Pub Date : 2024-10-11DOI: 10.1038/s41477-024-01820-x
Zhao Zhang, Tuo Yang, Yang Liu, Shan Wu, Honghe Sun, Jie Wu, Yonghong Li, Yi Zheng, Haoran Ren, Yuyong Yang, Shaochuan Shi, Wenyan Wang, Qi Pan, Lijuan Lian, Shaowen Duan, Yingxiong Zhu, Youming Cai, Hougao Zhou, Hao Zhang, Kaixue Tang, Jiaopeng Cui, Dan Gao, Liyang Chen, Yunhe Jiang, Xiaoming Sun, Xiaofeng Zhou, Zhangjun Fei, Nan Ma, Junping Gao
Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida ‘Samantha’ (‘JACmantha’) and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of ‘Samantha’ exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis ‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement. The haplotype-resolved genome of tetraploid modern rose, along with a variation map of 233 wild and cultivated Rosa accessions, reveals the complex genome composition of modern roses and elucidates the genomic bases of their origin and breeding.
{"title":"Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose","authors":"Zhao Zhang, Tuo Yang, Yang Liu, Shan Wu, Honghe Sun, Jie Wu, Yonghong Li, Yi Zheng, Haoran Ren, Yuyong Yang, Shaochuan Shi, Wenyan Wang, Qi Pan, Lijuan Lian, Shaowen Duan, Yingxiong Zhu, Youming Cai, Hougao Zhou, Hao Zhang, Kaixue Tang, Jiaopeng Cui, Dan Gao, Liyang Chen, Yunhe Jiang, Xiaoming Sun, Xiaofeng Zhou, Zhangjun Fei, Nan Ma, Junping Gao","doi":"10.1038/s41477-024-01820-x","DOIUrl":"10.1038/s41477-024-01820-x","url":null,"abstract":"Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida ‘Samantha’ (‘JACmantha’) and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of ‘Samantha’ exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis ‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement. The haplotype-resolved genome of tetraploid modern rose, along with a variation map of 233 wild and cultivated Rosa accessions, reveals the complex genome composition of modern roses and elucidates the genomic bases of their origin and breeding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1659-1671"},"PeriodicalIF":15.8,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-10DOI: 10.1038/s41477-024-01837-2
Guillaume Tena
{"title":"Translation and cytokinin for robust shapes","authors":"Guillaume Tena","doi":"10.1038/s41477-024-01837-2","DOIUrl":"10.1038/s41477-024-01837-2","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1440-1440"},"PeriodicalIF":15.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142397714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1038/s41477-024-01817-6
Xinya Du, Pengyue Li, Changqiu Fan, Jingjing Tian, Yang Lin, Jiatao Xie, Jiasen Cheng, Yanping Fu, Daohong Jiang, Meng Yuan, Xiao Yu, Kenichi Tsuda, Bo Li
A biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanisms of phytobacterial biofilm are still obscure. Here we found that the protein Ralstonia solanacearum resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by controlling systemic movement in tomato xylem. RuvC protein accumulates at the later stage of biofilm development and specifically targets Holliday junction (HJ)-like structures to disrupt the biofilm extracellular DNA (eDNA) lattice, thus facilitating biofilm dispersal. Recombinant RuvC protein can resolve extracellular HJ to prevent bacterial biofilm formation. Heterologous expression of R. solanacearum or Xanthomonas oryzae pv. oryzae RuvC with plant secretion signal in tomato or rice confers resistance to bacterial wilt or bacterial blight disease, respectively. Plant chloroplast-localized HJ resolvase monokaryotic chloroplast 1 (MOC1), which shares structural similarity with bacterial RuvC, shows a strong inhibitory effect on bacterial biofilm formation. Relocalization of SlMOC1 to apoplast in tomato roots leads to increased resistance to bacterial wilt. Our novel finding reveals a critical pathogenesis mechanism of R. solanacearum and provides an efficient biotechnology strategy to improve plant resistance to bacterial vascular disease. The bacterial pathogen Ralstonia solanacearum secretes endonuclease RuvC, which degrades mature biofilm by targeting the lattice formed by cruciform extracellular DNA. This helps bacterial dispersal, pathogen spread in plant xylem and virulence.
