{"title":"Spilling the beans on duplicated genes: Unravelling the mechanisms underlying transcriptional divergence in soybean.","authors":"Róisín Fattorini","doi":"10.1093/plcell/koaf283","DOIUrl":"https://doi.org/10.1093/plcell/koaf283","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145771571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Katie A Long, Ashleigh Lister, Maximillian R W Jones, Nikolai M Adamski, Rob E Ellis, Carole Chedid, Sophie J Carpenter, Xuemei Liu, Anna E Backhaus, Andrew Goldson, Vanda Knitlhoffer, Yuanrong Pei, Martin Vickers, Burkhard Steuernagel, Gemy G Kaithakottil, Jun Xiao, Wilfried Haerty, Iain C Macaulay, Cristóbal Uauy
The diversity of plant inflorescence architecture is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development compared to central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, gene expression patterns along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, we optimize Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localisation for 200 genes to cellular resolution across four stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organisation of spikelet and floral development, and characterising tissue-level gene markers. Using these domain- and cell-level maps, we characterise expression patterns of genes differentially expressed across the apical-basal axis. We identify distinct, spatially coordinated expression patterns distinguishing axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting factors patterning meristem identity and transition. To support the broader research community, all raw and processed data are publicly available, including through an interactive WebAtlas interface (www.wheat-spatial.com).
{"title":"Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution","authors":"Katie A Long, Ashleigh Lister, Maximillian R W Jones, Nikolai M Adamski, Rob E Ellis, Carole Chedid, Sophie J Carpenter, Xuemei Liu, Anna E Backhaus, Andrew Goldson, Vanda Knitlhoffer, Yuanrong Pei, Martin Vickers, Burkhard Steuernagel, Gemy G Kaithakottil, Jun Xiao, Wilfried Haerty, Iain C Macaulay, Cristóbal Uauy","doi":"10.1093/plcell/koaf282","DOIUrl":"https://doi.org/10.1093/plcell/koaf282","url":null,"abstract":"The diversity of plant inflorescence architecture is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development compared to central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, gene expression patterns along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, we optimize Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localisation for 200 genes to cellular resolution across four stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organisation of spikelet and floral development, and characterising tissue-level gene markers. Using these domain- and cell-level maps, we characterise expression patterns of genes differentially expressed across the apical-basal axis. We identify distinct, spatially coordinated expression patterns distinguishing axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting factors patterning meristem identity and transition. To support the broader research community, all raw and processed data are publicly available, including through an interactive WebAtlas interface (www.wheat-spatial.com).","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Célestine Belloeil,Vanesa Sanchez Garcia de la Torre,Rubén Contreras-Aguilera,Hendrik Küpper,Ophélie Courtin,Christophe Klopp,Céline Roques,Carole Iampietro,Céline Vandecasteele,Alexandra Launay-Avon,Wiebke Leemhuis,Jitpanu Yamjabok,Joost van den Heuvel,Mark G M Aarts,Celestino Quintela-Sabarís,Sébastien Thomine,Sylvain Merlot
Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporter genes, namely NcHMA3, NcHMA4 and NcIREG2, are consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in the roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participates in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of several metal transporters, including NcIREG2, and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.
{"title":"Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens.","authors":"Célestine Belloeil,Vanesa Sanchez Garcia de la Torre,Rubén Contreras-Aguilera,Hendrik Küpper,Ophélie Courtin,Christophe Klopp,Céline Roques,Carole Iampietro,Céline Vandecasteele,Alexandra Launay-Avon,Wiebke Leemhuis,Jitpanu Yamjabok,Joost van den Heuvel,Mark G M Aarts,Celestino Quintela-Sabarís,Sébastien Thomine,Sylvain Merlot","doi":"10.1093/plcell/koaf281","DOIUrl":"https://doi.org/10.1093/plcell/koaf281","url":null,"abstract":"Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporter genes, namely NcHMA3, NcHMA4 and NcIREG2, are consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in the roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participates in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of several metal transporters, including NcIREG2, and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene duplication is a major source of evolutionary innovation, enabling the emergence of novel expression patterns and functions. Leveraging single-cell genomics, we investigated the transcriptional and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), that has undergone two rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from the two rounds of whole-genome duplications and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Lastly, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics.
