BMC Plant Biology最新文献

{"title":"The landscape of fusion transcripts in plants: a new insight into genome complexity.","authors":"Pragya Chitkara, Ajeet Singh, Rashmi Gangwar, Rohan Bhardwaj, Shafaque Zahra, Simran Arora, Fiza Hamid, Ajay Arya, Namrata Sahu, Srija Chakraborty, Madhulika Ramesh, Shailesh Kumar","doi":"10.1186/s12870-024-05900-0","DOIUrl":"10.1186/s12870-024-05900-0","url":null,"abstract":"<p><strong>Background: </strong>Fusion transcripts (FTs), generated by the fusion of genes at the DNA level or RNA-level splicing events significantly contribute to transcriptome diversity. FTs are usually considered unique features of neoplasia and serve as biomarkers and therapeutic targets for multiple cancers. The latest findings show the presence of FTs in normal human physiology. Several discrete reports mentioned the presence of fusion transcripts in planta, has important roles in stress responses, morphological alterations, or traits (e.g. seed size, etc.).</p><p><strong>Results: </strong>In this study, we identified 169,197 fusion transcripts in 2795 transcriptome datasets of Arabidopsis thaliana, Cicer arietinum, and Oryza sativa by using a combination of tools, and confirmed the translational activity of 150 fusion transcripts through proteomic datasets. Analysis of the FT junction sequences and their association with epigenetic factors, as revealed by ChIP-Seq datasets, demonstrated an organised process of fusion formation at the DNA level. We investigated the possible impact of three-dimensional chromatin conformation on intra-chromosomal fusion events by leveraging the Hi-C datasets with the incidence of fusion transcripts. We further utilised the long-read RNA-Seq datasets to validate the most reoccurring fusion transcripts in each plant species followed by further authentication through RT-PCR and Sanger sequencing.</p><p><strong>Conclusions: </strong>Our findings suggest that a significant portion of fusion events may be attributed to alternative splicing during transcription, accounting for numerous fusion events without a proportional increase in the number of RNA pairs. Even non-nuclear DNA transcripts from mitochondria and chloroplasts can participate in intra- and inter-chromosomal fusion formation. Genes in close spatial proximity are more prone to undergoing fusion formation, especially in intra-chromosomal FTs. Most of the fusion transcripts may not undergo translation and serve as long non-coding RNAs. The low validation rate of FTs in plants indicated that the fusion transcripts are expressed at very low levels, like in the case of humans. FTs often originate from parental genes involved in essential biological processes, suggesting their relevance across diverse tissues and stress conditions. This study presents a comprehensive repository of fusion transcripts, offering valuable insights into their roles in vital physiological processes and stress responses.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1162"},"PeriodicalIF":4.3,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766317","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":"Genetic diversity analysis and core collection construction of tea plant from the Yunnan Province of China using ddRAD sequencing.","authors":"Weihua Sun, Chunlin Chen, Linlin Xu, Lingling Tao, Xiaoyan Tong, Yiping Tian, Huibing Jiang, Linbo Chen, Huilin Wen, Shengrui Liu, Chaoling Wei, Junyan Zhu","doi":"10.1186/s12870-024-05821-y","DOIUrl":"10.1186/s12870-024-05821-y","url":null,"abstract":"<p><p>Tea plants are economically important woody plants that originated in southwestern China. The Yunnan Province in China is regarded as the central origin of tea plants owing to the abundance and diversity of the tea germplasm present in this region. However, there is a lack of knowledge regarding the genetic diversity and evolutionary relationships among tea plants in this region. Here, a total of 266,397 high-quality single nucleotide polymorphisms were obtained using double digest restriction-site associated DNA sequencing from 468 tea accessions collected from Yunnan. The phylogenetic relationship and population structure of the 468 tea accessions revealed remarkable inter- and intraspecific introgression across different sect. Thea species. We found that Camellia taliensis (W. W. Smith) Melchior is the main genetic donor that greatly contributed to the domestication of C. sinensis (L.) O. Kuntze, as evidenced by the frequent generation of genetic intermediates derived from the hybridization between C. sinensis and C. taliensis in Lincang, Xishuangbanna, and Pu'er. Notable genetic differences were observed across the populations from distinct regions of Yunnan. Additionally, the Lancang River may have attenuated the genetic interflow between Lincang and Pu'er. Finally, a core collection of 50 tea accessions was constructed based on the genetic diversity of the 468 tea accessions. Our results provide novel insights into the evolutionary and domestication history of tea plants in Yunnan Province and can facilitate the development of strategies for the conservation, breeding, and utilization of the core collection.