Pub Date : 2023-11-17eCollection Date: 2024-01-01DOI: 10.1093/hr/uhad231
Ying Ye, Ru-Yi Liu, Xin Li, Xin-Qiang Zheng, Jian-Liang Lu, Yue-Rong Liang, Chao-Ling Wei, Yong-Quan Xu, Jian-Hui Ye
Flavonoids are important compounds in tea leaves imparting bitter and astringent taste, which also play key roles in tea plants responding to environmental stress. Our previous study showed that the expression level of CsMYB67 was positively correlated with the accumulation of flavonoids in tea leaves as exposed to sunlight. Here, we newly reported the function of CsMYB67 in regulating flavonoid biosynthesis in tea leaves. CsMYB67 was localized in the nucleus and responded to temperature. The results of transient expression assays showed the co-transformation of CsMYB67 and CsTTG1 promoted the transcription of CsANS promoter in the tobacco system. CsTTG1 was bound to the promoter of CsANS based on the results of yeast one-hybrid (Y1H) and transient expression assays, while CsMYB67 enhanced the transcription of CsANS through protein interaction with CsTTG1 according to the results of yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). Thus, CsMYB67-CsTTG1 module enhanced the anthocyanin biosynthesis through up-regulating the transcription of CsANS. Besides, CsMYB67 also enhanced the transcription of CsFLS and CsUFGT through forming transcription factor complexes. The function of CsMYB67 on flavonoid biosynthesis in tea leaves was validated by gene suppression assay. As CsMYB67 was suppressed, the transcriptional level of CsFLS was greatly reduced, leading to a significant increase in the contents of total catechins and total anthocyanidins. Hence, CsMYB67 plays an important role in regulating the downstream pathway of flavonoid biosynthesis in summer tea leaves.
{"title":"CsMYB67 participates in the flavonoid biosynthesis of summer tea leaves.","authors":"Ying Ye, Ru-Yi Liu, Xin Li, Xin-Qiang Zheng, Jian-Liang Lu, Yue-Rong Liang, Chao-Ling Wei, Yong-Quan Xu, Jian-Hui Ye","doi":"10.1093/hr/uhad231","DOIUrl":"10.1093/hr/uhad231","url":null,"abstract":"<p><p>Flavonoids are important compounds in tea leaves imparting bitter and astringent taste, which also play key roles in tea plants responding to environmental stress. Our previous study showed that the expression level of <i>CsMYB67</i> was positively correlated with the accumulation of flavonoids in tea leaves as exposed to sunlight. Here, we newly reported the function of CsMYB67 in regulating flavonoid biosynthesis in tea leaves. CsMYB67 was localized in the nucleus and responded to temperature. The results of transient expression assays showed the co-transformation of <i>CsMYB67</i> and <i>CsTTG1</i> promoted the transcription of <i>CsANS</i> promoter in the tobacco system. CsTTG1 was bound to the promoter of <i>CsANS</i> based on the results of yeast one-hybrid (Y1H) and transient expression assays, while CsMYB67 enhanced the transcription of <i>CsANS</i> through protein interaction with CsTTG1 according to the results of yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). Thus, CsMYB67-CsTTG1 module enhanced the anthocyanin biosynthesis through up-regulating the transcription of <i>CsANS</i>. Besides, CsMYB67 also enhanced the transcription of <i>CsFLS</i> and <i>CsUFGT</i> through forming transcription factor complexes. The function of <i>CsMYB67</i> on flavonoid biosynthesis in tea leaves was validated by gene suppression assay. As <i>CsMYB67</i> was suppressed, the transcriptional level of <i>CsFLS</i> was greatly reduced, leading to a significant increase in the contents of total catechins and total anthocyanidins. Hence, CsMYB67 plays an important role in regulating the downstream pathway of flavonoid biosynthesis in summer tea leaves.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139576821","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}
Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (CCD4) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in Lycium have not been discovered. Here, we annotated LbCCDs from the Lycium reference genome and found that LbCCD4.1 expression was significantly correlated with the carotenoid metabolites during Lycium five fruit developmental stages. Over-expression of LbCCD4.1 in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, LbERF5.1, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing ERF5.1 transgenic NQ's leaves. Over-expression or virus-induced gene silencing of LbERF5.1 in NQ's leaves induced a consistent up- or down-expression, respectively, of LbCCD4.1. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that ERF5.1 interacted with the promoter of CCD4.1 to increase its expression, and LbERF5.1 could bind to any one of the three predicted binding sites in the promoter of LbCCD4.1. A transcriptome analysis of LbERF5.1 and LbCCD4.1 over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between ERF5.1 and CCD4.1, which may be used to enhance carotenoid in Lycium.
