Pub Date : 2023-05-31eCollection Date: 2023-07-01DOI: 10.1093/hr/uhad111
Bi Ma, Honghong Wang, Jingchun Liu, Lin Chen, Xiaoyu Xia, Wuqi Wei, Zhen Yang, Jianglian Yuan, Yiwei Luo, Ningjia He
Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.
{"title":"The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes.","authors":"Bi Ma, Honghong Wang, Jingchun Liu, Lin Chen, Xiaoyu Xia, Wuqi Wei, Zhen Yang, Jianglian Yuan, Yiwei Luo, Ningjia He","doi":"10.1093/hr/uhad111","DOIUrl":"https://doi.org/10.1093/hr/uhad111","url":null,"abstract":"<p><p>Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, <i>Morus notabilis</i>, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that <i>M. notabilis</i> is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41122974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-31eCollection Date: 2023-07-01DOI: 10.1093/hr/uhad116
Wandi Liu, Chaohui Yan, Ruimin Li, Guanyu Chen, Xinqi Wang, Yingqiang Wen, Chaohong Zhang, Xiping Wang, Yan Xu, Yuejin Wang
Grapevine powdery mildew is caused by Erysiphe necator, which seriously harms grape production in the world. Stilbene synthase makes phytoalexins that contribute to the resistance of grapevine against powdery mildew. A novel VqNSTS3 was identified and cloned from Chinese wild Vitis quinquangularis accession Danfeng-2. The novel VqNSTS3 was transferred into susceptible 'Thompson Seedless' by Agrobacterium-mediated transformation. The transgenic plants showed resistance to the disease and activated other resistance-related genes. VqNSTS3 expression in grapevine is regulated by VqWRKY33, and which binds to TTGACC in the VqNSTS3 promoter. Furthermore, VqWRKY33 was phosphorylated by VqMAPK3/VqMAPK6 and thus led to enhanced signal transduction and increased VqNSTS3 expression. ProVqNSTS3::VqNSTS3-GFP of transgenic VqNSTS3 in Arabidopsis thaliana was observed to move to and wrap the pathogen's haustoria and block invasion by Golovinomyces cichoracearum. These results demonstrate that stilbene accumulation of novel VqNSTS3 of the Chinese wild Vitis quinquangularis accession Danfeng-2 prevented pathogen invasion and enhanced resistance to powdery mildew. Therefore, VqNSTS3 can be used in generating powdery mildew-resistant grapevines.
{"title":"VqMAPK3/VqMAPK6, VqWRKY33, and <i>VqNSTS3</i> constitute a regulatory node in enhancing resistance to powdery mildew in grapevine.","authors":"Wandi Liu, Chaohui Yan, Ruimin Li, Guanyu Chen, Xinqi Wang, Yingqiang Wen, Chaohong Zhang, Xiping Wang, Yan Xu, Yuejin Wang","doi":"10.1093/hr/uhad116","DOIUrl":"https://doi.org/10.1093/hr/uhad116","url":null,"abstract":"<p><p>Grapevine powdery mildew is caused by <i>Erysiphe necator</i>, which seriously harms grape production in the world. Stilbene synthase makes phytoalexins that contribute to the resistance of grapevine against powdery mildew. A novel <i>VqNSTS3</i> was identified and cloned from Chinese wild <i>Vitis quinquangularis</i> accession Danfeng-2. The novel <i>VqNSTS3</i> was transferred into susceptible 'Thompson Seedless' by <i>Agrobacterium</i>-mediated transformation. The transgenic plants showed resistance to the disease and activated other resistance-related genes. <i>VqNSTS3</i> expression in grapevine is regulated by VqWRKY33, and which binds to TTGACC in the <i>VqNSTS3</i> promoter. Furthermore, VqWRKY33 was phosphorylated by VqMAPK3/VqMAPK6 and thus led to enhanced signal transduction and increased <i>VqNSTS3</i> expression. <i>Pro</i><i>VqNSTS3::VqNSTS3</i>-GFP of transgenic <i>VqNSTS3</i> in <i>Arabidopsis thaliana</i> was observed to move to and wrap the pathogen's haustoria and block invasion by <i>Golovinomyces cichoracearum</i>. These results demonstrate that stilbene accumulation of novel <i>VqNSTS3</i> of the Chinese wild <i>Vitis quinquangularis</i> accession Danfeng-2 prevented pathogen invasion and enhanced resistance to powdery mildew. Therefore, <i>VqNSTS3</i> can be used in generating powdery mildew-resistant grapevines.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41180496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-16eCollection Date: 2023-07-01DOI: 10.1093/hr/uhad102
Jugou Liao, Xuemei Wei, Keliang Tao, Gang Deng, Jie Shu, Qin Qiao, Gonglin Chen, Zhuo Wei, Meihui Fan, Shah Saud, Shah Fahad, Suiyun Chen
Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.