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1163"},"PeriodicalIF":4.3,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766300","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":"Silicon-seed priming promotes seed germination under CA-induced autotoxicity by improving sucrose and respiratory metabolism in cucumber (Cucumis sativus L.).","authors":"Xin Meng, Ning Jin, Li Jin, Shuya Wang, Wang Zhao, Yandong Xie, Shuchao Huang, Zeyu Zhang, Zhiqi Xu, Zitong Liu, Jian Lyu, Jihua Yu","doi":"10.1186/s12870-024-05908-6","DOIUrl":"10.1186/s12870-024-05908-6","url":null,"abstract":"<p><p>Seed germination is one of the critical and sensitive stages of early plant growth, and its process is prevented by cinnamic acid (CA). Silicon (Si) plays a critical role in mitigating abiotic stresses and seed germination in plants, but little is known about its role in seed germination and physiology in CA-stressed cucumber. Here, we conducted experiments in the State Key Laboratory of Aridland Crop Science, Gansu Agricultural University from March to June 2021 to investigate the effects of Si-seed priming on growth, antioxidant capacity, sucrose mobilization and respiratory metabolism during germination under CA stress. Our results showed that seed soaking with Si (9 mmol/L) significantly reduced membrane lipid peroxidation and promoted post-germination growth of cucumber seeds under CA (2.0 mmol/L) stress. Si increased key enzyme activities in sucrose metabolism in CA-stressed seeds after germination, accelerating sucrose degradation and fructose synthesis. Si also enhanced the activities of key enzymes in the glycolytic pathway and pentose phosphate pathway in seeds, as well as in the post-germination tricarboxylic acid cycle, promoting glucose decomposition and ATP synthesis. Principal component analysis significantly separated the CK, Si, and CA + Si treatments from the CA treatment in the first principal component after 48 h of treatment. In addition, qRT-PCR analysis showed that Si induced overexpression of genes related to sucrose and respiratory metabolism in seeds treated with CA for 48 h. In conclusion, our findings provide evidence that Si priming may be an effective method to reverse CA inhibition of cucumber seeds, which effectively improve germination under CA stress by attenuating membrane lipid peroxidation and enhancing sucrose mobilization and respiratory metabolism in cucumber.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1164"},"PeriodicalIF":4.3,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766313","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":"Characterization of tae-miR156(s) and their response to abiotic stress in wheat (Triticum aestivum L.).","authors":"Shuang Ruan, Juan Lin, Tiantian Li, Yingjie Wu, Cheng Xu, Li Mu, Wei Liu, Can Chen, Jie Lu, Chuanxi Ma, Hongqi Si","doi":"10.1186/s12870-024-05899-4","DOIUrl":"10.1186/s12870-024-05899-4","url":null,"abstract":"<p><p>The microRNA156 (miR156) has been widely studied in plants, however, the characterization of the miR156 family of genes in wheat and their expression patterns under abiotic stress are not completely clear. In this study, a total of 20 miR156 family members, referred to as tae-miR156a to tae-miR156t, were identified in wheat with their loci mapped to various chromosomes. These members were divided into five subgroups: miR156a/b/c/d/e/f, miR156g/h/i, miR156j/k, miR156l/m/n/o/p/q, and miR156r/s/t. They were highly conserved during evolution. The prediction of cis-elements in the tae-MIR156(s) promoter region revealed that the tae-MIR156(s) had diverse cis-acting elements; of these, 15 tae-MIR156(s) and 6 tae-MIR156(s) were found to be drought-responsive elements and cold-responsive elements, respectively. And the prediction target genes of tae-miR156(s) are mainly SPL transcription factor genes. Expression analysis based on quantitative real-time polymerase chain reaction (qRT‒PCR) showed that miR156(s) have different expression levels in the various wheat tissues, and the subgroups' response to abiotic stress varied. Among them, miR156g/h/i were strongly induced in the root of cold and heat stress, and miR156a/b/c/d/e/f were significantly increased in roots after drought stress, whereas miR156r/s/t were highly inhibited in leaves and roots after salt stress. These findings imply that tae-miR156(s) are involved in stress response in wheat, and they provide new fundamental knowledge for further analysis of the function of miR156 and its regulatory mechanism in response to abiotic stress.