{"title":"<i>ERF5.1</i> modulates carotenoid accumulation by interacting with <i>CCD4.1 in Lycium</i>.","authors":"Jianhua Zhao, Yuhui Xu, Haoxia Li, Xinlei Zhu, Yue Yin, Xiyan Zhang, Xiaoya Qin, Jun Zhou, Linyuan Duan, Xiaojie Liang, Ting Huang, Bo Zhang, Ru Wan, Zhigang Shi, Youlong Cao, Wei An","doi":"10.1093/hr/uhad230","DOIUrl":"https://doi.org/10.1093/hr/uhad230","url":null,"abstract":"<p><p>Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (<i>CCD4</i>) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in <i>Lycium</i> have not been discovered. Here, we annotated <i>LbCCD</i>s from the <i>Lycium</i> reference genome and found that <i>LbCCD4.1</i> expression was significantly correlated with the carotenoid metabolites during <i>Lycium</i> five fruit developmental stages. Over-expression of <i>LbCCD4.1</i> in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, <i>LbERF5.1</i>, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing <i>ERF5.1</i> transgenic NQ's leaves. Over-expression or virus-induced gene silencing of <i>LbERF5.1</i> in NQ's leaves induced a consistent up- or down-expression, respectively, of <i>LbCCD4.1</i>. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that <i>ERF5.1</i> interacted with the promoter of <i>CCD4.1</i> to increase its expression, and <i>LbERF5.1</i> could bind to any one of the three predicted binding sites in the promoter of <i>LbCCD4.1</i>. A transcriptome analysis of <i>LbERF5.1</i> and <i>LbCCD4.1</i> over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between <i>ERF5.1</i> and <i>CCD4.1</i>, which may be used to enhance carotenoid in <i>Lycium</i>.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10745278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032830","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}
Scutellaria baicalensis Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensis contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensis through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450) gene family, three genes (SbFBH1, 2, and 5) encoding flavonoid 3'-hydroxylases (F3'Hs) and one gene (SbFBH7) encoding flavonoid 3'5'-hydroxylase (F3'5'H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.
{"title":"Gap-free genome assembly and <i>CYP450</i> gene family analysis reveal the biosynthesis of anthocyanins in <i>Scutellaria baicalensis</i>.","authors":"Tianlin Pei, Sanming Zhu, Weizhi Liao, Yumin Fang, Jie Liu, Yu Kong, Mengxiao Yan, Mengying Cui, Qing Zhao","doi":"10.1093/hr/uhad235","DOIUrl":"10.1093/hr/uhad235","url":null,"abstract":"<p><p><i>Scutellaria baicalensis</i> Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from <i>S. baicalensis</i> contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on <i>S. baicalensis</i>. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of <i>S. baicalensis</i> through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of <i>Cytochrome P450 (CYP450)</i> gene family, three genes (<i>SbFBH1</i>, <i>2</i>, and <i>5</i>) encoding flavonoid 3'-hydroxylases (F3'Hs) and one gene (<i>SbFBH7</i>) encoding flavonoid 3'5'-hydroxylase (F3'5'H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering <i>CYP450</i> genes involved in the flavonoid decoration.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10753160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139059193","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 : 2023-11-17eCollection Date: 2023-12-01DOI: 10.1093/hr/uhad232
Qi Gao, Shaoqiang Hu, Xiaoli Wang, Fu Han, Huifeng Luo, Zhongchi Liu, Chunying Kang
Light is an important environmental signal that influences plant growth and development. Among the photoreceptors, phytochromes can sense red/far-red light to coordinate various biological processes. However, their functions in strawberry are not yet known. In this study, we identified an EMS mutant, named P8, in woodland strawberry (Fragaria vesca) that showed greatly increased plant height and reduced anthocyanin content. Mapping-by-sequencing revealed that the causal mutation in FvePhyB leads to premature termination of translation. The light treatment assay revealed that FvePhyB is a bona fide red/far-red light photoreceptor, as it specifically