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Luna-García V, Bernal Gallardo JJ, Rethoret-Pasty M, Pasha A, Provart NJ, de Folter S. A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. PLANT PHYSIOLOGY 2024; 195:410-429. [PMID: 38088205 DOI: 10.1093/plphys/kiad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 05/02/2024]
Abstract
Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.
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Affiliation(s)
- Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Judith Jazmin Bernal Gallardo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Martin Rethoret-Pasty
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
- Polytech Nice Sophia, Université Côte d'Azur, 930 Rte des Colles, 06410 Biot, France
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
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2
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Manrique S, Cavalleri A, Guazzotti A, Villarino GH, Simonini S, Bombarely A, Higashiyama T, Grossniklaus U, Mizzotti C, Pereira AM, Coimbra S, Sankaranarayanan S, Onelli E, Masiero S, Franks RG, Colombo L. HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation. PLANT PHYSIOLOGY 2024; 194:2117-2135. [PMID: 38060625 PMCID: PMC10980524 DOI: 10.1093/plphys/kiad629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/29/2023] [Indexed: 04/01/2024]
Abstract
The gynoecium is critical for the reproduction of flowering plants as it contains the ovules and the tissues that foster pollen germination, growth, and guidance. These tissues, known as the reproductive tract (ReT), comprise the stigma, style, and transmitting tract (TT). The ReT and ovules originate from the carpel margin meristem (CMM) within the pistil. SHOOT MERISTEMLESS (STM) is a key transcription factor for meristem formation and maintenance. In all above-ground meristems, including the CMM, local STM downregulation is required for organ formation. However, how this downregulation is achieved in the CMM is unknown. Here, we have studied the role of HISTONE DEACETYLASE 19 (HDA19) in Arabidopsis (Arabidopsis thaliana) during ovule and ReT differentiation based on the observation that the hda19-3 mutant displays a reduced ovule number and fails to differentiate the TT properly. Fluorescence-activated cell sorting coupled with RNA-sequencing revealed that in the CMM of hda19-3 mutants, genes promoting organ development are downregulated while meristematic markers, including STM, are upregulated. HDA19 was essential to downregulate STM in the CMM, thereby allowing ovule formation and TT differentiation. STM is ectopically expressed in hda19-3 at intermediate stages of pistil development, and its downregulation by RNA interference alleviated the hda19-3 phenotype. Chromatin immunoprecipitation assays indicated that STM is a direct target of HDA19 during pistil development and that the transcription factor SEEDSTICK is also required to regulate STM via histone acetylation. Thus, we identified factors required for the downregulation of STM in the CMM, which is necessary for organogenesis and tissue differentiation.
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Affiliation(s)
- Silvia Manrique
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Andrea Guazzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Gonzalo H Villarino
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Sara Simonini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Aureliano Bombarely
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Chiara Mizzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Ana Marta Pereira
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Silvia Coimbra
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Elisabetta Onelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Robert G Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
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3
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Rieu P, Beretta VM, Caselli F, Thévénon E, Lucas J, Rizk M, Franchini E, Caporali E, Paleni C, Nanao MH, Kater MM, Dumas R, Zubieta C, Parcy F, Gregis V. The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development. Proc Natl Acad Sci U S A 2024; 121:e2310464121. [PMID: 38412122 DOI: 10.1073/pnas.2310464121] [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: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 02/29/2024] Open
Abstract
The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | | | - Francesca Caselli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Emmanuel Thévénon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Mahmoud Rizk
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Chiara Paleni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Max H Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
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Zhao S, Rong J. Single-cell RNA-seq reveals a link of ovule abortion and sugar transport in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2024; 15:1274013. [PMID: 38371413 PMCID: PMC10869455 DOI: 10.3389/fpls.2024.1274013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Camellia oleifera is the most important woody oil crop in China. Seed number per fruit is an important yield trait in C. oleifera. Ovule abortion is generally observed in C. oleifera and significantly decreases the seed number per fruit. However, the mechanisms of ovule abortion remain poorly understood at present. Single-cell RNA sequencing (scRNA-seq) was performed using mature ovaries of two C. oleifera varieties with different ovule abortion rates (OARs). In total, 20,526 high-quality cells were obtained, and 18 putative cell clusters were identified. Six cell types including female gametophyte, protoxylem, protophloem, procambium, epidermis, and parenchyma cells were identified from three main tissue types of ovule, placenta, and pericarp inner layer. A comparative analysis on scRNA-seq data between high- and low-OAR varieties demonstrated that the overall expression of CoSWEET and CoCWINV in procambium cells, and CoSTP in the integument was significantly upregulated in the low-OAR variety. Both the infertile ovule before pollination and the abortion ovule producing after compatible pollination might be attributed to selective abortion caused by low sugar levels in the apoplast around procambium cells and a low capability of hexose uptake in the integument. Here, the first single-cell transcriptional landscape is reported in woody crop ovaries. Our investigation demonstrates that ovule abortion may be related to sugar transport in placenta and ovules and sheds light on further deciphering the mechanism of regulating sugar transport and the improvement of seed yield in C. oleifera.
