Pub Date : 2024-06-27DOI: 10.1038/s41477-024-01738-4
Michael John Passalacqua, Jesse Gillis
Single-cell RNA sequencing is increasingly used to investigate cross-species differences driven by gene expression and cell-type composition in plants. However, the frequent expansion of plant gene families due to whole-genome duplications makes identification of one-to-one orthologues difficult, complicating integration. Here we demonstrate that coexpression can be used to trim many-to-many orthology families down to identify one-to-one gene pairs with proxy expression profiles, improving the performance of traditional integration methods and reducing barriers to integration across a diverse array of plant species. To enhance cross-species single-cell analysis, the authors find gene pairs with similar expression patterns across 13 species. These coexpression proxies serve as common features in datasets, improving integrative and comparative cell-type analysis.
{"title":"Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species","authors":"Michael John Passalacqua, Jesse Gillis","doi":"10.1038/s41477-024-01738-4","DOIUrl":"10.1038/s41477-024-01738-4","url":null,"abstract":"Single-cell RNA sequencing is increasingly used to investigate cross-species differences driven by gene expression and cell-type composition in plants. However, the frequent expansion of plant gene families due to whole-genome duplications makes identification of one-to-one orthologues difficult, complicating integration. Here we demonstrate that coexpression can be used to trim many-to-many orthology families down to identify one-to-one gene pairs with proxy expression profiles, improving the performance of traditional integration methods and reducing barriers to integration across a diverse array of plant species. To enhance cross-species single-cell analysis, the authors find gene pairs with similar expression patterns across 13 species. These coexpression proxies serve as common features in datasets, improving integrative and comparative cell-type analysis.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01738-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461797","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}
MicroRNAs (miRNAs) are produced from highly structured primary transcripts (pri-miRNAs) and regulate numerous biological processes in eukaryotes. Due to the extreme heterogeneity of these structures, the initial processing sites of plant pri-miRNAs and the structural rules that determine their processing have been predicted for many miRNAs but remain elusive for others. Here we used semi-active DCL1 mutants and advanced degradome-sequencing strategies to accurately identify the initial processing sites for 147 of 326 previously annotated Arabidopsis miRNAs and to illustrate their associated pri-miRNA cleavage patterns. Elucidating the in vivo RNA secondary structures of 73 pri-miRNAs revealed that about 95% of them differ from in silico predictions, and that the revised structures offer clearer interpretation of the processing sites and patterns. Finally, DCL1 partners Serrate and HYL1 could synergistically and independently impact processing patterns and in vivo RNA secondary structures of pri-miRNAs. Together, our work sheds light on the precise processing mechanisms of plant pri-miRNAs. Parallel degradome sequencing and DMS-MaPseq pinpoint the first cleavage sites on bona fide pri-miRNAs, decode their in vivo structure and provide better interpretation of the cleavage modes and impact of DCL1 cofactors in the process in Arabidopsis.
{"title":"Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis","authors":"Xingxing Yan, Changhao Li, Kaiye Liu, Tianru Zhang, Qian Xu, Xindi Li, Jiaying Zhu, Ziying Wang, Anikah Yusuf, Shuqing Cao, Xu Peng, James J. Cai, Xiuren Zhang","doi":"10.1038/s41477-024-01725-9","DOIUrl":"10.1038/s41477-024-01725-9","url":null,"abstract":"MicroRNAs (miRNAs) are produced from highly structured primary transcripts (pri-miRNAs) and regulate numerous biological processes in eukaryotes. Due to the extreme heterogeneity of these structures, the initial processing sites of plant pri-miRNAs and the structural rules that determine their processing have been predicted for many miRNAs but remain elusive for others. Here we used semi-active DCL1 mutants and advanced degradome-sequencing strategies to accurately identify the initial processing sites for 147 of 326 previously annotated Arabidopsis miRNAs and to illustrate their associated pri-miRNA cleavage patterns. Elucidating the in vivo RNA secondary structures of 73 pri-miRNAs revealed that about 95% of them differ from in silico predictions, and that the revised structures offer clearer interpretation of the processing sites and patterns. Finally, DCL1 partners Serrate and HYL1 could synergistically and independently impact processing patterns and in vivo RNA secondary structures of pri-miRNAs. Together, our work sheds light on the precise processing mechanisms of plant pri-miRNAs. Parallel degradome sequencing and DMS-MaPseq pinpoint the first cleavage sites on bona fide pri-miRNAs, decode their in vivo structure and provide better interpretation of the cleavage modes and impact of DCL1 cofactors in the process in Arabidopsis.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141448325","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 : 2024-06-21DOI: 10.1038/s41477-024-01729-5