inhibits hypocotyl length under red light. Transcriptome analysis showed that the FvePhyB mutation affects the expression levels of genes involved in hormone synthesis and signaling and anthocyanin biosynthesis in petioles and fruits. The srl mutant with a longer internode is caused by a mutation in the DELLA gene FveRGA1 (Repressor of GA1) in the gibberellin pathway. We found that the P8 srl double mutant has much longer internodes than srl, suggesting a synergistic role of FvePhyB and FveRGA1 in this process. Taken together, these results demonstrate the important role of FvePhyB in regulating plant architecture and anthocyanin content in woodland strawberry.
{"title":"The red/far-red light photoreceptor FvePhyB regulates tissue elongation and anthocyanin accumulation in woodland strawberry.","authors":"Qi Gao, Shaoqiang Hu, Xiaoli Wang, Fu Han, Huifeng Luo, Zhongchi Liu, Chunying Kang","doi":"10.1093/hr/uhad232","DOIUrl":"https://doi.org/10.1093/hr/uhad232","url":null,"abstract":"<p><p>Light is an important environmental signal that influences plant growth and development. Among the photoreceptors, phytochromes can sense red/far-red light to coordinate various biological processes. However, their functions in strawberry are not yet known. In this study, we identified an EMS mutant, named P8, in woodland strawberry (<i>Fragaria vesca</i>) that showed greatly increased plant height and reduced anthocyanin content. Mapping-by-sequencing revealed that the causal mutation in <i>FvePhyB</i> leads to premature termination of translation. The light treatment assay revealed that FvePhyB is a bona fide red/far-red light photoreceptor, as it specifically inhibits hypocotyl length under red light. Transcriptome analysis showed that the <i>FvePhyB</i> mutation affects the expression levels of genes involved in hormone synthesis and signaling and anthocyanin biosynthesis in petioles and fruits. The <i>srl</i> mutant with a longer internode is caused by a mutation in the DELLA gene <i>FveRGA1</i> (<i>Repressor of GA1</i>) in the gibberellin pathway. We found that the P8 <i>srl</i> double mutant has much longer internodes than <i>srl</i>, suggesting a synergistic role of <i>FvePhyB</i> and <i>FveRGA1</i> in this process. Taken together, these results demonstrate the important role of <i>FvePhyB</i> in regulating plant architecture and anthocyanin content in woodland strawberry.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10745270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032831","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 : 2023-11-14eCollection Date: 2023-12-01DOI: 10.1093/hr/uhad239
Sangkyu Park, Hyo Lee, Jaeeun Song, Chan Ju Lim, Jinpyo Oh, Sang Hoon Lee, Saet Buyl Lee, Jong-Yeol Lee, Sunhyung Lim, Jin A Kim, Beom-Gi Kim
Flavonols are the major class of flavonoids of green Chinese cabbage (Brassica rapa subsp. pekinensis). The B. rapa genome harbors seven flavonol synthase genes (BrFLSs), but they have not been functionally characterized. Here, transcriptome analysis showed four BrFLSs mainly expressed in Chinese cabbage. Among them, only BrFLS1 showed major FLS activity and additional flavanone 3β-hydroxylase (F3H) activity, while BrFLS2 and BrFLS3.1 exhibited only marginal F3H activities. We generated BrFLS1-knockout (BrFLS1-KO) Chinese cabbages using CRISPR/Cas9-mediated genome editing and obtained transgene-free homozygous plants without off-target mutation in the T1 generation, which were further advanced to the T2 generation showing normal phenotype. UPLC-ESI-QTOF-MS analysis revealed that flavonol glycosides were dramatically decreased in the T2 plants, while dihydroflavonol glycosides accumulated concomitantly to levels corresponding to the reduced levels of flavonols. Quantitative PCR analysis revealed that the early steps of phenylpropanoid and flavonoid biosynthetic pathway were upregulated in the BrFLS1-KO plants. In accordance, total phenolic contents were slightly enhanced in the BrFLS1-KO plants, which suggests a negative role of flavonols in phenylpropanoid and flavonoid biosynthesis in Chinese cabbage. Phenotypic surveys revealed that the BrFLS1-KO Chinese cabbages showed normal head formation and reproductive phenotypes, but subtle morphological changes in their heads were observed. In addition, their seedlings were susceptible to osmotic stress compared to the controls, suggesting that flavonols play a positive role for osmotic stress tolerance in B.rapa seedling. In this study, we showed that CRISPR/Cas9-mediated BrFLS1-KO successfully generated a valuable breeding resource of Chinese cabbage with distinctive metabolic traits and that CRISPR/Cas9 can be efficiently applied in functional Chinese cabbage breeding.