{"title":"Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants.","authors":"Jugou Liao, Xuemei Wei, Keliang Tao, Gang Deng, Jie Shu, Qin Qiao, Gonglin Chen, Zhuo Wei, Meihui Fan, Shah Saud, Shah Fahad, Suiyun Chen","doi":"10.1093/hr/uhad102","DOIUrl":"https://doi.org/10.1093/hr/uhad102","url":null,"abstract":"<p><p>Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41145241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Carrot (Daucus carota) is an Apiaceae plant with multi-colored fleshy roots that provides a model system for carotenoid research. In this study, we assembled a 430.40 Mb high-quality gapless genome to the telomere-to-telomere (T2T) level of “Kurodagosun” carrot. In total, 36 268 genes were identified and 34 961 of them were functionally annotated. The proportion of repeat sequences in the genome was 55.3%, mainly long terminal repeats. Depending on the coverage of the repeats, 14 telomeres and 9 centromeric regions on the chromosomes were predicted. A phylogenetic analysis showed that carrots evolved early in the family Apiaceae. Based on the T2T genome, we reconstructed the carotenoid metabolic pathway and identified the structural genes that regulate carotenoid biosynthesis. Among the 65 genes that were screened, 9 were newly identified. Additionally, some gene sequences overlapped with transposons, suggesting replication and functional differentiation of carotenoid-related genes during carrot evolution. Given that some gene copies were barely expressed during development, they might be functionally redundant. Comparison of 24 cytochrome P450 genes associated with carotenoid biosynthesis revealed the tandem or proximal duplication resulting in expansion of CYP gene family. These results provided molecular information for carrot carotenoid accumulation and contributed to a new genetic resource.
{"title":"Telomere-to-telomere carrot (<i>Daucus carota</i>) genome assembly reveals carotenoid characteristics.","authors":"Ya-Hui Wang, Pei-Zhuo Liu, Hui Liu, Rong-Rong Zhang, Yi Liang, Zhi-Sheng Xu, Xiao-Jie Li, Qing Luo, Guo-Fei Tan, Guang-Long Wang, Ai-Sheng Xiong","doi":"10.1093/hr/uhad103","DOIUrl":"https://doi.org/10.1093/hr/uhad103","url":null,"abstract":"Abstract Carrot (Daucus carota) is an Apiaceae plant with multi-colored fleshy roots that provides a model system for carotenoid research. In this study, we assembled a 430.40 Mb high-quality gapless genome to the telomere-to-telomere (T2T) level of “Kurodagosun” carrot. In total, 36 268 genes were identified and 34 961 of them were functionally annotated. The proportion of repeat sequences in the genome was 55.3%, mainly long terminal repeats. Depending on the coverage of the repeats, 14 telomeres and 9 centromeric regions on the chromosomes were predicted. A phylogenetic analysis showed that carrots evolved early in the family Apiaceae. Based on the T2T genome, we reconstructed the carotenoid metabolic pathway and identified the structural genes that regulate carotenoid biosynthesis. Among the 65 genes that were screened, 9 were newly identified. Additionally, some gene sequences overlapped with transposons, suggesting replication and functional differentiation of carotenoid-related genes during carrot evolution. Given that some gene copies were barely expressed during development, they might be functionally redundant. Comparison of 24 cytochrome P450 genes associated with carotenoid biosynthesis revealed the tandem or proximal duplication resulting in expansion of CYP gene family. These results provided molecular information for carrot carotenoid accumulation and contributed to a new genetic resource.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.
