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Cervantes-Pérez SA, Zogli P, Amini S, Thibivilliers S, Tennant S, Hossain MS, Xu H, Meyer I, Nooka A, Ma P, Yao Q, Naldrett MJ, Farmer A, Martin O, Bhattacharya S, Kläver J, Libault M. Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process. PLANT COMMUNICATIONS 2024:100984. [PMID: 38845198 DOI: 10.1016/j.xplc.2024.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens-infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.
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Affiliation(s)
| | - Prince Zogli
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sahand Amini
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA
| | - Sandra Thibivilliers
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA
| | - Sutton Tennant
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA
| | - Md Sabbir Hossain
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA
| | - Hengping Xu
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA
| | - Ian Meyer
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Akash Nooka
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Pengchong Ma
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Qiuming Yao
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Olivier Martin
- INRAE, Université Paris-Saclay, Institut des Sciences des Plantes de Paris Saclay, IPS2, Batiment 630 Plateau du Moulon, Rue Noetzlin, 91192 Gif sur Yvette Cedex, France
| | | | | | - Marc Libault
- Division of Plant Science and Technology, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65211, USA; Interdisciplinary Plant Group of Missouri-Columbia, Columbia, MO 65211, USA.
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López-García CM, Ávila-Hernández CA, Quintana-Rodríguez E, Aguilar-Hernández V, Lozoya-Pérez NE, Rojas-Raya MA, Molina-Torres J, Araujo-León JA, Brito-Argáez L, González-Sánchez AA, Ramírez-Chávez E, Orona-Tamayo D. Extracellular Self- and Non-Self DNA Involved in Damage Recognition in the Mistletoe Parasitism of Mesquite Trees. Int J Mol Sci 2023; 25:457. [PMID: 38203628 PMCID: PMC10778891 DOI: 10.3390/ijms25010457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/16/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Psittacanthus calyculatus parasitizes mesquite trees through a specialized structure called a haustorium, which, in the intrusive process, can cause cellular damage in the host tree and release DAMPs, such as ATP, sugars, RNA, and DNA. These are highly conserved molecules that primarily function as signals that trigger and activate the defense responses. In the present study, we generate extracellular DNA (exDNA) from mesquite (P. laevigata) tree leaves (self-exDNA) and P. calyculatus (non-self exDNA) mistletoe as DAMP sources to examine mesquite trees' capacity to identify specific self or non-self exDNA. We determined that mesquite trees perceive self- and non-self exDNA with the synthesis of O2•-, H2O2, flavonoids, ROS-enzymes system, MAPKs activation, spatial concentrations of JA, SA, ABA, and CKs, and auxins. Our data indicate that self and non-self exDNA application differs in oxidative burst, JA signaling, MAPK gene expression, and scavenger systems. This is the first study to examine the molecular biochemistry effects in a host tree using exDNA sources derived from a mistletoe.
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Affiliation(s)
- Claudia Marina López-García
- Medio Ambiente y Biotecnología, Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), León 37545, Guanajuato, Mexico; (C.M.L.-G.)
| | - César Alejandro Ávila-Hernández
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Instituto Politécnico Nacional, Irapuato 36821, Guanajuato, Mexico; (C.A.Á.-H.); (M.A.R.-R.); (E.R.-C.)
| | - Elizabeth Quintana-Rodríguez
- Medio Ambiente y Biotecnología, Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), León 37545, Guanajuato, Mexico; (C.M.L.-G.)
| | - Víctor Aguilar-Hernández
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán (CICY), Mérida 97205, Yucatán, Mexico (J.A.A.-L.)
| | - Nancy Edith Lozoya-Pérez
- Medio Ambiente y Biotecnología, Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), León 37545, Guanajuato, Mexico; (C.M.L.-G.)
| | - Mariana Atzhiry Rojas-Raya
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Instituto Politécnico Nacional, Irapuato 36821, Guanajuato, Mexico; (C.A.Á.-H.); (M.A.R.-R.); (E.R.-C.)
| | - Jorge Molina-Torres
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Instituto Politécnico Nacional, Irapuato 36821, Guanajuato, Mexico; (C.A.Á.-H.); (M.A.R.-R.); (E.R.-C.)
| | - Jesús Alfredo Araujo-León
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán (CICY), Mérida 97205, Yucatán, Mexico (J.A.A.-L.)
| | - Ligia Brito-Argáez
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán (CICY), Mérida 97205, Yucatán, Mexico (J.A.A.-L.)
| | | | - Enrique Ramírez-Chávez
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Instituto Politécnico Nacional, Irapuato 36821, Guanajuato, Mexico; (C.A.Á.-H.); (M.A.R.-R.); (E.R.-C.)
| | - Domancar Orona-Tamayo
- Medio Ambiente y Biotecnología, Centro de Innovación Aplicada en Tecnologías Competitivas (CIATEC), León 37545, Guanajuato, Mexico; (C.M.L.-G.)
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