses to abiotic stress. In this study, we identified that strawberry transcription factor FaMYB63 exhibited a significant upregulation in its expression under salt stress conditions. An analysis using yeast assay demonstrated that FaMYB63 exhibited the ability to activate transcriptional activity. Compared with those in the wild-type (WT) plants, the seed germination rate, root length, contents of chlorophyll and proline, and antioxidant activities (SOD, CAT, and POD) were significantly higher in FaMYB63-overexpressing Arabidopsis plants exposed to salt stress. Conversely, the levels of malondialdehyde (MDA) were considerably lower. Additionally, the FaMYB63-overexpressed Arabidopsis plants displayed a substantially improved capacity to scavenge active oxygen. Furthermore, the activation of stress-related genes by FaMYB63 bolstered the tolerance of transgenic Arabidopsis to salt stress. It was also established that FaMYB63 binds directly to the promoter of the salt overly sensitive gene SOS1, thereby activating its expression. These findings identified FaMYB63 as a possible and important regulator of salt stress tolerance in strawberries.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140185192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrative omics studies revealed synergistic link between sucrose metabolic isogenes and carbohydrates in poplar roots infected by Fusarium wilt 综合全局研究揭示了受镰刀菌枯萎病感染的杨树根系中蔗糖代谢同源物与碳水化合物之间的协同联系
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-19 DOI: 10.1007/s11103-024-01426-z
Xianglei Xu, Haikun Wei, Kejun Yao, Hao Wu, Tingting Huang, Mei Han, Tao Su, Fuliang Cao
{"title":"Integrative omics studies revealed synergistic link between sucrose metabolic isogenes and carbohydrates in poplar roots infected by Fusarium wilt","authors":"Xianglei Xu, Haikun Wei, Kejun Yao, Hao Wu, Tingting Huang, Mei Han, Tao Su, Fuliang Cao","doi":"10.1007/s11103-024-01426-z","DOIUrl":"https://doi.org/10.1007/s11103-024-01426-z","url":null,"abstract":"<p>Advances in carbohydrate metabolism prompted its essential role in defense priming and sweet immunity during plant-pathogen interactions. Nevertheless, upstream responding enzymes in the sucrose metabolic pathway and associated carbohydrate derivatives underlying fungal pathogen challenges remain to be deciphered in <i>Populus</i>, a model tree species. In silico deduction of genomic features, including phylogenies, exon/intron distributions, <i>cis</i>-regulatory elements, and chromosomal localization, identified 59 enzyme genes (11 families) in the <i>Populus</i> genome. Spatiotemporal expression of the transcriptome and the quantitative real-time PCR revealed a minuscule number of isogenes that were predominantly expressed in roots. Upon the pathogenic <i>Fusarium solani</i> (Fs) exposure, dynamic changes in the transcriptomics atlas and experimental evaluation verified Susy (<i>PtSusy2</i> and <i>3</i>), CWI (<i>PtCWI3</i>), VI (<i>PtVI2</i>), HK (<i>PtHK6</i>), FK (<i>PtFK6</i>), and UGPase (<i>PtUGP2</i>) families, displaying promotions in their expressions at 48 and 72 h of post-inoculation (hpi). Using the gas chromatography-mass spectrometry (GC–MS)-based non-targeted metabolomics combined with a high-performance ion chromatography system (HPICS), approximately 307 metabolites (13 categories) were annotated that led to the quantification of 46 carbohydrates, showing marked changes between three compared groups. By contrast, some sugars (e.g., sorbitol, L-arabitol, trehalose, and galacturonic acid) exhibited a higher accumulation at 72 hpi than 0 hpi, while levels of α-lactose and glucose decreased, facilitating them as potential signaling molecules. The systematic overview of multi-omics approaches to dissect the effects of Fs infection provides theoretical cues for understanding defense immunity depending on fine-tuned Suc metabolic gene clusters and synergistically linked carbohydrate pools in trees.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140167757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Coordination between two cis-elements of WRKY33, bound by the same transcription factor, confers humid adaption in Arabidopsis thaliana 由同一转录因子结合的 WRKY33 的两个顺式元件之间的协调赋予拟南芥湿度适应能力