{"title":"Gene editing of authentic <i>Brassica rapa flavonol synthase 1</i> generates dihydroflavonol-accumulating Chinese cabbage.","authors":"Sangkyu Park, Hyo Lee, Jaeeun Song, Chan Ju Lim, Jinpyo Oh, Sang Hoon Lee, Saet Buyl Lee, Jong-Yeol Lee, Sunhyung Lim, Jin A Kim, Beom-Gi Kim","doi":"10.1093/hr/uhad239","DOIUrl":"https://doi.org/10.1093/hr/uhad239","url":null,"abstract":"<p><p>Flavonols are the major class of flavonoids of green Chinese cabbage (<i>Brassica rapa</i> subsp. <i>pekinensis</i>). The <i>B. rapa</i> genome harbors seven <i>flavonol synthase</i> genes (<i>BrFLS</i>s), but they have not been functionally characterized. Here, transcriptome analysis showed four <i>BrFLS</i>s mainly expressed in Chinese cabbage. Among them, only BrFLS1 showed major FLS activity and additional flavanone 3<i>β</i>-hydroxylase (F3H) activity, while BrFLS2 and BrFLS3.1 exhibited only marginal F3H activities. We generated <i>BrFLS1</i>-knockout (<i>BrFLS1-</i>KO) Chinese cabbages using CRISPR/Cas9-mediated genome editing and obtained transgene-free homozygous plants without off-target mutation in the T<sub>1</sub> generation, which were further advanced to the T<sub>2</sub> generation showing normal phenotype. UPLC-ESI-QTOF-MS analysis revealed that flavonol glycosides were dramatically decreased in the T<sub>2</sub> plants, while dihydroflavonol glycosides accumulated concomitantly to levels corresponding to the reduced levels of flavonols. Quantitative PCR analysis revealed that the early steps of phenylpropanoid and flavonoid biosynthetic pathway were upregulated in the <i>BrFLS1-</i>KO plants. In accordance, total phenolic contents were slightly enhanced in the <i>BrFLS1-</i>KO plants, which suggests a negative role of flavonols in phenylpropanoid and flavonoid biosynthesis in Chinese cabbage. Phenotypic surveys revealed that the <i>BrFLS1-KO</i> Chinese cabbages showed normal head formation and reproductive phenotypes, but subtle morphological changes in their heads were observed. In addition, their seedlings were susceptible to osmotic stress compared to the controls, suggesting that flavonols play a positive role for osmotic stress tolerance in <i>B.rapa</i> seedling. In this study, we showed that CRISPR/Cas9-mediated <i>BrFLS1</i>-KO successfully generated a valuable breeding resource of Chinese cabbage with distinctive metabolic traits and that CRISPR/Cas9 can be efficiently applied in functional Chinese cabbage breeding.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138814098","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}
Scutellaria baicalensis Georgi, also known as huang-qin in traditional Chinese medicine, is a widely used herbal remedy due to its anticancer, antivirus, and hepatoprotective properties. The S. baicalensis genome was sequenced many years ago; by contrast, the proteome as the executer of most biological processes of S. baicalensis in the aerial parts, as well as the secondary structure of the roots (xylem, phloem, and periderm), is far less comprehensively characterized. Here we attempt to depict the molecular landscape of the non-model plant S. baicalensis through a multi-omics approach, with the goal of constructing a highly informative and valuable reference dataset. Furthermore, we provide an in-depth characterization dissection to explain the two distinct flavonoid biosynthesis pathways that exist in the aerial parts and root, at the protein and phosphorylated protein levels. Our study provides detailed spatial proteomic and phosphoproteomic information in the context of secondary structures, with implications for the molecular profiling of secondary metabolite biosynthesis in non-model medicinal plants.
