{"title":"The genome of the medicinal plant Uncaria rhynchophylla provides new insights into monoterpenoid indole alkaloid metabolism and its molecular regulatory mechanism.","authors":"Detian Mu, Lingyun Wan, Yingying Shao, Limei Pan, Xinghui Liu, Iain W Wilson, Zhixing Qing, Yu Zhou, Ying Lu, Yingjie He, Lina Zhu, Jine Fu, Shugen Wei, Xiaojun Ma, Chi Song, Deyou Qiu, Qi Tang","doi":"10.1186/s43897-025-00187-7","DOIUrl":"10.1186/s43897-025-00187-7","url":null,"abstract":"<p><p>The high-quality chromosomal-level genome assembly (627.72 Mb, contig N50 1.80 Mb) of Uncaria rhynchophylla, a Chinese herb used for hypertension and Alzheimer's disease. Integrated genomic and transcriptomic analyses identified 46,909 genes, including 72 UrWRKY transcription factors. Sixty-four candidate genes for monoterpenoid indole alkaloid (MIA) biosynthesis were screened. Functional validation confirmed UrTDC6 catalyzes tryptamine formation and UrLAMT1/UrLAMT2 catalyze loganin production. Correlation analysis linked MIA content with UrWRKY expression, identifying UrWRKY37 as a key regulator. UrWRKY37 directly activates UrTDC and UrSGD transcription. Overexpression in hairy roots upregulated MIA pathway genes and significantly increased accumulation of isocorynoxeine, corynoxeine, and isorhynchophylline. This work elucidates MIA biosynthesis and its transcriptional regulation in U. rhynchophylla.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"9"},"PeriodicalIF":8.1,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12866418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146107614","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}
{"title":"The telomere-to-telomere haplotype genome provides in-depth insights into the molecular mechanisms of the anthocyanin deficiency phenotype in Prunus mume.","authors":"Pengyu Zhou, Xiao Huang, Wei Tan, Feng Gao, Yang Bai, Chengdong Ma, Ximeng Lin, Yufan Ma, Minglu Li, Zhaojun Ni, Ting Shi, Faisal Hayat, Jing Shao, Zhihong Gao","doi":"10.1186/s43897-025-00186-8","DOIUrl":"10.1186/s43897-025-00186-8","url":null,"abstract":"<p><p>Prunus mume originated from China and is highly valued for its remarkable combination of ornamental blossoms and high economic value. Previously published P. mume genomes contain unanchored genetic regions and excessive gaps. Here, we report the P. mume f. viridicalyx gap-free telomere-to-telomere (T2T) haplotype genome. The LE_hap1 and LE_hap2 genomes were 229.29 and 228.36 Mb in length, respectively, with an N50 length of the contig between 27.65 and 27.79 Mb and 24,318 and 24,316 protein-coding genes, respectively. The completeness, continuity, and accuracy of the P. mume f. viridicalyx genome was significantly improved over the previous P. mume genomes. The key mutated genes during P. mume f. viridicalyx cultivar domestication were identified by comparative genomic, population evolution, and selective sweep analyses to be significantly enriched in the anthocyanin metabolism process, glutathione metabolism process, and carotenoid biosynthesis. Further analysis revealed that early codon termination of the PmGSTF2 gene, which is the key gene for the characteristic production of P. mume f. viridicalyx, reduced anthocyanin accumulation. We assembled a complete T2T gap-free haplotype P. mume genome, which provides a reference for gene mining and genome evolution of the anthocyanin deficiency phenotype in P. mume.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"8"},"PeriodicalIF":8.1,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12862912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100746","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}
Yan Zheng, Danni Yang, Landi Luo, Xin Yin, Xingyu Yang, Yunqiang Yang, Xiangxiang Kong, Yongping Yang
{"title":"A functional FRIa variant drives turnip adaptation to the Qinghai-Xizang Plateau.","authors":"Yan Zheng, Danni Yang, Landi Luo, Xin Yin, Xingyu Yang, Yunqiang Yang, Xiangxiang Kong, Yongping Yang","doi":"10.1186/s43897-025-00185-9","DOIUrl":"10.1186/s43897-025-00185-9","url":null,"abstract":"<p><p>Flowering time is crucial for plant adaptation to regional climate conditions and for reproduction in agricultural production. Turnip (Brassica rapa ssp. rapa) is a traditional adaptive vegetable cultivated on the Qinghai-Xizang Plateau. However, little is known about the potential molecular mechanisms underlying the adaptive evolution of flowering time in turnip in different regions, especially on the Qinghai-Xizang Plateau. In this study, the key adaptive trait of flowering time, which is positively correlated with altitude, was analyzed in 104 turnip accessions grown worldwide. Whole-genome resequencing and Sanger sequencing discovered that the FRIa gene, a key regulator of flowering time in turnip, had sequence variations, with five distinct alleles and eight genotypes being defined. By combining the association analyses of FRIa genotypes and flowering time as well as genetic validation, FRIa1 was identified as a highly functional allele that contributes to delayed flowering of turnip for adaptation to the Qinghai-Xizang Plateau. Four specific SNP variations were determined to be critical for the strong function of FRIa in turnip. Our results provide new insights into the adaptation of flowering time in turnip along altitudinal gradients and shed light on the adaptive evolution of FRIa in turnip on the Qinghai-Xizang Plateau.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"6"},"PeriodicalIF":8.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12794460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145953306","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}