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Affiliation(s)
- Songzi Zhao
- Jiangxi Province Key Laboratory of Camellia Germplasm Conservation and Utilization, Jiangxi Academy of Forestry, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
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5
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He S, Min Y, Liu Z, Zhi F, Ma R, Ge A, Wang S, Zhao Y, Peng D, Zhang D, Jin M, Song B, Wang J, Guo Y, Chen M. Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:121-142. [PMID: 38146678 DOI: 10.1111/jipb.13606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in seeds. Thus far, the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely unknown. Here, we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK (STK) and SEPALLATA3 (SEP3), which bridges several key genes to regulate oil accumulation in seeds. We found that STK, highly expressed in the developing embryo, positively regulates seed oil accumulation in Arabidopsis (Arabidopsis thaliana). Furthermore, we discovered that SEP3 physically interacts with STK in vivo and in vitro. Seed oil content is increased by the SEP3 mutation, while it is decreased by SEP3 overexpression. The chromatin immunoprecipitation, electrophoretic mobility shift assay, and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5, SEP3, and SEED FATTY ACID REDUCER 4 (SFAR4). Moreover, genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5, SEP3, and SFAR4. Additionally, we demonstrated that TRANSPARENT TESTA 8 (TT8) and ACYL-ACYL CARRIER PROTEIN DESATURASE 3 (AAD3) are direct targets of MYB5 during seed oil accumulation in Arabidopsis. Together, our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3, which fine tunes oil accumulation in seeds.
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Affiliation(s)
- Shuangcheng He
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yuanchang Min
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Zijin Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Fang Zhi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Rong Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Ankang Ge
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shixiang Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yu Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Danshuai Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Da Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Minshan Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Bo Song
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jianjun Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yuan Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Mingxun Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, College of Agronomy, Northwest A&F University, Yangling, 712100, China
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Ramos-Pulido J, de Folter S. Organogenic events during gynoecium and fruit development in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102440. [PMID: 37633079 DOI: 10.1016/j.pbi.2023.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 08/04/2023] [Indexed: 08/28/2023]
Abstract
Angiosperms are the most successful group of land plants. This success is mainly due to the gynoecium, the innermost whorl of the flower. In Arabidopsis, the gynoecium is a syncarpic structure formed by two congenitally fused carpels. At the fusion edges of the carpels, the carpel margin meristem forms. This quasi-meristem is important for medial-tissue development, including the ovules. After the double fertilization, both the seeds and fruit begin to develop. Due to the importance of seeds and fruits as major food sources worldwide, it has been an important task for the scientific community to study gynoecium development. In this review, we present the most recent advances in Arabidopsis gynoecium patterning, as well as some questions that remain unanswered.
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Affiliation(s)
- Juan Ramos-Pulido
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, Mexico.
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7
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Xu T, Liu Z, Zhan D, Pang Z, Zhang S, Li C, Kang X, Yang J. Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:117. [PMID: 37480079 PMCID: PMC10360242 DOI: 10.1186/s13068-023-02366-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Lignin is a major restriction factor for the industrial production of biomass resources, such as pulp and bioenergy. Eucalyptus is one of the most important sources of pulp and bioenergy. After polyploidization, the lignin content of forest trees is generally reduced, which is considered a beneficial genetic improvement. However, the differences in the lignin content between triploid and diploid Eucalyptus and the underlying regulatory mechanism are still unclear. RESULTS We conducted a comprehensive analysis at the phenotypic, transcriptional and metabolite levels between Eucalyptus urophylla triploids and diploids to reveal the effects of polyploidization on the lignin content and lignin metabolic pathway. The results showed that the lignin content of Eucalyptus urophylla triploid stems was significantly lower than that of diploids. Lignin-related metabolites were differentially accumulated between triploids and diploids, among which coniferaldehyde, p-coumaryl alcohol, sinapaldehyde and coniferyl alcohol had significant positive correlations with lignin content, indicating that they might be primarily contributing metabolites. Most lignin biosynthetic genes were significantly downregulated, among which 11 genes were significantly positively correlated with the lignin content and above metabolites. Furthermore, we constructed a co-expression network between lignin biosynthetic genes and transcription factors based on weighted gene co-expression network analysis. The network identified some putative orthologues of secondary cell wall (SCW)-related transcription factors, among which MYB52, MYB42, NAC076, and LBD15 were significantly downregulated in Eucalyptus urophylla triploids. In addition, potential important transcription factors, including HSL1, BEE3, HHO3, and NAC046, also had high degrees of connectivity and high edge weights with lignin biosynthetic genes, indicating that they might also be involved in the variation of lignin accumulation between triploid and diploid Eucalyptus urophylla. CONCLUSIONS The results demonstrated that some lignin-related metabolites, lignin biosynthetic genes and transcription factors in Eucalyptus urophylla triploids may be relatively sensitive in response to the polyploidization effect, significantly changing their expression levels, which ultimately correlated with the varied lignin content. The analysis of the underlying formation mechanism could provide beneficial information for the development and utilization of polyploid biomass resources, which will be also valuable for genetic improvement in other bioenergy plants.