生物膜生活方式对于细菌病原体在动植物中定植并保护自身免受宿主免疫和抗菌化学物质的侵害至关重要。植物细菌生物膜的形成和调控机制尚不清楚。在这里，我们发现 Ralstonia solanacearum 对紫外线 C 的抗性蛋白（RuvC）在生物膜中含量很高，并通过控制番茄木质部的系统运动来正向调节致病性。RuvC 蛋白在生物膜发育后期积累，并特异性地靶向霍利迪接合点（HJ）样结构，破坏生物膜胞外 DNA（eDNA）晶格，从而促进生物膜的扩散。重组 RuvC 蛋白可解决细胞外 HJ 问题，防止细菌形成生物膜。在番茄或水稻中异源表达带有植物分泌信号的 R. solanacearum 或 Xanthomonas oryzae pv. oryzae RuvC，可分别获得对细菌枯萎病或细菌性疫病的抗性。植物叶绿体定位的 HJ 分解酶单核叶绿体 1（MOC1）与细菌 RuvC 结构相似，对细菌生物膜的形成有很强的抑制作用。将 SlMOC1 重新定位到番茄根的细胞外质可增强对细菌枯萎病的抵抗力。我们的新发现揭示了 R. solanacearum 的关键致病机制，为提高植物对细菌性维管束病害的抗性提供了一种有效的生物技术策略。
{"title":"Holliday junction resolvase RuvC targets biofilm eDNA and confers plant resistance to vascular pathogens","authors":"Xinya Du, Pengyue Li, Changqiu Fan, Jingjing Tian, Yang Lin, Jiatao Xie, Jiasen Cheng, Yanping Fu, Daohong Jiang, Meng Yuan, Xiao Yu, Kenichi Tsuda, Bo Li","doi":"10.1038/s41477-024-01817-6","DOIUrl":"10.1038/s41477-024-01817-6","url":null,"abstract":"A biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanisms of phytobacterial biofilm are still obscure. Here we found that the protein Ralstonia solanacearum resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by controlling systemic movement in tomato xylem. RuvC protein accumulates at the later stage of biofilm development and specifically targets Holliday junction (HJ)-like structures to disrupt the biofilm extracellular DNA (eDNA) lattice, thus facilitating biofilm dispersal. Recombinant RuvC protein can resolve extracellular HJ to prevent bacterial biofilm formation. Heterologous expression of R. solanacearum or Xanthomonas oryzae pv. oryzae RuvC with plant secretion signal in tomato or rice confers resistance to bacterial wilt or bacterial blight disease, respectively. Plant chloroplast-localized HJ resolvase monokaryotic chloroplast 1 (MOC1), which shares structural similarity with bacterial RuvC, shows a strong inhibitory effect on bacterial biofilm formation. Relocalization of SlMOC1 to apoplast in tomato roots leads to increased resistance to bacterial wilt. Our novel finding reveals a critical pathogenesis mechanism of R. solanacearum and provides an efficient biotechnology strategy to improve plant resistance to bacterial vascular disease. The bacterial pathogen Ralstonia solanacearum secretes endonuclease RuvC, which degrades mature biofilm by targeting the lattice formed by cruciform extracellular DNA. This helps bacterial dispersal, pathogen spread in plant xylem and virulence.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1710-1723"},"PeriodicalIF":15.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1038/s41477-024-01816-7
Our extensive, multi-year regional study reveals that prolonged exposure to heavy wildfire smoke results in significant and persistent reductions in non-structural carbohydrates in trees, and that these effects continue for months following the fires (including into the dormancy period and next season’s bloom). Furthermore, trees that are subjected to high levels of smoke exhibit substantial yield reductions in the following year.