{"title":"From duplication to divergence: single-cell insights into transcriptional and cis -regulatory landscapes in soybean","authors":"Xiang Li, Xuan Zhang, Robert J Schmitz","doi":"10.1093/plcell/koaf279","DOIUrl":"https://doi.org/10.1093/plcell/koaf279","url":null,"abstract":"Gene duplication is a major source of evolutionary innovation, enabling the emergence of novel expression patterns and functions. Leveraging single-cell genomics, we investigated the transcriptional and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), that has undergone two rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from the two rounds of whole-genome duplications and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Lastly, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"141 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145593504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Auxenochlorella: The green algal reference we've been waiting for.","authors":"Regina Mencia","doi":"10.1093/plcell/koaf278","DOIUrl":"https://doi.org/10.1093/plcell/koaf278","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"160 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unearthing a legacy from the green revolution: Rht-D1b contributes to larger roots in modern Bread Wheat varieties.","authors":"Christian Damian Lorenzo","doi":"10.1093/plcell/koaf277","DOIUrl":"https://doi.org/10.1093/plcell/koaf277","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"371 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hui Tao, Ruyi Wang, Feng He, Chongyang Zhang, Su Jiang, Min Wang, Xiao Xu, Jisong Wang, Xiaoman You, Dan Wang, Jiangbo Fan, Hailong Guo, Kabin Xie, Guo-Liang Wang, Yuese Ning
Plant respiratory burst oxidase homologs (Rbohs) contribute to the production of reactive oxygen species (ROS), which are crucial defense signals in plants. However, the regulation of rice (Oryza sativa) OsRboh homeostasis has remained unclear. In this study, we reported that overexpression of OsRbohB confers resistance to Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae. Mechanistically, the calcium-dependent protein kinase OsCPK4 interacts with and phosphorylates OsRbohB at Ser322 and Ser326, thereby reducing immune responses. OsRbohB phosphomimic modifications at these two sites disrupt OsRbohB-mediated disease resistance. Moreover, the RING-type E3 ubiquitin ligase OsRING142 interacts with and ubiquitinates OsRbohB at Lys266, targeting it for degradation by the 26S proteasome pathway and compromising the immune response. Overexpression of OsRbohBK266R further increased resistance compared to OsRbohB overexpression plants. Remarkably, phosphorylation at OsRbohB facilitates OsRING142-mediated ubiquitination and degradation of OsRbohB. OsRbohBK266R×S2A overexpression plants with reduced ubiquitination and phosphorylation levels of OsRbohB exhibit stronger resistance against M. oryzae. Overall, our study highlights the critical role of Rbohs in broad-spectrum resistance and demonstrates that phosphorylation and ubiquitination synergistically fine-tune Rboh protein stability and immunity.
{"title":"Phosphorylation and ubiquitination synergistically promote the degradation of OsRbohB to modulate rice immunity","authors":"Hui Tao, Ruyi Wang, Feng He, Chongyang Zhang, Su Jiang, Min Wang, Xiao Xu, Jisong Wang, Xiaoman You, Dan Wang, Jiangbo Fan, Hailong Guo, Kabin Xie, Guo-Liang Wang, Yuese Ning","doi":"10.1093/plcell/koaf276","DOIUrl":"https://doi.org/10.1093/plcell/koaf276","url":null,"abstract":"Plant respiratory burst oxidase homologs (Rbohs) contribute to the production of reactive oxygen species (ROS), which are crucial defense signals in plants. However, the regulation of rice (Oryza sativa) OsRboh homeostasis has remained unclear. In this study, we reported that overexpression of OsRbohB confers resistance to Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae. Mechanistically, the calcium-dependent protein kinase OsCPK4 interacts with and phosphorylates OsRbohB at Ser322 and Ser326, thereby reducing immune responses. OsRbohB phosphomimic modifications at these two sites disrupt OsRbohB-mediated disease resistance. Moreover, the RING-type E3 ubiquitin ligase OsRING142 interacts with and ubiquitinates OsRbohB at Lys266, targeting it for degradation by the 26S proteasome pathway and compromising the immune response. Overexpression of OsRbohBK266R further increased resistance compared to OsRbohB overexpression plants. Remarkably, phosphorylation at OsRbohB facilitates OsRING142-mediated ubiquitination and degradation of OsRbohB. OsRbohBK266R×S2A overexpression plants with reduced ubiquitination and phosphorylation levels of OsRbohB exhibit stronger resistance against M. oryzae. Overall, our study highlights the critical role of Rbohs in broad-spectrum resistance and demonstrates that phosphorylation and ubiquitination synergistically fine-tune Rboh protein stability and immunity.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"114 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Melon (Cucumis melo L.) is a globally important fruit crop, but progress in molecular breeding has been hampered by limited functional dissection of genes associated with agronomic traits. Therefore, we developed a comprehensive genome resource based on the C. melo ssp. agrestis accession 13C. This resource includes a complete telomere-to-telomere (T2T) genome assembly, including accurate quantification of 45S rDNA copy number in melon, a transcriptome atlas from 31 tissue samples, a phenotypically diverse EMS-induced mutant library and a stable transformation system. By sequencing 1,125 M₂ families, we identified about 660,000 variants, which cover 97.33% of the annotated gene space. Leveraging these integrated resources, we identified and functionally characterized several key genes, including CLAVATA3 INSENSITIVE RECEPTOR KINASES 2 (CmCIK2), which regulates carpel number; PARA-AMINOBENZOIC ACID SYNTHASE (CmACDS), a central regulator of folate biosynthesis; and a mutant allele of the known gynoecious gene WIP DOMAIN PROTEIN 1 (CmWIP1). In addition, we discovered a specific EMS-induced variant in the fruit ripening regulator CmNAC-NOR, and further validated its function by generating targeted mutants. The CmNAC-NOR mutants exhibited delayed fruit ripening, thus providing a valuable resource for improving ripening traits in agrestis accessions. To facilitate broader utilization, we developed the Melon Information Resource (MIR), available at https://zhanglab.qau.edu.cn/melon/index.php, an integrated platform housing 13C comprehensive genome resources and associated convenient analysis tools. This unified and accession-specific resource offers unprecedented opportunities to accelerate gene discovery and trait improvement in melon through functional genomics and molecular breeding.