{"title":"LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by <i>Colletotrichum gloeosporioides</i>.","authors":"Rui Zhou, Yuhui Dong, Changxi Wang, Jianning Liu, Qiang Liang, Xiaoye Meng, Xinya Lang, Shengyi Xu, Wenjun Liu, Shuhui Zhang, Nan Wang, Ke Qiang Yang, Hongcheng Fang","doi":"10.1093/hr/uhad086","DOIUrl":"https://doi.org/10.1093/hr/uhad086","url":null,"abstract":"<p><p>Walnut anthracnose induced by <i>Colletotrichum gloeosporioides</i> is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a <i>C. gloeosporioides</i>-induced lncRNA, lncRNA109897, located upstream from the target gene <i>JrCCR4</i>, upregulated the expression of <i>JrCCR4</i>. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of <i>lncRNA109897</i> to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of <i>Arabidopsis thaliana</i> further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of <i>C. gloeosporioides</i>. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-15eCollection Date: 2023-05-01DOI: 10.1093/hr/uhad048
Giovanni Battista Tornielli, Marco Sandri, Marianna Fasoli, Alessandra Amato, Mario Pezzotti, Paola Zuccolotto, Sara Zenoni
Fruit growth and development consist of a continuous succession of physical, biochemical, and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like grapevine (Vitis vinifera L.) to scale the development of its fruit across genotypes and growing conditions. In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the complex dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time. The MPhS allowed the alignment of time-series fruit samples proving to be a complementary method for mapping the progression of grape berry development with higher detail compared to classic time- or phenotype-based approaches.
{"title":"A molecular phenology scale of grape berry development.","authors":"Giovanni Battista Tornielli, Marco Sandri, Marianna Fasoli, Alessandra Amato, Mario Pezzotti, Paola Zuccolotto, Sara Zenoni","doi":"10.1093/hr/uhad048","DOIUrl":"https://doi.org/10.1093/hr/uhad048","url":null,"abstract":"<p><p>Fruit growth and development consist of a continuous succession of physical, biochemical, and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like grapevine (<i>Vitis vinifera</i> L.) to scale the development of its fruit across genotypes and growing conditions. In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the complex dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time. The MPhS allowed the alignment of time-series fruit samples proving to be a complementary method for mapping the progression of grape berry development with higher detail compared to classic time- or phenotype-based approaches.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41107235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter, and the activation of the GA signaling pathway is the key to breaking endodormancy. GA signal transduction is involved in many physiological processes. Although the GA-GID1-DELLA regulatory module is conserved in many plants, it has a set of specific components that add complexity to the GA response mechanism. DELLA proteins are key switches in GA signaling. Therefore, there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy release. In this study, the prolonged chilling increased the content of endogenously active gibberellins. PsRGL1 among three DELLA proteins was significantly downregulated during chilling- and exogenous GA3-induced bud dormancy release by cell-free degradation assay, and a high level of polyubiquitination was detected. Silencing PsRGL1 accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release, including PsCYCD, PsEBB1, PsEBB3, PsBG6, and PsBG9. Three F-box protein family members responded to chilling and GA3 treatments, resulting in PsF-box1 induction. Yeast two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1, and the binding site was in the C-terminal domain. PsF-box1 overexpression promoted dormancy release and upregulated the expression of the dormancy-related genes. In addition, yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin ligase. These findings enriched the molecular mechanism of the GA signaling pathway during dormancy release, and enhanced the understanding of tree peony bud endodormancy.