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1165"},"PeriodicalIF":4.3,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779402","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":"Expansion of Pleioblastus amarus in tea plantations significantly enhances the appearance and nutritional composition of bamboo shoots but adversely affects palatability.","authors":"Lili Fan, Shuanglin Chen, Zongming Cai, Ziwu Guo, Jie Yang, Rong Zheng, Ruicai Hu","doi":"10.1186/s12870-024-05856-1","DOIUrl":"10.1186/s12870-024-05856-1","url":null,"abstract":"<p><p>The expansion of Pleioblastus amarus into tea plantations introduces environmental heterogeneity, significantly influencing the growth and quality of bamboo shoots. This study examined the effects of bamboo expansion on the appearance, nutrition, and palatability of bamboo shoots, utilizing partial least squares structural equation modeling (PLS-SEM) to identify key influencing factors. Results revealed that bamboo expansion increased shoot diameter, length, and fresh weight, enhancing overall size and edibility, particularly in the tea-bamboo mixed forest center zone (TBC), where appearance quality peaked. Nutritional analysis revealed substantial increases in protein, fat, starch, and vitamin C content after bamboo expansion, along with the improvements in amino acid score (AAS), essential amino acid index (EAAI), and nutritional index (NI), indicating elevated nutritional value. However, despite the rise in soluble sugars and flavor-enhancing amino acids, higher levels of total acids, oxalic acid, tannins, and cellulose diminished the palatability, notably in TBC site. PLS-SEM further indicated that while bamboo expansion positively influenced shoot appearance and nutrition, soil factors predominantly drove these changes and concurrently detracted from overall palatability. These findings provide a framework for enhancing bamboo shoot quality and optimizing management practices in tea plantation ecosystems.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1161"},"PeriodicalIF":4.3,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766221","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":"Comparative study of seed germination, phenology, and reproductive fitness in Melilotus sulcatus populations from Israel.","authors":"Maor Matzrafi, Shaharit Ziv, Jackline Abu-Nassar, Daryl Gillett, Abraham Gamliel","doi":"10.1186/s12870-024-05857-0","DOIUrl":"10.1186/s12870-024-05857-0","url":null,"abstract":"<p><strong>Background: </strong>Melilotus sulcatus (Fabaceae) is an annual weed species prevalent in the Mediterranean Basin and Asia, characterized by a hard seed coat, indicating physical seed dormancy and long seed-bank longevity. This weed exhibits high phenotypic plasticity, thriving across various climatic regions in Israel. This study investigates seed germination of M. sulcatus populations under different temperatures. Moreover, we have studied the phenology, and reproductive biology of M. sulcatus populations in a common garden experiment. Seeds of M. sulcatus were collected from onion fields at Kibbutz Grofit located in the hyper-arid Southern Arava region, with ~ 30 mm average annual rainfall, and from Kibbutz Yifat, in the Jezreel Valley, where annual rainfall is 450-650 mm. Progeny generations were grown in pollen-proof cages at Newe Ya'ar Research Center also located at the Jezreel Valley.</p><p><strong>Results: </strong>Differences in seed area and average weight were observed among populations and generations, with field populations producing heavier seeds compared to progeny populations. The optimal temperature (T₀) for seed germination varied among populations, with the highest T₀ recorded for the Grofit field population (23.40℃) collected at the warm site and the lowest for the Yifat field population (17.67℃) collected at the cold site, while the two progeny populations showed similar T₀ values. Phenology and reproductive biology were tested using seeds of the two field populations. Despite the vigorous growth of the Grofit population, there were no significant differences in average final weight (4.59 g for Grofit and 4.23 g for Yifat) and height (51.8 cm for Grofit and 50.3 cm for Yifat) between populations. Grofit progeny plants exhibited a statistically significantly higher number of seeds per pod, combined with larger seed area and average weight.</p><p><strong>Conclusions: </strong>Overall, our findings underscore the adaptive strategies employed by M. sulcatus populations in response to their environment. Vigorous plant growth, a higher number of seeds per pod, and larger seed area and average weight were observed in individuals from the Grofit population compared to the Yifat population. The greater fitness of Grofit population, originated from hyper-arid conditions, highlights the significant impact of environmental factors on species adaptation.