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-19 DOI: 10.1007/s11103-024-01428-x
Bao Liu, Yudan Zheng, Shangling Lou, Meng Liu, Weiwei Wang, Xiaoqin Feng, Han Zhang, Yan Song, Huanhuan Liu
{"title":"Coordination between two cis-elements of WRKY33, bound by the same transcription factor, confers humid adaption in Arabidopsis thaliana","authors":"Bao Liu, Yudan Zheng, Shangling Lou, Meng Liu, Weiwei Wang, Xiaoqin Feng, Han Zhang, Yan Song, Huanhuan Liu","doi":"10.1007/s11103-024-01428-x","DOIUrl":"https://doi.org/10.1007/s11103-024-01428-x","url":null,"abstract":"<p>To cope with flooding-induced hypoxia, plants have evolved different strategies. Molecular strategies, such as the N-degron pathway and transcriptional regulation, are known to be crucial for <i>Arabidopsis thaliana</i>’s hypoxia response. Our study uncovered a novel molecular strategy that involves a single transcription factor interacting with two identical cis-elements, one located in the promoter region and the other within the intron. This unique double-element adjustment mechanism has seldom been reported in previous studies. In humid areas, WRKY70 plays a crucial role in <i>A. thaliana</i>’s adaptation to submergence-induced hypoxia by binding to identical cis-elements in both the promoter and intron regions of <i>WRKY33</i>. This dual binding enhances <i>WRKY33</i> expression and the activation of hypoxia-related genes. Conversely, in arid regions lacking the promoter cis-element, WRKY70 only binds to the intron cis-element, resulting in limited <i>WRKY33</i> expression during submergence stress. The presence of a critical promoter cis-element in humid accessions, but not in dry accessions, indicates a coordinated regulation enabling <i>A. thaliana</i> to adapt and thrive in humid habitats.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140168521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The dicot homolog of maize PPR103 carries a C-terminal DYW domain and may have a role in C-to-U editing of some chloroplast RNA transcripts. 玉米 PPR103 的双子叶植物同源物带有一个 C 端 DYW 结构域,可能在某些叶绿体 RNA 转录本的 C 到 U 编辑过程中发挥作用。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-15 DOI: 10.1007/s11103-024-01424-1
Tyra N McCray, Mohammad F Azim, Tessa M Burch-Smith
{"title":"The dicot homolog of maize PPR103 carries a C-terminal DYW domain and may have a role in C-to-U editing of some chloroplast RNA transcripts.","authors":"Tyra N McCray, Mohammad F Azim, Tessa M Burch-Smith","doi":"10.1007/s11103-024-01424-1","DOIUrl":"10.1007/s11103-024-01424-1","url":null,"abstract":"<p><p>In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria- and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain. IPI1/emb175/PPR103 is a nuclear gene encoding a PLS-type PPR protein essential for survival in Arabidopsis thaliana and maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis and Nicotiana IPI1 orthologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. In this study we examined the function of IPI1 in chloroplast RNA processing in N. benthamiana to gain insight into the importance of the DYW domain to the function of the EMB175/PPR103/ IPI1 proteins. Structural predictions suggest that evolutionary loss of residues identified as critical for catalyzing C-to-U editing in other members of this class of proteins, were likely to lead to reduced or absent editing activity in the Nicotiana and Arabidopsis IPI1 orthologs. Virus-induced gene silencing of NbIPI1 led to defects in chloroplast ribosomal RNA processing and changes to stability of rpl16 transcripts, revealing conserved function with its maize ortholog. NbIPI1-silenced plants also had defective C-to-U RNA editing in several chloroplast transcripts, a contrast from the finding that maize PPR103 had no role in editing. The results indicate that in addition to its role in transcript stability, NbIPI1 may contribute to C-to-U editing in N. benthamiana chloroplasts.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10940495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132205","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
Arginine inhibits the arginine biosynthesis rate-limiting enzyme and leads to the accumulation of intracellular aspartate in Synechocystis sp. PCC 6803 精氨酸抑制精氨酸生物合成限速酶,导致 Synechocystis sp.