{"title":"PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony.","authors":"Linqiang Gao, Demei Niu, Tianyu Chi, Yanchao Yuan, Chunying Liu, Shupeng Gai, Yuxi Zhang","doi":"10.1093/hr/uhad044","DOIUrl":"https://doi.org/10.1093/hr/uhad044","url":null,"abstract":"<p><p>Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter, and the activation of the GA signaling pathway is the key to breaking endodormancy. GA signal transduction is involved in many physiological processes. Although the GA-GID1-DELLA regulatory module is conserved in many plants, it has a set of specific components that add complexity to the GA response mechanism. DELLA proteins are key switches in GA signaling. Therefore, there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy release. In this study, the prolonged chilling increased the content of endogenously active gibberellins. PsRGL1 among three DELLA proteins was significantly downregulated during chilling- and exogenous GA<sub>3</sub>-induced bud dormancy release by cell-free degradation assay, and a high level of polyubiquitination was detected. Silencing <i>PsRGL1</i> accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release, including <i>PsCYCD, PsEBB1</i>, <i>PsEBB3</i>, <i>PsBG6</i>, and <i>PsBG9</i>. Three F-box protein family members responded to chilling and GA<sub>3</sub> treatments, resulting in <i>PsF-box1</i> induction. Yeast two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1, and the binding site was in the C-terminal domain. <i>PsF-box1</i> overexpression promoted dormancy release and upregulated the expression of the dormancy-related genes. In addition, yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin ligase. These findings enriched the molecular mechanism of the GA signaling pathway during dormancy release, and enhanced the understanding of tree peony bud endodormancy.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41122975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The hydrophobic cuticle encasing the fruit skin surface plays critical roles during fruit development and post-harvest. Skin failure often results in the fruit surface cracking and forming a wound-periderm tissue made of suberin and lignin. The factors that make the fruit skin susceptible to cracking have yet to be fully understood. Herein, we investigated two varieties of chili peppers (Capsicum annuum L.), Numex Garnet, whose fruit has intact skin, and Vezena Slatka, whose fruit has cracked skin. Microscopical observations, gas chromatography-mass spectrometry, biochemical and gene expression assays revealed that Vezena Slatka fruit form a thicker cuticle with greater levels of cutin monomers and hydroxycinnamic acids, and highly express key cutin-related genes. The skin of these fruit also had a lower epidermal cell density due to cells with very large perimeters, and highly express genes involved in epidermal cell differentiation. We demonstrate that skin cracking in the Vezena Slatka fruit is accompanied by a spatial accumulation of lignin-like polyphenolic compounds, without the formation of a typical wound-periderm tissues made of suberized cells. Lastly, we establish that skin cracking in chili-type pepper significantly affects fruit quality during post-harvest storage in a temperature-dependent manner. In conclusion, our data highlight cuticle thickness and epidermal cell density as two critical factors determining fruit skin susceptibility to cracking in chili-type pepper fruit.
{"title":"Microscopic and metabolic investigations disclose the factors that lead to skin cracking in chili-type pepper fruit varieties.","authors":"Ofir Marinov, Gal Nomberg, Sutanni Sarkar, Gulab Chand Arya, Eldad Karavani, Einat Zelinger, Ekaterina Manasherova, Hagai Cohen","doi":"10.1093/hr/uhad036","DOIUrl":"10.1093/hr/uhad036","url":null,"abstract":"<p><p>The hydrophobic cuticle encasing the fruit skin surface plays critical roles during fruit development and post-harvest. Skin failure often results in the fruit surface cracking and forming a wound-periderm tissue made of suberin and lignin. The factors that make the fruit skin susceptible to cracking have yet to be fully understood. Herein, we investigated two varieties of chili peppers (<i>Capsicum annuum</i> L.), Numex Garnet, whose fruit has intact skin, and Vezena Slatka, whose fruit has cracked skin. Microscopical observations, gas chromatography-mass spectrometry, biochemical and gene expression assays revealed that Vezena Slatka fruit form a thicker cuticle with greater levels of cutin monomers and hydroxycinnamic acids, and highly express key cutin-related genes. The skin of these fruit also had a lower epidermal cell density due to cells with very large perimeters, and highly express genes involved in epidermal cell differentiation. We demonstrate that skin cracking in the Vezena Slatka fruit is accompanied by a spatial accumulation of lignin-like polyphenolic compounds, without the formation of a typical wound-periderm tissues made of suberized cells. Lastly, we establish that skin cracking in chili-type pepper significantly affects fruit quality during post-harvest storage in a temperature-dependent manner. In conclusion, our data highlight cuticle thickness and epidermal cell density as two critical factors determining fruit skin susceptibility to cracking in chili-type pepper fruit.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-28eCollection Date: 2023-04-01DOI: 10.1093/hr/uhad035