{"title":"Multi-omics landscape to decrypt the distinct flavonoid biosynthesis of <i>Scutellaria baicalensis</i> across multiple tissues.","authors":"Dandan Guo, Zhenyu Zhu, Zhe Wang, Fei Feng, Qi Cao, Zhewei Xia, Xinlei Jia, Diya Lv, Ting Han, Xiaofei Chen","doi":"10.1093/hr/uhad258","DOIUrl":"10.1093/hr/uhad258","url":null,"abstract":"<p><p><i>Scutellaria baicalensis</i> Georgi, also known as huang-qin in traditional Chinese medicine, is a widely used herbal remedy due to its anticancer, antivirus, and hepatoprotective properties. The <i>S. baicalensis</i> genome was sequenced many years ago; by contrast, the proteome as the executer of most biological processes of <i>S. baicalensis</i> in the aerial parts, as well as the secondary structure of the roots (xylem, phloem, and periderm), is far less comprehensively characterized. Here we attempt to depict the molecular landscape of the non-model plant <i>S. baicalensis</i> through a multi-omics approach, with the goal of constructing a highly informative and valuable reference dataset. Furthermore, we provide an in-depth characterization dissection to explain the two distinct flavonoid biosynthesis pathways that exist in the aerial parts and root, at the protein and phosphorylated protein levels. Our study provides detailed spatial proteomic and phosphoproteomic information in the context of secondary structures, with implications for the molecular profiling of secondary metabolite biosynthesis in non-model medicinal plants.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10828779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652292","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}
Nymphaea is a key genus of the ANA grade (Amborellales, Nymphaeales, and Austrobaileyales) of basal flowering plants, which serve as a key model to study the early evolution of floral traits. In this study, we comprehensively investigated the emission, biosynthesis, and biological function of the floral scent in a night-blossoming waterlily Nymphaea prolifera. The headspace volatile collection combined with GC-MS analysis showed that the floral scent of N. prolifera is predominately comprised by methylated benzenoids including anisole, veratrole, guaiacol, and methoxyanisole. Moreover, the emission of these floral benzenoids in N. prolifera exhibited temporal and spatial pattern with circadian rhythm and tissue specificity. By creating and mining transcriptomes of N. prolifera flowers, 12 oxygen methyltransferases (NpOMTs) were functionally identified. By in vitro enzymatic assay, NpOMT3, 6, and 7 could produce anisole and NpOMT5, 7, 9, produce guaiacol, whereas NpOMT3, 6, 9, 11 catalyzed the formation of veratrole. Methoxyanisole was identified as the universal product of all NpOMTs. Expression patterns of NpOMTs provided implication for their roles in the production of the respective benzenoids. Phylogenetic analysis of OMTs suggested a Nymphaea-specific expansion of the OMT family, indicating the evolution of lineage-specific functions. In bioassays, anisole, veratrole, and guaiacol in the floral benzenoids were revealed to play the critical role in repelling waterlily aphids. Overall, this study indicates that the basal flowering plant N. prolifera has evolved a diversity and complexity of OMT genes for the biosynthesis of methylated benzenoids that can repel insects from feeding the flowers. These findings provide new insights into the evolutional mechanism and ecological significance of the floral scent from early-diverged flowering plants.