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1160"},"PeriodicalIF":4.3,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766266","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":"Reproductive biology of Lasiurus sindicus: a vital perennial fodder grass for arid ecosystem.","authors":"Reena Rani, Archana Sanyal","doi":"10.1186/s12870-024-05803-0","DOIUrl":"10.1186/s12870-024-05803-0","url":null,"abstract":"<p><strong>Background: </strong>In the arid conditions of Thar desert, only the plants which are adapted to the extreme conditions can grow and reproduce. Rangelands are important fodder resources which are needed to be improved for their long-term productivity and sustainability through conservation and utilization of indigenous plant species (Lasiurus sindicus, Cenchrus ciliaris, Cenchrus setigerus, etc.). In this first ever study; we investigated the reproductive features of L. sindicus, which will assist in breeding related improvement programs of L. sindicus. The findings will also enhance our understanding about the survival strategies of L. sindicus in the extreme arid conditions.</p><p><strong>Results: </strong>Flowers of L. sindicus are of both types, staminate and bisexual with off- white colored corolla. Results of outcrossing index (OCI), pollen-to-ovule (P/O) ratio, pollen count and different pollination treatments, indicated for cross- pollination mechanism in L. sindicus. Absence of nectar secreting tissues for nectar production and fragrance, suggested for wind-mediated pollination system. Lower grain germination rate of self-pollination than that of geitonogamous pollination and open pollination, further supported the prevalence of outcrossing in the breeding system.</p><p><strong>Conclusions: </strong>Different aspects of reproductive biology of L. sindicus, were examined which provided insight into conservation and management of this unique plant species for rangeland management programs. Floral traits, such as large pollen count, high grain setting in open pollination treatment and absence of pollinators in L. sindicus indicated towards wind-mediated out-crossing. Our findings have laid a solid foundation for various genetic studies and improvement programs of L. sindicus.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1159"},"PeriodicalIF":4.3,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766308","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":"Evaluation of genetic diversity in some hybrid individuals of honeyberry (Lonicera caerulea L.) based on fruit characteristics, leaf morphology, vitamin C, antioxidant activity, and biochemical and nutritional contents.","authors":"Kahraman Gürcan, Kadir Uğurtan Yılmaz, Yazgan Tunç, Mehmet Yaman, Adem Güneş, Ercan Yıldız, Fatih Demirel, Serap Demirel, Ali Khadivi","doi":"10.1186/s12870-024-05846-3","DOIUrl":"10.1186/s12870-024-05846-3","url":null,"abstract":"<p><strong>Background: </strong>Genetic diversity is a prerequisite for breeding programs, and one of the main goals here is to obtain quality products. Therefore, this study aims to evaluate the genetic diversity in some hybrid individuals of honeyberry (Lonicera caerulea L.) based on fruit characteristics, leaf morphology, vitamin C, antioxidant activity, biochemical, and nutritional content. In this context, superior quality individuals have been identified based on the 42 variables examined in our study. These hybrid individuals can be economically incorporated into production after the registration stages, and their sustainability for use in breeding programs can also be ensured.</p><p><strong>Results: </strong>The fruit weight ranged from 0.71 ('H11') to 1.66 g ('H6'). The ascorbic acid varied between 17.13 ('H7') and 20.64 mg AAE/100 g ('H15'). The antioxidant activity changed between 12.59 ('Store') and 15.03 µmol Trolox g^-1 ('Aurea'). The total anthocyanins were found to be highest in 'Borrel Beast' (163.79 mg cyn-3-gluc 100 g^-1), followed by 'H8' (163.20 mg cyn-3-gluc 100 g^-1). The highest nutrient levels in the fruits were found in the 'H10' individual, with calcium (2445.77 mg kg^-1), potassium (2274.36 mg kg^-1), phosphorus (2123.27 mg kg^-1), magnesium (1263.95 mg kg^-1), and sulfur (859.62 mg kg^-1), respectively. The highest nutrient levels in the leaves were found in the 'H14' individual for calcium (19,493.21 mg kg^-1), 'H5' for magnesium (5643.52 mg kg^-1), 'H8' for sulfur (2312.11 mg kg^-1), 'H6' for phosphorus (2007.51 mg kg^-1), and 'H6' for potassium (1099.32 mg kg^-1). In general, the nutrients in the fruit exhibited significant correlations among themselves at different levels (*, **, ***). Within the scope of principal component analysis, the first 8 principal components explained 80.69% of the total variance. According to the cluster and population analyses, it was determined that there was a high variation in subgroup B2. Additionally, although honeyberry is a relatively new fruit in Türkiye, efforts have begun to develop new cultivars through hybrid breeding.</p><p><strong>Conclusions: </strong>When 42 variables were evaluated together to determine genetic diversity, hybrid individuals 'H14', 'H5', 'H8', and 'H1' were identified as superior individuals, respectively.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1158"},"PeriodicalIF":4.