{"title":"Wildfire smoke exposure reduces tree carbon reserves and yield","authors":"","doi":"10.1038/s41477-024-01816-7","DOIUrl":"10.1038/s41477-024-01816-7","url":null,"abstract":"Our extensive, multi-year regional study reveals that prolonged exposure to heavy wildfire smoke results in significant and persistent reductions in non-structural carbohydrates in trees, and that these effects continue for months following the fires (including into the dormancy period and next season’s bloom). Furthermore, trees that are subjected to high levels of smoke exhibit substantial yield reductions in the following year.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1623-1624"},"PeriodicalIF":15.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1038/s41477-024-01813-w
By studying the structure and function of a protein from the green alga Chlorella that drives phase separation of Rubisco, we revealed the protein’s ability to interact with Rubiscos from plants. This overcomes a major challenge in adding pyrenoids, which are carbon-fixing superchargers, to crops.
{"title":"Algal pyrenoid protein can condense plant Rubiscos: a step towards boosting carbon fixation in crops","authors":"","doi":"10.1038/s41477-024-01813-w","DOIUrl":"10.1038/s41477-024-01813-w","url":null,"abstract":"By studying the structure and function of a protein from the green alga Chlorella that drives phase separation of Rubisco, we revealed the protein’s ability to interact with Rubiscos from plants. This overcomes a major challenge in adding pyrenoids, which are carbon-fixing superchargers, to crops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1625-1626"},"PeriodicalIF":15.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1038/s41477-024-01812-x
James Barrett, Mihris I. S. Naduthodi, Yuwei Mao, Clément Dégut, Sabina Musiał, Aidan Salter, Mark C. Leake, Michael J. Plevin, Alistair J. McCormick, James N. Blaza, Luke C. M. Mackinder
CO2 fixation is commonly limited by inefficiency of the CO2-fixing enzyme Rubisco. Eukaryotic algae concentrate and fix CO2 in phase-separated condensates called pyrenoids, which complete up to one-third of global CO2 fixation. Condensation of Rubisco in pyrenoids is dependent on interaction with disordered linker proteins that show little conservation between species. We developed a sequence-independent bioinformatic pipeline to identify linker proteins in green algae. We report the linker from Chlorella and demonstrate that it binds a conserved site on the Rubisco large subunit. We show that the Chlorella linker phase separates Chlamydomonas Rubisco and that despite their separation by ~800 million years of evolution, the Chlorella linker can support the formation of a functional pyrenoid in Chlamydomonas. This cross-species reactivity extends to plants, with the Chlorella linker able to drive condensation of some native plant Rubiscos in vitro and in planta. Our results represent an exciting frontier for pyrenoid engineering in plants, which is modelled to increase crop yields. Barrett et al. identify a key Rubisco phase-separating protein in the CO2-fixing pyrenoid of Chlorella algae. This protein’s broad promiscuity for green lineage Rubiscos may aid in engineering CO2-supercharging pyrenoids in plants to boost yields.