{"title":"Diverse <i>O</i>-methyltransferases catalyze the biosynthesis of floral benzenoids that repel aphids from the flowers of waterlily <i>Nymphaea prolifera</i>.","authors":"Guanhua Liu, Jianyu Fu, Lingyun Wang, Mingya Fang, Wanbo Zhang, Mei Yang, Xuemin Yang, Yingchun Xu, Lin Shi, Xiaoying Ma, Qian Wang, Hui Chen, Cuiwei Yu, Dongbei Yu, Feng Chen, Yifan Jiang","doi":"10.1093/hr/uhad237","DOIUrl":"10.1093/hr/uhad237","url":null,"abstract":"<p><p><i>Nymphaea</i> is a key genus of the ANA grade (Amborellales, Nymphaeales, and Austrobaileyales) of basal flowering plants, which serve as a key model to study the early evolution of floral traits. In this study, we comprehensively investigated the emission, biosynthesis, and biological function of the floral scent in a night-blossoming waterlily <i>Nymphaea prolifera</i>. The headspace volatile collection combined with GC-MS analysis showed that the floral scent of <i>N. prolifera</i> is predominately comprised by methylated benzenoids including anisole, veratrole, guaiacol, and methoxyanisole. Moreover, the emission of these floral benzenoids in <i>N. prolifera</i> exhibited temporal and spatial pattern with circadian rhythm and tissue specificity. By creating and mining transcriptomes of <i>N. prolifera</i> flowers, 12 oxygen methyltransferases (<i>NpOMTs</i>) were functionally identified. By <i>in vitro</i> enzymatic assay, NpOMT3, 6, and 7 could produce anisole and NpOMT5, 7, 9, produce guaiacol, whereas NpOMT3, 6, 9, 11 catalyzed the formation of veratrole. Methoxyanisole was identified as the universal product of all NpOMTs. Expression patterns of <i>NpOMTs</i> provided implication for their roles in the production of the respective benzenoids. Phylogenetic analysis of OMTs suggested a <i>Nymphaea</i>-specific expansion of the OMT family, indicating the evolution of lineage-specific functions. In bioassays, anisole, veratrole, and guaiacol in the floral benzenoids were revealed to play the critical role in repelling waterlily aphids. Overall, this study indicates that the basal flowering plant <i>N. prolifera</i> has evolved a diversity and complexity of OMT genes for the biosynthesis of methylated benzenoids that can repel insects from feeding the flowers. These findings provide new insights into the evolutional mechanism and ecological significance of the floral scent from early-diverged flowering plants.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10753166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139059192","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}
Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.
{"title":"Telomere-to-telomere genome assembly of melon (<i>Cucumis melo</i> L. var. <i>inodorus</i>) provides a high-quality reference for meta-QTL analysis of important traits.","authors":"Minghua Wei, Ying Huang, Changjuan Mo, Haiyan Wang, Qingguo Zeng, Wenli Yang, Jihao Chen, Xuejun Zhang, Qiusheng Kong","doi":"10.1093/hr/uhad189","DOIUrl":"https://doi.org/10.1093/hr/uhad189","url":null,"abstract":"<p><p>Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (<i>Cucumis melo</i> L. var. <i>inodorus</i>) was <i>de novo</i> assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was <i>de novo</i> assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615816/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429608","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 : 2023-09-26eCollection Date: 2023-10-01DOI: 10.1093/hr/uhad186
Kang Du, Shenxiu Jiang, Hao Chen, Yufei Xia, Ruihua Guo, Aoyu Ling, Ting Liao, Wenqi Wu, Xiangyang Kang
Poplar is an important afforestation and urban greening species. Poplar leaf development occurs in stages, from young to mature and then from mature to senescent; these are accompanied by various phenotypic and physiological changes. However, the associated transcriptional regulatory network is relatively unexplored. We first used principal component analysis to classify poplar leaves at different leaf positions into two stages: developmental maturity (the stage of maximum photosynthetic capacity); and the stage when photosynthetic capacity started to decline and gradually changed to senescence. The two stages were then further subdivided into five intervals by gene expression clustering analysis: young leaves, the period of cell genesis and functional differentiation (L1); young leaves, the period of development and initial formation of photosynthetic capacity (L3-L7); the period of maximum photosynthetic capacity of functional leaves (L9-L13); the period of decreasing photosynthetic capacity of functional leaves (L15-L27); and the period of senescent leaves (L29). Using a weighted co-expression gene network analysis of regulatory genes, high-resolution spatiotemporal transcriptional regulatory networks were constructed to reveal the core regulators that regulate leaf development. Spatiotemporal transcriptome data of poplar leaves revealed dynamic changes in genes and miRNAs during leaf development and identified several core regulators of leaf development, such as GRF5 and MYB5. This in-depth analysis of transcriptional regulation during leaf development provides a theoretical basis for exploring the biological basis of the transcriptional regulation of leaf development and the molecular design of breeding for delaying leaf senescence.