Tengfei Liu, Md Abu Kawochar, Shahnewaz Begum, Enshuang Wang, Tingting Zhou, Shenglin Jing, Tiantian Liu, Liu Yu, Bihua Nie, Botao Song
Cold-induced sweetening (CIS), the undesirable sugar accumulation in cold-stored potato (Solanum tuberosum L.) tubers, is a severe postharvest issue in the potato processing industry. Although the process of sucrose hydrolysis by vacuolar invertase during potato CIS is well understood, there is limited knowledge about the transportation of sucrose from the cytosol to the vacuole during postharvest cold storage. Here, we report that among the three potato tonoplast sugar transporters (TSTs), StTST1 exhibits the highest expression in tubers during postharvest cold storage. Subcellular localization analysis demonstrates that StTST1 is a tonoplast-localized protein. StTST1 knockdown decreases reducing sugar accumulation in tubers during low-temperature storage. Compared to wild-type, potato chips produced from StTST1-silenced tubers displayed significantly lower acrylamide levels and lighter color after cold storage. Transcriptome analysis manifests that suppression of StTST1 promotes starch synthesis and inhibits starch degradation in cold-stored tubers. We further establish that the increased sucrose content in the StTST1-silenced tubers might cause a decrease in the ABA content, thereby inhibiting the ABA-signaling pathway. We demonstrate that the down-regulation of β-amylase StBAM1 in StTST1-silenced tubers might be directly controlled by ABA-responsive element-binding proteins (AREBs). Altogether, we have shown that StTST1 plays a critical role in sugar accumulation and starch metabolism regulation during postharvest cold storage. Thus, our findings provide a new strategy to improve the frying quality of cold-stored tubers and reduce the acrylamide content in potato chips.
{"title":"Potato tonoplast sugar transporter 1 controls tuber sugar accumulation during postharvest cold storage.","authors":"Tengfei Liu, Md Abu Kawochar, Shahnewaz Begum, Enshuang Wang, Tingting Zhou, Shenglin Jing, Tiantian Liu, Liu Yu, Bihua Nie, Botao Song","doi":"10.1093/hr/uhad035","DOIUrl":"10.1093/hr/uhad035","url":null,"abstract":"<p><p>Cold-induced sweetening (CIS), the undesirable sugar accumulation in cold-stored potato (<i>Solanum tuberosum</i> L.) tubers, is a severe postharvest issue in the potato processing industry. Although the process of sucrose hydrolysis by vacuolar invertase during potato CIS is well understood, there is limited knowledge about the transportation of sucrose from the cytosol to the vacuole during postharvest cold storage. Here, we report that among the three potato tonoplast sugar transporters (TSTs), <i>StTST1</i> exhibits the highest expression in tubers during postharvest cold storage. Subcellular localization analysis demonstrates that StTST1 is a tonoplast-localized protein. S<i>tTST1</i> knockdown decreases reducing sugar accumulation in tubers during low-temperature storage. Compared to wild-type, potato chips produced from <i>StTST1</i>-silenced tubers displayed significantly lower acrylamide levels and lighter color after cold storage. Transcriptome analysis manifests that suppression of <i>StTST1</i> promotes starch synthesis and inhibits starch degradation in cold-stored tubers. We further establish that the increased sucrose content in the <i>StTST1</i>-silenced tubers might cause a decrease in the ABA content, thereby inhibiting the ABA-signaling pathway. We demonstrate that the down-regulation of β-amylase <i>StBAM1</i> in <i>StTST1</i>-silenced tubers might be directly controlled by ABA-responsive element-binding proteins (AREBs). Altogether, we have shown that <i>StTST1</i> plays a critical role in sugar accumulation and starch metabolism regulation during postharvest cold storage. Thus, our findings provide a new strategy to improve the frying quality of cold-stored tubers and reduce the acrylamide content in potato chips.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41145257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-28eCollection Date: 2023-04-01DOI: 10.1093/hr/uhad038
Hongtao Song, Qi Wang, Zhonghua Zhang, Kui Lin, Erli Pang
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
{"title":"Identification of clade-wide putative <i>cis</i>-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes.","authors":"Hongtao Song, Qi Wang, Zhonghua Zhang, Kui Lin, Erli Pang","doi":"10.1093/hr/uhad038","DOIUrl":"10.1093/hr/uhad038","url":null,"abstract":"<p><p><i>Cis</i>-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as <i>cis</i>-regulatory elements. They control the development of various lineages. However, predicting clade-wide <i>cis</i>-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and <i>cis</i>-regulatory elements, we present a computational approach that predicts the clade-wide putative <i>cis</i>-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide <i>cis</i>-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide <i>cis</i>-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41174381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}