Xiaojing Xue, Xiao Chen, Xin Wang, Tao Wang, Rui Liao, Haifeng Liu, Changxiang Zhu, Jonathan D G Jones, Zhaohui Chu
{"title":"Two Phytophthora effectors mitigate plant immunity by manipulating intracellular pH through interaction with V-ATPase in potato.","authors":"Xiaojing Xue, Xiao Chen, Xin Wang, Tao Wang, Rui Liao, Haifeng Liu, Changxiang Zhu, Jonathan D G Jones, Zhaohui Chu","doi":"10.1186/s43897-025-00184-w","DOIUrl":"10.1186/s43897-025-00184-w","url":null,"abstract":"<p><p>Plant V-ATPase serves as a primary active proton pump of the endomembrane system and is crucial for the stress response. However, the role of the C subunit of V-ATPase (VHA-C) in effector-triggered immunity remains poorly understood. Here, we reveal that Phytophthora infestans evolved a pair of RxLR effectors, AL3 and Avr2, which are expressed sequentially and both target the host VHA-C (StATP6V1C1) and StBSL1. In the early stage of P. infestans infection, AL3 promotes the assembly of StATP6V1C1 with subunits G and E, leading to increased V-ATPase activity and cytoplasmic acidification. Subsequently, Avr2 inhibits the StWNK10-catalyzed Ser-261 phosphorylation of StATP6V1C1, thereby retarding V-ATPase activity and causing intracellular alkalinization. In cultivars absence of two immune receptors, this pH shift facilitates the interactions of the two effectors with downstream susceptibility factors of StBSL1 at various stages of infection, which may promote the onset and development of the disease. As coping strategy, plants independently evolve two NLRs, R2 and Rpi-mcq1, guard both StATP6V1C1 and StBSLs to perceive effectors thereby mitigating the risk of late blight. Our findings establish a new arms race battlefield between plants and oomycetes, highlighting the role of intracellular pH homeostasis in both effector-triggered susceptibility (ETS) and effector-triggered immunity (ETI).</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"4"},"PeriodicalIF":8.1,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12784495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145935489","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}
Lin Weng, Li Wang, Enbai Zhou, Guixiang Wang, Xiaoyan Wang, Rong Li, Yuan Sun, Meng Li, Han Xiao
{"title":"Compound Inflorescence (S) represses fruit growth and seed development in tomato.","authors":"Lin Weng, Li Wang, Enbai Zhou, Guixiang Wang, Xiaoyan Wang, Rong Li, Yuan Sun, Meng Li, Han Xiao","doi":"10.1186/s43897-025-00183-x","DOIUrl":"10.1186/s43897-025-00183-x","url":null,"abstract":"<p><p>In most fruit-bearing plants, the growth and ripening of the fruit are highly coordinated with its seeds. In tomato (Solanum lycopersicum), fruit growth is regulated by a number of transcription factors. The WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor COMPOUND INFLORESCENCE (S)/SlWOX9 is a key regulator of inflorescence branching and embryogenesis. In this study, we show that S activity is indispensable for fruit and seed development. Ectopic S expression led to a decrease in seed weight and markedly suppressed endoreduplication-associated fruit growth. Conversely, the s-classic allele promoted fruit growth in the small-fruited S. pimpinellifolium accession LA1781 though the promotion was offset by fruit overload and vegetative reversion of flowers in large-fruited cultivars. Through transcriptome profiling and DNA affinity purification sequencing (DAP-seq), we discovered that S targeted a set of genes involved in seed development. Moreover, we demonstrate that S regulates fruit and seed development mainly through direct transcriptional repression of the Mei2-like gene SlTEL1 (Solanum lycopersicum TERMINAL EAR-LIKE 1). These findings uncover a new aspect of transcription regulation of fruit growth and seed development by WOX transcription factors in tomato.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"5"},"PeriodicalIF":8.1,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12781540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145918700","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}
{"title":"Integrated genome-wide domestication and association analyses reveal the complex genetic basis of parthenocarpy during cucumber domestication.","authors":"Pinyu Zhu, Shiyou Wang, Yongjiao Meng, Weiping Diao, Xiaqing Yu, Yuhui Wang, Ji Li, Jinfeng Chen","doi":"10.1186/s43897-025-00182-y","DOIUrl":"10.1186/s43897-025-00182-y","url":null,"abstract":"<p><p>Parthenocarpy is an important target trait for the yield and quality of fruit crops. It has been used and selected in cucumber breeding for more than a hundred years, which has led to variation in parthenocarpic ability among different cucumber groups and thus resulted in a complex genetic basis. Here, we performed deep resequencing of 236 cucumbers from six cucumber groups and investigated parthenocarpic phenotypes over three years and six seasons to explore the genetic basis of parthenocarpy in cucumber. Among the 34 loci associated with parthenocarpy identified through a genome-wide association study (GWAS), 17 (50%) were correlated with reported quantitative trait loci (QTLs), and 27 (79.4%) were selected during cucumber domestication. We found that favorable parthenocarpic alleles continuously accumulated in cultivated cucumbers, and our data pinpoint that different favorable alleles were selected in the cucumber groups, leading to variations in parthenocarpic ability among them. To validate the favorable alleles detected by GWAS, we cloned three genes, CsACA10, CsCaM, and CsERT2, and verified their roles in the regulation of parthenocarpy for the first time. Our study elucidated the genetic basis and molecular mechanism of parthenocarpy, providing important germplasms for improving parthenocarpy in cucumber breeding.