Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment
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TL;DR: In central infected zone of nodule, it is found that uninfected cells specialize into functionally distinct sub-groups during nodule development and revealed a transitional subtype of infected cells with enriched nodulation-related genes.
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Abstract: Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zone of nodule, we found that uninfected cells specialize into functionally distinct sub-groups during nodule development and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.
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Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security?
Min-Yao Jhu,Giles E. D. Oldroyd +1 more
TL;DR: In this paper , the root nodule symbiosis from legumes to other crops is explored and future research directions that might help to overcome the barrier of achieving self-fertilising crops are highlighted.
Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.
Carolin Grones,Thomas Eekhout,Dongbo Shi,Manuel Neumann,L. S. Berg,Yuji Ke,Rachel Shahan,Kevin L. Cox,Fabio Gomez-Cano,Hilde Nelissen,Jan U. Lohmann,Stefania Giacomello,Olivier C. Martin,Benjamin Cole,Jia-Wei Wang,Kerstin Kaufmann,Michael T. Raissig,Gergo Palfalvi,Thomas Greb,Marc Libault,Bert De Rybel +20 more
TL;DR: Common challenges associated with the use of single-cell transcriptomics in plants are discussed and general guidelines to improve reproducibility, quality, comparability, and interpretation are proposed to make the data readily available to the community in this fast-developing field of research.
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Recent progresses in plant single-cell transcriptomics
Dihuai Zheng,Jiwei Xu,Yaqian Lu,Hongyu Chen,Qinjie Chu,Longjiang Fan +5 more
TL;DR: Recent advances in single-cell transcriptomics reveal a new plant cell landscape, with high-throughput sequencing technologies applied in multiple tissues, highlighting advantages and weaknesses of scRNA, scATAC, and spatial transcriptome sequencing approaches.
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Deep generative modeling for single-cell transcriptomics.
TL;DR: Single-cell variational inference (scVI) is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.
Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation
Sonali Roy,Wei Liu,Raja Sekhar Nandety,Ashley D. Crook,Kirankumar S. Mysore,Catalina I. Pislariu,Julia Frugoli,Rebecca Dickstein,Michael K. Udvardi +8 more
TL;DR: This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean).
Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection
Marc Libault,Andrew Farmer,Laurent Brechenmacher,Jenny Drnevich,Raymond J. Langley,Damla D. Bilgin,Osman Radwan,David J. Neece,Steven J. Clough,Gregory D. May,Gary Stacey +10 more
TL;DR: A large-scale transcriptome analysis of B. japonicum-inoculated and mock- inoculated soybean root hairs identified genes involved in root hair cell infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN.
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Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula.
Jeremy D. Murray,Rajasekhara Reddy Duvvuru Muni,Ivone Torres-Jerez,Yuhong Tang,Stacy N. Allen,Megan Andriankaja,Guangming Li,Ashverya Laxmi,Xiaofei Cheng,Jiangqi Wen,David Vaughan,Michael Schultze,Jongho Sun,Myriam Charpentier,Giles E. D. Oldroyd,Million Tadege,Pascal Ratet,Kirankumar S. Mysore,Rujin Chen,Michael K. Udvardi +19 more
TL;DR: It is shown by analyses of mutants that the Vapyrin (VPY) gene is also required for rhizobial colonization and nodulation, and elevation of VPY transcripts upon application of Nod factors indicates that VPY acts downstream of the common signalling pathway.
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A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants
Uwe Ohler,Sam H Jiang +1 more
TL;DR: In this article , an organ-scale atlas of gene expression dynamics across root cell types and developmental time was built to investigate the spatiotemporal transcriptional signatures underlying developmental trajectories.
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