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-13 DOI: 10.1007/s11103-024-01416-1
Noriaki Katayama, Takashi Osanai
{"title":"Arginine inhibits the arginine biosynthesis rate-limiting enzyme and leads to the accumulation of intracellular aspartate in Synechocystis sp. PCC 6803","authors":"Noriaki Katayama, Takashi Osanai","doi":"10.1007/s11103-024-01416-1","DOIUrl":"https://doi.org/10.1007/s11103-024-01416-1","url":null,"abstract":"<p>Cyanobacteria are oxygen-evolving photosynthetic prokaryotes that affect the global carbon and nitrogen turnover. <i>Synechocystis</i> sp. PCC 6803 (<i>Synechocystis</i> 6803) is a model cyanobacterium that has been widely studied and can utilize and uptake various nitrogen sources and amino acids from the outer environment and media. l-arginine is a nitrogen-rich amino acid used as a nitrogen reservoir in <i>Synechocystis</i> 6803, and its biosynthesis is strictly regulated by feedback inhibition. Argininosuccinate synthetase (ArgG; EC 6.3.4.5) is the rate-limiting enzyme in arginine biosynthesis and catalyzes the condensation of citrulline and aspartate using ATP to produce argininosuccinate, which is converted to l-arginine and fumarate through argininosuccinate lyase (ArgH). We performed a biochemical analysis of <i>Synechocystis</i> 6803 ArgG (<i>Sy</i>ArgG) and obtained a <i>Synechocystis</i> 6803 mutant overexpressing <i>Sy</i>ArgG and ArgH of <i>Synechocystis</i> 6803 (<i>Sy</i>ArgH). The specific activity of <i>Sy</i>ArgG was lower than that of other arginine biosynthesis enzymes and <i>Sy</i>ArgG was inhibited by arginine, especially among amino acids and organic acids. Both arginine biosynthesis enzyme-overexpressing strains grew faster than the wild-type <i>Synechocystis</i> 6803. Based on previous reports and our results, we suggest that <i>Sy</i>ArgG is the rate-limiting enzyme in the arginine biosynthesis pathway in cyanobacteria and that arginine biosynthesis enzymes are similarly regulated by arginine in this cyanobacterium. Our results contribute to elucidating the regulation of arginine biosynthesis during nitrogen metabolism.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140114857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Moving forward to understand the alteration of physiological mechanism by seed priming with different halo-agents under salt stress. 进一步了解盐胁迫下不同卤素试剂对种子引诱生理机制的改变。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-08 DOI: 10.1007/s11103-024-01425-0
Alivia Paul, Subhankar Mondal, Koushik Chakraborty, Asok K Biswas
{"title":"Moving forward to understand the alteration of physiological mechanism by seed priming with different halo-agents under salt stress.","authors":"Alivia Paul, Subhankar Mondal, Koushik Chakraborty, Asok K Biswas","doi":"10.1007/s11103-024-01425-0","DOIUrl":"10.1007/s11103-024-01425-0","url":null,"abstract":"<p><p>Soil salinity hampers the survival and productivity of crops. To minimize salt-associated damages in plant, better salt management practices in agriculture have become a prerequisite. Seed priming with different halo-agents is a technique, which improves the primed plant's endurance to tackle sodium. Salt tolerance is achieved in tolerant plants through fundamental physiological mechanisms- ion-exclusion and tissue tolerance, and salt-tolerant plants may (Na<sup>+</sup> accumulators) or may not (Na<sup>+</sup> excluders) allow sodium movement to leaves. While Na<sup>+</sup> excluders depend on ion exclusion in roots, Na<sup>+</sup> accumulators are proficient Na<sup>+</sup> managers that can compartmentalize Na<sup>+</sup> in leaves and use them beneficially as inexpensive osmoticum. Salt-sensitive plants are Na<sup>+</sup> accumulators, but their inherent tissue tolerance ability and ion-exclusion process are insufficient for tolerance. Seed priming with different halo-agents aids in 'rewiring' of the salt tolerance mechanisms of plants. The resetting of the salt tolerance mechanism is not universal for every halo-agent and might vary with halo-agents. Here, we review the physiological mechanisms that different halo-agents target to confer enhanced salt tolerance in primed plants. Calcium and potassium-specific halo-agents trigger Na<sup>+</sup> exclusion in roots, thus ensuring a low amount of Na<sup>+</sup> in leaves. In contrast, Na<sup>+</sup>-specific priming agents favour processes for Na<sup>+</sup> inclusion in leaves, improve plant tissue tolerance or vacuolar sequestration, and provide the greatest benefit to salt-sensitive and sodium accumulating plants. Overall, this review will help to understand the underlying mechanism behind plant's inherent nature towards salt management and its amelioration with different halo-agents, which helps to optimize crop stress performance.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment. 生物源纳米锌处理下蔷薇嫩枝培养物中蛋白质的功能注释。
IF 3.9 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-08 DOI: 10.1007/s11103-024-01432-1
Shaghufta Perveen, Matthew P Padula, Naila Safdar, Sidra Abbas