Rose A. Marks, Llewelyn Van Der Pas, Jenny Schuster, Ian S. Gilman, Robert VanBuren
Desiccation tolerance has evolved repeatedly in plants as an adaptation to survive extreme environments. Plants use similar biophysical and cellular mechanisms to survive life without water, but convergence at the molecular, gene and regulatory levels remains to be tested. Here we explore the evolutionary mechanisms underlying the recurrent evolution of desiccation tolerance across grasses. We observed substantial convergence in gene duplication and expression patterns associated with desiccation. Syntenic genes of shared origin are activated across species, indicative of parallel evolution. In other cases, similar metabolic pathways are induced but using different gene sets, pointing towards phenotypic convergence. Species-specific mechanisms supplement these shared core mechanisms, underlining the complexity and diversity of evolutionary adaptations to drought. Our findings provide insight into the evolutionary processes driving desiccation tolerance and highlight the roles of parallel and convergent evolution in response to environmental challenges. Marks et al. explore the repeated evolution of desiccation tolerance in grasses. Their analysis of diverse resurrection grasses reveals significant genetic convergence and parallel evolution, suggesting a shared foundation for adapting to extreme drought.
{"title":"Convergent evolution of desiccation tolerance in grasses","authors":"Rose A. Marks, Llewelyn Van Der Pas, Jenny Schuster, Ian S. Gilman, Robert VanBuren","doi":"10.1038/s41477-024-01729-5","DOIUrl":"10.1038/s41477-024-01729-5","url":null,"abstract":"Desiccation tolerance has evolved repeatedly in plants as an adaptation to survive extreme environments. Plants use similar biophysical and cellular mechanisms to survive life without water, but convergence at the molecular, gene and regulatory levels remains to be tested. Here we explore the evolutionary mechanisms underlying the recurrent evolution of desiccation tolerance across grasses. We observed substantial convergence in gene duplication and expression patterns associated with desiccation. Syntenic genes of shared origin are activated across species, indicative of parallel evolution. In other cases, similar metabolic pathways are induced but using different gene sets, pointing towards phenotypic convergence. Species-specific mechanisms supplement these shared core mechanisms, underlining the complexity and diversity of evolutionary adaptations to drought. Our findings provide insight into the evolutionary processes driving desiccation tolerance and highlight the roles of parallel and convergent evolution in response to environmental challenges. Marks et al. explore the repeated evolution of desiccation tolerance in grasses. Their analysis of diverse resurrection grasses reveals significant genetic convergence and parallel evolution, suggesting a shared foundation for adapting to extreme drought.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141435847","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 : 2024-06-21DOI: 10.1038/s41477-024-01733-9
Technological advances have demonstrated the possibility of chemical synthesis of a multicellular plant genome. What does this mean for humans and how should we prepare for this breakthrough?
{"title":"Synthetic moss","authors":"","doi":"10.1038/s41477-024-01733-9","DOIUrl":"10.1038/s41477-024-01733-9","url":null,"abstract":"Technological advances have demonstrated the possibility of chemical synthesis of a multicellular plant genome. What does this mean for humans and how should we prepare for this breakthrough?","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01733-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437255","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 : 2024-06-19DOI: 10.1038/s41477-024-01718-8
Tom O’Hara, Andrew Steed, Rachel Goddard, Kumar Gaurav, Sanu Arora, Jesús Quiroz-Chávez, Ricardo Ramírez-González, Roshani Badgami, David Gilbert, Javier Sánchez-Martín, Luzie Wingen, Cong Feng, Mei Jiang, Shifeng Cheng, Susanne Dreisigacker, Beat Keller, Brande B. H. Wulff, Cristóbal Uauy, Paul Nicholson
Wheat blast, caused by the fungus Magnaporthe oryzae, threatens global cereal production since its emergence in Brazil in 1985 and recently spread to Bangladesh and Zambia. Here we demonstrate that the AVR-Rmg8 effector, common in wheat-infecting isolates, is recognized by the gene Pm4, previously shown to confer resistance to specific races of Blumeria graminis f. sp. tritici, the cause of powdery mildew of wheat. We show that Pm4 alleles differ in their recognition of different AVR-Rmg8 alleles, and some confer resistance only in seedling leaves but not spikes, making it important to select for those alleles that function in both tissues. This study has identified a gene recognizing an important virulence factor present in wheat blast isolates in Bangladesh and Zambia and represents an important first step towards developing durably resistant wheat cultivars for these regions. The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast carrying the effector AVR-Rmg8. The authors propose the Pm4f allele as the most effective allele to deploy in Bangladesh and Zambia.