{"title":"A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage","authors":"James Barrett, Mihris I. S. Naduthodi, Yuwei Mao, Clément Dégut, Sabina Musiał, Aidan Salter, Mark C. Leake, Michael J. Plevin, Alistair J. McCormick, James N. Blaza, Luke C. M. Mackinder","doi":"10.1038/s41477-024-01812-x","DOIUrl":"10.1038/s41477-024-01812-x","url":null,"abstract":"CO2 fixation is commonly limited by inefficiency of the CO2-fixing enzyme Rubisco. Eukaryotic algae concentrate and fix CO2 in phase-separated condensates called pyrenoids, which complete up to one-third of global CO2 fixation. Condensation of Rubisco in pyrenoids is dependent on interaction with disordered linker proteins that show little conservation between species. We developed a sequence-independent bioinformatic pipeline to identify linker proteins in green algae. We report the linker from Chlorella and demonstrate that it binds a conserved site on the Rubisco large subunit. We show that the Chlorella linker phase separates Chlamydomonas Rubisco and that despite their separation by ~800 million years of evolution, the Chlorella linker can support the formation of a functional pyrenoid in Chlamydomonas. This cross-species reactivity extends to plants, with the Chlorella linker able to drive condensation of some native plant Rubiscos in vitro and in planta. Our results represent an exciting frontier for pyrenoid engineering in plants, which is modelled to increase crop yields. Barrett et al. identify a key Rubisco phase-separating protein in the CO2-fixing pyrenoid of Chlorella algae. This protein’s broad promiscuity for green lineage Rubiscos may aid in engineering CO2-supercharging pyrenoids in plants to boost yields.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 11","pages":"1801-1813"},"PeriodicalIF":15.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01812-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-08DOI: 10.1038/s41477-024-01835-4
Catherine Walker
{"title":"Global impacts of the European Green Deal","authors":"Catherine Walker","doi":"10.1038/s41477-024-01835-4","DOIUrl":"10.1038/s41477-024-01835-4","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1439-1439"},"PeriodicalIF":15.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-08DOI: 10.1038/s41477-024-01822-9
The secondary structure of pri-miRNAs determines the efficiency and accuracy of miRNA production. RNA helicase Brr2a, a key component of spliceosomes in Arabidopsis, can interact with the pri-miRNA processing machinery component HYL1 and fine-tune the structures of pri-miRNAs to enhance miRNA production, whether the pri-miRNAs contain introns or not.
{"title":"The spliceosome factor and RNA helicase Brr2a moonlights in miRNA production","authors":"","doi":"10.1038/s41477-024-01822-9","DOIUrl":"10.1038/s41477-024-01822-9","url":null,"abstract":"The secondary structure of pri-miRNAs determines the efficiency and accuracy of miRNA production. RNA helicase Brr2a, a key component of spliceosomes in Arabidopsis, can interact with the pri-miRNA processing machinery component HYL1 and fine-tune the structures of pri-miRNAs to enhance miRNA production, whether the pri-miRNAs contain introns or not.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1444-1445"},"PeriodicalIF":15.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-04DOI: 10.1038/s41477-024-01799-5
Xiner Chen, Yuxiu Li, Man Liu, Gongli Ai, Xian Zhang, Jiafa Wang, Shujuan Tian, Li Yuan
Seedless watermelon production relies on triploid cultivation or the application of plant growth regulators. However, challenges such as chromosomal imbalances in triploid varieties and concerns about food safety with growth regulator application impede progress. To tackle these challenges, we developed a sexually and vegetatively reproducible inducer line of diploid seedless watermelon by disrupting the double fertilization process. This innovative approach has enabled the successful induction of diploid seedless watermelon across diverse varieties. A study developed a universal seedless watermelon inducer line using CRISPR/Cas9 to knock out the HAP2 gene, simplifying the breeding process and addressing food safety concerns. This method may also apply to other crops such as cherries or grapes.
{"title":"A sexually and vegetatively reproducible diploid seedless watermelon inducer via ClHAP2 mutation","authors":"Xiner Chen, Yuxiu Li, Man Liu, Gongli Ai, Xian Zhang, Jiafa Wang, Shujuan Tian, Li Yuan","doi":"10.1038/s41477-024-01799-5","DOIUrl":"10.1038/s41477-024-01799-5","url":null,"abstract":"Seedless watermelon production relies on triploid cultivation or the application of plant growth regulators. However, challenges such as chromosomal imbalances in triploid varieties and concerns about food safety with growth regulator application impede progress. To tackle these challenges, we developed a sexually and vegetatively reproducible inducer line of diploid seedless watermelon by disrupting the double fertilization process. This innovative approach has enabled the successful induction of diploid seedless watermelon across diverse varieties. A study developed a universal seedless watermelon inducer line using CRISPR/Cas9 to knock out the HAP2 gene, simplifying the breeding process and addressing food safety concerns. This method may also apply to other crops such as cherries or grapes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 10","pages":"1446-1452"},"PeriodicalIF":15.8,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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