{"title":"Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment.","authors":"Shaghufta Perveen, Matthew P Padula, Naila Safdar, Sidra Abbas","doi":"10.1007/s11103-024-01432-1","DOIUrl":"10.1007/s11103-024-01432-1","url":null,"abstract":"<p><p>Nano-interactions are well known for their positive as well as negative impacts on the morphological and physiological systems of plants. Keeping in mind, the conformational changes in plant proteins as one of the key mechanisms for stress adaptation responses, the current project was designed to explore the effect of glutathione-capped and uncapped zinc nano-entities on Catharanthus roseus shoot cultures. Zinc nanotreatment (0.05 μg/mL) significantly induced ester production in C. roseus shoots as detected by Gas Chromatography-Mass spectrometry. These nanotreated shoots were further subjected to peptide-centric nano-LC-MS/MS analysis. Mass spectrometry followed by a Heat map revealed a significant effect of zinc nanoparticles on 59 distinct classes of proteins as compared to control. Proteins involved in regulating stress scavenging, transport, and secondary metabolite biosynthesis were robustly altered under capped zinc nanotreatment. UniProt database identified majority of the localization of the abundantly altered protein in cell membranes and chloroplasts. STRING and Cytoscape analysis assessed inter and intra coordination of triosephosphate isomerase with other identified proteins and highlighted its role in the regulation of protein abundance under applied stress. This study highlights the understanding of complex underlying mechanisms and regulatory networks involved in proteomic alterations and interactions within the plant system to cope with the nano-effect.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140065674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Methylomes as key features for predicting recombination in some plant species. 甲基组是预测某些植物物种重组的关键特征。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-08 DOI: 10.1007/s11103-023-01396-8
Mauricio Peñuela, Jorge Finke, Camilo Rocha
{"title":"Methylomes as key features for predicting recombination in some plant species.","authors":"Mauricio Peñuela, Jorge Finke, Camilo Rocha","doi":"10.1007/s11103-023-01396-8","DOIUrl":"10.1007/s11103-023-01396-8","url":null,"abstract":"<p><p>Knowing how chromosome recombination works is essential for plant breeding. It enables the design of crosses between different varieties to combine desirable traits and create new ones. This is because the meiotic crossovers between homologous chromatids are not purely random, and various strategies have been developed to describe and predict such exchange events. Recent studies have used methylation data to predict chromosomal recombination in rice using machine learning models. This approach proved successful due to the presence of a positive correlation between the CHH context cytosine methylation and recombination rates in rice chromosomes. This paper assesses the question if methylation can be used to predict recombination in four plant species: Arabidopsis, maize, sorghum, and tomato. The results indicate a positive association between CHH context methylation and recombination rates in certain plant species, with varying degrees of strength in their relationships. The CG and CHG methylation contexts show negative correlation with recombination. Methylation data was key effectively in predicting recombination in sorghum and tomato, with a mean determination coefficient of 0.65 ± 0.11 and 0.76 ± 0.05, respectively. In addition, the mean correlation values between predicted and experimental recombination rates were 0.83 ± 0.06 for sorghum and 0.90 ± 0.05 for tomato, confirming the significance of methylomes in both monocotyledonous and dicotyledonous species. The predictions for Arabidopsis and maize were not as accurate, likely due to the comparatively weaker relationships between methylation contexts and recombination, in contrast to sorghum and tomato, where stronger associations were observed. To enhance the accuracy of predictions, further evaluations using data sets closely related to each other might prove beneficial. In general, this methylome-based method holds great potential as a reliable strategy for predicting recombination rates in various plant species, offering valuable insights to breeders in their quest to develop novel and improved varieties.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10924001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060175","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
Characterization of CYP82 genes involved in the biosynthesis of structurally diverse benzylisoquinoline alkaloids in Corydalis yanhusuo. 参与延胡索堇菜中结构多样的苄基异喹啉生物碱生物合成的 CYP82 基因的特征。
IF 5.1 2区 生物学
Plant Molecular Biology Pub Date : 2024-03-07 DOI: 10.1007/s11103-023-01397-7
Xiuyu Liu, Ying Ma, Junling Bu, Conglong Lian, Rui Ma, Qishuang Li, Xiang Jiao, Zhimin Hu, Yun Chen, Suiqing Chen, Juan Guo, Luqi Huang
{"title":"Characterization of CYP82 genes involved in the biosynthesis of structurally diverse benzylisoquinoline alkaloids in Corydalis yanhusuo.","authors":"Xiuyu Liu, Ying Ma, Junling Bu, Conglong Lian, Rui Ma, Qishuang Li, Xiang Jiao, Zhimin Hu, Yun Chen, Suiqing Chen, Juan Guo, Luqi Huang","doi":"10.1007/s11103-023-01397-7","DOIUrl":"10.1007/s11103-023-01397-7","url":null,"abstract":"<p><p>Benzylisoquinoline alkaloids (BIAs) represent a significant class of secondary metabolites with crucial roles in plant physiology and substantial potential for clinical applications. CYP82 genes are involved in the formation and modification of various BIA skeletons, contributing to the structural diversity of compounds. In this study, Corydalis yanhusuo, a traditional Chinese medicine rich in BIAs, was investigated to identify the catalytic function of CYP82s during BIA formation. Specifically, 20 CyCYP82-encoding genes were cloned, and their functions were identified in vitro. Ten of these CyCYP82s were observed to catalyze hydroxylation, leading to the formation of protopine and benzophenanthridine scaffolds. Furthermore, the correlation between BIA accumulation and the expression of CyCYP82s in different tissues of C. yanhusuo was assessed their. The identification and characterization of CyCYP82s provide novel genetic elements that can advance the synthetic biology of BIA compounds such as protopine and benzophenanthridine, and offer insights into the biosynthesis of BIAs with diverse structures in C. yanhusuo.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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