{"title":"The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast","authors":"Tom O’Hara, Andrew Steed, Rachel Goddard, Kumar Gaurav, Sanu Arora, Jesús Quiroz-Chávez, Ricardo Ramírez-González, Roshani Badgami, David Gilbert, Javier Sánchez-Martín, Luzie Wingen, Cong Feng, Mei Jiang, Shifeng Cheng, Susanne Dreisigacker, Beat Keller, Brande B. H. Wulff, Cristóbal Uauy, Paul Nicholson","doi":"10.1038/s41477-024-01718-8","DOIUrl":"10.1038/s41477-024-01718-8","url":null,"abstract":"Wheat blast, caused by the fungus Magnaporthe oryzae, threatens global cereal production since its emergence in Brazil in 1985 and recently spread to Bangladesh and Zambia. Here we demonstrate that the AVR-Rmg8 effector, common in wheat-infecting isolates, is recognized by the gene Pm4, previously shown to confer resistance to specific races of Blumeria graminis f. sp. tritici, the cause of powdery mildew of wheat. We show that Pm4 alleles differ in their recognition of different AVR-Rmg8 alleles, and some confer resistance only in seedling leaves but not spikes, making it important to select for those alleles that function in both tissues. This study has identified a gene recognizing an important virulence factor present in wheat blast isolates in Bangladesh and Zambia and represents an important first step towards developing durably resistant wheat cultivars for these regions. The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast carrying the effector AVR-Rmg8. The authors propose the Pm4f allele as the most effective allele to deploy in Bangladesh and Zambia.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01718-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425297","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}
Wheat blast, a devastating disease having spread recently from South America to Asia and Africa, is caused by Pyricularia oryzae (synonym of Magnaporthe oryzae) pathotype Triticum, which first emerged in Brazil in 1985. Rmg8 and Rmg7, genes for resistance to wheat blast found in common wheat and tetraploid wheat, respectively, recognize the same avirulence gene, AVR-Rmg8. Here we show that an ancestral resistance gene, which had obtained an ability to recognize AVR-Rmg8 before the differentiation of Triticum and Aegilops, has expanded its target pathogens. Molecular cloning revealed that Rmg7 was an allele of Pm4, a gene for resistance to wheat powdery mildew on 2AL, whereas Rmg8 was its homoeologue on 2BL ineffective against wheat powdery mildew. Rmg8 variants with the ability to recognize AVR-Rmg8 were distributed not only in Triticum spp. but also in Aegilops speltoides, Aegilops umbellulata and Aegilops comosa. This result suggests that the origin of resistance gene(s) recognizing AVR-Rmg8 dates back to the time before differentiation of A, B, S, U and M genomes, that is, ~5 Myr before the emergence of its current target, the wheat blast fungus. Phylogenetic analyses suggested that, in the evolutionary process thereafter, some of their variants gained the ability to recognize the wheat powdery mildew fungus and evolved into genes controlling dual resistance to wheat powdery mildew and wheat blast. Rmg8 and Rmg7, genes for resistance to wheat blast, proved to be a homoeologue and an allele of Pm4, a gene for resistance to powdery mildew. Their functional homologues were also found in Aegilops spp., suggesting that their origin dates back to the time before differentiation of Triticum and Aegilops.