{"title":"Spatiotemporal miRNA and transcriptomic network dynamically regulate the developmental and senescence processes of poplar leaves.","authors":"Kang Du, Shenxiu Jiang, Hao Chen, Yufei Xia, Ruihua Guo, Aoyu Ling, Ting Liao, Wenqi Wu, Xiangyang Kang","doi":"10.1093/hr/uhad186","DOIUrl":"https://doi.org/10.1093/hr/uhad186","url":null,"abstract":"<p><p>Poplar is an important afforestation and urban greening species. Poplar leaf development occurs in stages, from young to mature and then from mature to senescent; these are accompanied by various phenotypic and physiological changes. However, the associated transcriptional regulatory network is relatively unexplored. We first used principal component analysis to classify poplar leaves at different leaf positions into two stages: developmental maturity (the stage of maximum photosynthetic capacity); and the stage when photosynthetic capacity started to decline and gradually changed to senescence. The two stages were then further subdivided into five intervals by gene expression clustering analysis: young leaves, the period of cell genesis and functional differentiation (L1); young leaves, the period of development and initial formation of photosynthetic capacity (L3-L7); the period of maximum photosynthetic capacity of functional leaves (L9-L13); the period of decreasing photosynthetic capacity of functional leaves (L15-L27); and the period of senescent leaves (L29). Using a weighted co-expression gene network analysis of regulatory genes, high-resolution spatiotemporal transcriptional regulatory networks were constructed to reveal the core regulators that regulate leaf development. Spatiotemporal transcriptome data of poplar leaves revealed dynamic changes in genes and miRNAs during leaf development and identified several core regulators of leaf development, such as GRF5 and MYB5. This in-depth analysis of transcriptional regulation during leaf development provides a theoretical basis for exploring the biological basis of the transcriptional regulation of leaf development and the molecular design of breeding for delaying leaf senescence.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10611553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415487","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 : 2023-09-25eCollection Date: 2023-10-01DOI: 10.1093/hr/uhad193
Felipe Pérez de Los Cobos, Eva Coindre, Naima Dlalah, Bénédicte Quilot-Turion, Ignasi Batlle, Pere Arús, Iban Eduardo, Henri Duval
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
{"title":"Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time.","authors":"Felipe Pérez de Los Cobos, Eva Coindre, Naima Dlalah, Bénédicte Quilot-Turion, Ignasi Batlle, Pere Arús, Iban Eduardo, Henri Duval","doi":"10.1093/hr/uhad193","DOIUrl":"10.1093/hr/uhad193","url":null,"abstract":"<p><p>Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed <i>Prudul26A013473</i> as a candidate gene responsible for the main QTL found in crack-out percentage, <i>Prudul26A012082</i> and <i>Prudul26A017782</i> as candidate genes for the QTLs found in double kernels percentage, and <i>Prudul26A000954</i> as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10623407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489485","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}