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766291","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":"Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit.","authors":"Li-Zhen Ling, Xiao-Di Hu, Shu-Dong Zhang","doi":"10.1186/s12870-024-05877-w","DOIUrl":"https://doi.org/10.1186/s12870-024-05877-w","url":null,"abstract":"<p><strong>Background: </strong>MicroRNA (miRNA) is a crucial post-transcriptional regulatory factor in plant growth and development. Duplicated genes often exhibit functional divergence due to competition for the identical miRNA binding sites. Kiwifruit (Actinidia spp.) is an economically significant horticultural crop renowned for its distinctive flavor, which is largely attributable to elevated citrate levels during fruit development. However, the mechanisms through which miRNA-targeted modules evolve following duplication events and regulate citrate biosynthesis, thereby influencing the unique flavor profile of kiwifruits, remain poorly understood.</p><p><strong>Results: </strong>In this study, we examined the expression patterns of miRNAs and interactions with their targets in kiwifruit fruit samples from various pulp tissues and developmental stages. Our analysis identified 46 miRNAs, comprising 44 known miRNAs and two novel/kiwifruit-specific miRNAs, which targeted a total of 1,474 genes. Correlation analysis revealed weak relationships between the expression levels of miRNAs and their target genes. Among these targets, 27 tandemly duplicated genes, and 782 whole genome duplication (WGD) genes exhibited a loss of miRNA binding sites in one of their duplicated copies. Furthermore, weighted gene co-expression network analysis demonstrated that most duplicated genes clustered into distinct gene modules. These findings suggest that the loss of miRNA targets following duplications contributes to expression divergence among gene duplicates, thereby facilitating stable gene expression within the miRNA-targeted network. For instance, the aconitate hydratase genes AchAco4 and AchAco6 were each targeted by different miRNAs, ach-miR-3774 and ach-miR-10371, respectively. Notably, these genes exhibited distinct expression patterns compared to their duplicated counterparts.</p><p><strong>Conclusions: </strong>This study enhances our understanding of how the miRNA-AchAco module regulates citrate content and provides insights into the molecular network that influences the flavor profile of kiwifruit.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1157"},"PeriodicalIF":4.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of ANS gene regulating fruit color in jujube (Ziziphus jujuba Mill. cv. Lingwuchangzao) and analysis of its expression under elevated temperature and drought stress.","authors":"Botao Wang, Lei Zhang, Ting Zhang, Yaping Ma, Lihua Song","doi":"10.1186/s12870-024-05837-4","DOIUrl":"https://doi.org/10.1186/s12870-024-05837-4","url":null,"abstract":"<p><strong>Background: </strong>The anthocyanin synthase (ANS) gene is pivotal in plant anthocyanin biosynthesis, significantly influencing fruit coloration. Despite extensive on various studies, there remains a notable absence of research on the regulatory functions of the ANS gene in the 'Lingwuchangzao' variety under elevated temperature and drought stress.</p><p><strong>Results: </strong>In this study, 107 ZjANS genes were identified. Analyses of their physicochemical properties and gene structures revealed that most are localized in the cytosol and nucleus, with only seven ZjANS genes exhibiting basic characteristics. All genes contained the conserved domains 2OG-FeII_Oxy and DIOX-N. Chromosomal localization and Ka/Ks analysis indicated that these genes are distributed across 12 chromosomes, with 22 tandem gene pairs, suggesting purifying selection. Phylogenetic and synteny analysis demonstrated that ZjANS genes are evolutionarily conserved, forming collinear gene pairs with four species. Cis-acting element analysis identified elements related to anthocyanin synthesis and environmental stress, such as LTR and MBS. Predictions of protein interaction indicated that certain ZjANS proteins interact with MYB, CHI, and GA proteins, potentially involved in the anthocyanin synthesis pathway. Transcriptome and qRT-PCR analysis revealed that thirteen ZjANS genes positively respond to coloring in jujube under elevated temperature and drought stress, with ZjANS17 identified as particularly significant.</p><p><strong>Conclusion: </strong>This study identified 107 ZjANS genes and systematically analyzed their evolutionary conservation. Thirteen ZjANS genes were found to positively influence fruit coloring in 'Lingwuchangzao' under elevated temperature and drought stress. These findings provide a foundation for further investigations into ZjANS genes and the breeding new jujube varieties.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1156"},"PeriodicalIF":4.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766304","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}