{"title":"Evolution of wheat blast resistance gene Rmg8 accompanied by differentiation of variants recognizing the powdery mildew fungus","authors":"Soichiro Asuke, Kohei Morita, Motoki Shimizu, Fumitaka Abe, Ryohei Terauchi, Chika Nago, Yoshino Takahashi, Mai Shibata, Motohiro Yoshioka, Mizuki Iwakawa, Mitsuko Kishi-Kaboshi, Zhuo Su, Shuhei Nasuda, Hirokazu Handa, Masaya Fujita, Makoto Tougou, Koichi Hatta, Naoki Mori, Yoshihiro Matsuoka, Kenji Kato, Yukio Tosa","doi":"10.1038/s41477-024-01711-1","DOIUrl":"10.1038/s41477-024-01711-1","url":null,"abstract":"Wheat blast, a devastating disease having spread recently from South America to Asia and Africa, is caused by Pyricularia oryzae (synonym of Magnaporthe oryzae) pathotype Triticum, which first emerged in Brazil in 1985. Rmg8 and Rmg7, genes for resistance to wheat blast found in common wheat and tetraploid wheat, respectively, recognize the same avirulence gene, AVR-Rmg8. Here we show that an ancestral resistance gene, which had obtained an ability to recognize AVR-Rmg8 before the differentiation of Triticum and Aegilops, has expanded its target pathogens. Molecular cloning revealed that Rmg7 was an allele of Pm4, a gene for resistance to wheat powdery mildew on 2AL, whereas Rmg8 was its homoeologue on 2BL ineffective against wheat powdery mildew. Rmg8 variants with the ability to recognize AVR-Rmg8 were distributed not only in Triticum spp. but also in Aegilops speltoides, Aegilops umbellulata and Aegilops comosa. This result suggests that the origin of resistance gene(s) recognizing AVR-Rmg8 dates back to the time before differentiation of A, B, S, U and M genomes, that is, ~5 Myr before the emergence of its current target, the wheat blast fungus. Phylogenetic analyses suggested that, in the evolutionary process thereafter, some of their variants gained the ability to recognize the wheat powdery mildew fungus and evolved into genes controlling dual resistance to wheat powdery mildew and wheat blast. Rmg8 and Rmg7, genes for resistance to wheat blast, proved to be a homoeologue and an allele of Pm4, a gene for resistance to powdery mildew. Their functional homologues were also found in Aegilops spp., suggesting that their origin dates back to the time before differentiation of Triticum and Aegilops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425194","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 : 2024-06-19DOI: 10.1038/s41477-024-01690-3
Tofazzal Islam, Rojana Binte Azad
Characterization of Rmg8, the major resistance gene for wheat blast found in common wheat, brought a surprise: it is a variant of Pm4, a resistance gene for powdery mildew disease. Both genes recognize the AVR-Rmg8 gene of the wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT), which results in resistance against this pathogen. This discovery opens avenues for developing wheat varieties to combat wheat blast disease.
{"title":"Rmg8 gene against wheat blast","authors":"Tofazzal Islam, Rojana Binte Azad","doi":"10.1038/s41477-024-01690-3","DOIUrl":"10.1038/s41477-024-01690-3","url":null,"abstract":"Characterization of Rmg8, the major resistance gene for wheat blast found in common wheat, brought a surprise: it is a variant of Pm4, a resistance gene for powdery mildew disease. Both genes recognize the AVR-Rmg8 gene of the wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT), which results in resistance against this pathogen. This discovery opens avenues for developing wheat varieties to combat wheat blast disease.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425278","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 : 2024-06-17DOI: 10.1038/s41477-024-01701-3
Georg Oberhofer, Michelle L. Johnson, Tobin Ivy, Igor Antoshechkin, Bruce A. Hay
Gene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed. Gene drive elements spread linked traits and can be used to change the composition or fate of populations. Here Oberhofer and colleagues engineer gene drive in the plant Arabidopsis thaliana. Applications include genetic biocontrol and conservation.
{"title":"Cleave and Rescue gamete killers create conditions for gene drive in plants","authors":"Georg Oberhofer, Michelle L. Johnson, Tobin Ivy, Igor Antoshechkin, Bruce A. Hay","doi":"10.1038/s41477-024-01701-3","DOIUrl":"10.1038/s41477-024-01701-3","url":null,"abstract":"Gene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed. Gene drive elements spread linked traits and can be used to change the composition or fate of populations. Here Oberhofer and colleagues engineer gene drive in the plant Arabidopsis thaliana. Applications include genetic biocontrol and conservation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141333758","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：