甜瓜（Cucumis melo L.）是一种全球性的重要水果作物，但由于对农艺性状相关基因的功能解剖有限，分子育种的进展受到阻碍。因此，我们开发了一个全面的甜瓜基因组资源。第13C条。该资源包括完整的端粒到端粒（T2T）基因组组装，包括甜瓜45S rDNA拷贝数的精确定量，31个组织样本的转录组图谱，表型多样的ems诱导突变文库和稳定的转化系统。通过对1125个M₂家族进行测序，我们发现了大约66万个变异，覆盖了97.33%的注释基因空间。利用这些整合的资源，我们鉴定并功能表征了几个关键基因，包括调节心皮数量的CLAVATA3不敏感受体激酶2 (CmCIK2)；对氨基苯甲酸合成酶（CmACDS），叶酸生物合成的中心调节因子；以及已知的雌同体基因WIP DOMAIN PROTEIN 1 （CmWIP1）的突变等位基因。此外，我们在果实成熟调节因子CmNAC-NOR中发现了一个特定的ems诱导变异，并通过产生靶向突变进一步验证了其功能。CmNAC-NOR突变体表现出果实成熟延迟的特性，为改良青花苜蓿的成熟性状提供了宝贵的资源。为了促进更广泛的利用，我们开发了甜瓜信息资源（MIR），可在https://zhanglab.qau.edu.cn/melon/index.php上获得，这是一个集成平台，包含13C全面的基因组资源和相关的便捷分析工具。这种统一的、特异的资源为通过功能基因组学和分子育种加速甜瓜基因发现和性状改良提供了前所未有的机会。
{"title":"A comprehensive omics resource and genetic tools for genetic research and precision breeding of Cucumis melo ssp. agrestis","authors":"Yuanchao Xu, Bin Liu, Yang Li, Xinxiu Chen, Chao Yan, Yue Liu, Huihui Wang, Jie Wang, Wenjing Dong, Shijun Deng, Naonao Wang, Hangyu Wu, Huixin Guo, Zekai Zhang, Xiuhua Yao, Jing Feng, Jinjing Sun, Huimin Zhang, Bingsheng Lv, Kuipeng Xu, Xiaofeng Liu, Xuejun Zhang, Zhonghua Zhang, Sen Chai","doi":"10.1093/plcell/koaf272","DOIUrl":"https://doi.org/10.1093/plcell/koaf272","url":null,"abstract":"Melon (Cucumis melo L.) is a globally important fruit crop, but progress in molecular breeding has been hampered by limited functional dissection of genes associated with agronomic traits. Therefore, we developed a comprehensive genome resource based on the C. melo ssp. agrestis accession 13C. This resource includes a complete telomere-to-telomere (T2T) genome assembly, including accurate quantification of 45S rDNA copy number in melon, a transcriptome atlas from 31 tissue samples, a phenotypically diverse EMS-induced mutant library and a stable transformation system. By sequencing 1,125 M₂ families, we identified about 660,000 variants, which cover 97.33% of the annotated gene space. Leveraging these integrated resources, we identified and functionally characterized several key genes, including CLAVATA3 INSENSITIVE RECEPTOR KINASES 2 (CmCIK2), which regulates carpel number; PARA-AMINOBENZOIC ACID SYNTHASE (CmACDS), a central regulator of folate biosynthesis; and a mutant allele of the known gynoecious gene WIP DOMAIN PROTEIN 1 (CmWIP1). In addition, we discovered a specific EMS-induced variant in the fruit ripening regulator CmNAC-NOR, and further validated its function by generating targeted mutants. The CmNAC-NOR mutants exhibited delayed fruit ripening, thus providing a valuable resource for improving ripening traits in agrestis accessions. To facilitate broader utilization, we developed the Melon Information Resource (MIR), available at https://zhanglab.qau.edu.cn/melon/index.php, an integrated platform housing 13C comprehensive genome resources and associated convenient analysis tools. This unified and accession-specific resource offers unprecedented opportunities to accelerate gene discovery and trait improvement in melon through functional genomics and molecular breeding.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Branching out: Increased specialization of young genes during seed maturation explained by new \"out of the seed\" hypothesis.","authors":"Julie Robinson","doi":"10.1093/plcell/koaf275","DOIUrl":"https://doi.org/10.1093/plcell/koaf275","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"182 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145499605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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