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"7"},"PeriodicalIF":8.1,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12777003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145913207","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}
Yoshiharu Mimata, Ruhai Gong, Xuanxuan Pei, Guochen Qin, Wenxiu Ye
{"title":"A drought stress-responsive metabolite malate modulates stomatal responses through G-protein-dependent pathway in grapevine and Arabidopsis.","authors":"Yoshiharu Mimata, Ruhai Gong, Xuanxuan Pei, Guochen Qin, Wenxiu Ye","doi":"10.1186/s43897-025-00181-z","DOIUrl":"10.1186/s43897-025-00181-z","url":null,"abstract":"<p><p>Drought stress is a significant environmental threat to global agricultural production and distribution. Plant adaptation to dehydration stress involves intricate biological processes with substantial changes in metabolite composition. In this study, we investigated the role of tricarboxylic acid (TCA) cycle metabolites in drought tolerance in grapevine and Arabidopsis by metabolome, live cell imaging, electrophysiological and pharmacological approaches. Metabolome analysis revealed that amount of malate, citrate, and isocitrate increased over time in detached grapevine leaves. Ca<sup>2+</sup> imaging and ion channel measurements indicated that fumarate, malate, and α-ketoglutarate induced cytosolic free Ca<sup>2+</sup> concentration ([Ca<sup>2+</sup>]<sub>cyt</sub>) elevation in guard cells and directly activated a guard-cell anion channel SLOW ANION CHANNEL-ASSOCIATED 1 (SLAC1). However, only malate induced stomatal closure, which required increases in [Ca<sup>2+</sup>]<sub>cyt</sub> in guard cells and activation of SLAC1. Through pharmacological experiments and reverse genetics analyses, G-proteins were identified as essential components of malate signaling by regulating second messenger production. These results indicate that TCA cycle metabolites are sensed individually by guard cells and that malate plays a key role in connecting metabolic regulation and drought tolerance through G-protein-dependent signal cascades.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"2"},"PeriodicalIF":8.1,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12772033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906709","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}
Naila Mir Baz, Jiahui Wang, Xulei Zhao, Asia Maqbool, Caizhen Gao, Pengfei Wang, Haijiang Chen, Hongbo Cao
{"title":"Carotenoid biosynthesis in Prunus species: from pathway and accumulation structure to diverse pigmentation.","authors":"Naila Mir Baz, Jiahui Wang, Xulei Zhao, Asia Maqbool, Caizhen Gao, Pengfei Wang, Haijiang Chen, Hongbo Cao","doi":"10.1186/s43897-025-00188-6","DOIUrl":"10.1186/s43897-025-00188-6","url":null,"abstract":"<p><p>Prunus species, also known as stone fruits, include several eye-catching fruits such as cherries, plums, apricots, peaches, nectarines, etc., which have significant economic value and are widely cultivated worldwide. Carotenoids are important secondary metabolites contributing to stone fruits' aesthetic appeal and nutritional value. Carotenoids contribute hues ranging from pastel yellow to rich orange in Prunus fruits. Carotenoids accumulate in Prunus tissues through the action of chromoplasts, particular structures that store and stabilize these pigments, giving rise to their vibrant colors. The diversity in carotenoid types and levels among Prunus species and cultivars leads to diverse tissue colors, reflecting their genetic diversity and evolutionary adaptations. The most important genes related to coloration are PSY, LCYB/E, and BCH1, which are responsible for carotenoid biosynthesis, whereas CCDs and NCEDs are involved in the degradation of carotenoids. PSY leads to increased carotenoid accumulation, providing yellow and orange pigmentation. LCYB involved in β-carotene accumulation results in an orange color. LCYE can lead to lutein biosynthesis and contribute to yellow coloration. BCH1 contributes to yellow pigmentation. CCD4 plays an essential role in the flesh color of the fruit, leading to white flesh in Prunus fruits, especially peaches. NCED is involved in abscisic acid formation by degrading carotenoids. Despite the importance of carotenoids, the connection between carotenoid profiles and the diversity of Prunus fruits has received little attention in the past. This review outlines the present knowledge regarding the molecular diversity mechanisms of the carotenoid biosynthesis pathway in Prunus fruits.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"6 1","pages":"3"},"PeriodicalIF":10.0,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12765319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145896310","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}