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Affiliation(s)
- Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dingju Zhan
- Guangxi Bagui R&D Institute for Forest Tree and Flower Breeding, Nanning, 530025, China
| | - Zhenwu Pang
- Guangxi Bagui R&D Institute for Forest Tree and Flower Breeding, Nanning, 530025, China
| | - Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenhe Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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8
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Du Q, Wu Z, Liu P, Qing J, He F, Du L, Sun Z, Zhu L, Zheng H, Sun Z, Yang L, Wang L, Du H. The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1118363. [PMID: 37063180 PMCID: PMC10102601 DOI: 10.3389/fpls.2023.1118363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.
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Affiliation(s)
- Qingxin Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Zixian Wu
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Panfeng Liu
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Jun Qing
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Feng He
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Lanying Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Zhiqiang Sun
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Lili Zhu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Hongchu Zheng
- Product Department, Henan Jinduzhong Agricultural Science and Technology Co., Ltd., Yanling, China
| | - Zongyi Sun
- Operation Department, Grandomics Biosciences Co., Ltd., Wuhan, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Lu Wang
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
| | - Hongyan Du
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
- Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
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9
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Herrera-Ubaldo H, Campos SE, López-Gómez P, Luna-García V, Zúñiga-Mayo VM, Armas-Caballero GE, González-Aguilera KL, DeLuna A, Marsch-Martínez N, Espinosa-Soto C, de Folter S. The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis. MOLECULAR PLANT 2023; 16:260-278. [PMID: 36088536 DOI: 10.1016/j.molp.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. The gynoecium is the flower's female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. In this study, we used a systems biology approach to understand the formation of a complex reproductive unit-as the gynoecium-by mapping binary interactions between well-characterized TFs. We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. In addition, we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs. Furthermore, we analyzed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Taken together, all these results serve as a valuable resource for the plant community.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Sergio E Campos
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Pablo López-Gómez
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Víctor M Zúñiga-Mayo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Gerardo E Armas-Caballero
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Karla L González-Aguilera
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato 36824, México
| | - Carlos Espinosa-Soto
- Instituto de Física, Universidad de San Luis Potosí, San Luis Potosí, SLP 78290, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México.
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10
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Gao P, Qiu S, Ma X, Parkin IAP, Xiang D, Datla R. Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax. PLANTS 2022; 11:plants11152031. [PMID: 35956508 PMCID: PMC9370790 DOI: 10.3390/plants11152031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/24/2022] [Accepted: 07/30/2022] [Indexed: 11/16/2022]
Abstract
Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8, Canada
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Shuqing Qiu
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Xingliang Ma
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Isobel A. P. Parkin
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
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11
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Li C, Cai X, Shen Q, Chen X, Xu M, Ye T, Si D, Wu L, Chen D, Han Z, Si J. Genome-wide analysis of basic helix-loop-helix genes in Dendrobium catenatum and functional characterization of DcMYC2 in jasmonate-mediated immunity to Sclerotium delphinii. FRONTIERS IN PLANT SCIENCE 2022; 13:956210. [PMID: 35982703 PMCID: PMC9378844 DOI: 10.3389/fpls.2022.956210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium catenatum, belonging to the Orchidaceae, is a precious Chinese herbal medicine. Sclerotium delphinii (P1) is a broad-spectrum fungal disease, which causes widespread loss in the near-wild cultivation of D. catenatum. Thus, resistance breeding of D. catenatum has become the key to solve this problem. The basic helix-loop-helix (bHLH) gene family is closely related to plant resistance to external stresses, but the related research in D. catenatum is not deep enough yet. Phylogenetic analysis showed that 108 DcbHLH genes could be divided into 23 subgroups. Promoter cis-acting elements revealed that DcbHLHs contain a large number of stress-related cis-acting elements. Transcriptome analysis of MeJA and P1 treatment manifested that exogenous MeJA can change the expression pattern of most bHLH genes, especially the IIIe subgroup, including inhibiting the expression of DcbHLH026 (MYC2a) and promoting the expression of DcbHLH027 (MYC2b). Subcellular localization indicated that they were located in the nucleus. Furthermore, exogenous MeJA treatment significantly delayed disease time and reduced lesion size after infection with P1. DcMYC2b-overexpression Arabidopsis lines showed significantly smaller lesions after being infected with P1 than the wild type, indicating that DcMYC2b functions as an important positive regulator in D. catenatum defense against P1. Our findings shed more insights into the critical role of the DcbHLH family in plants and the resistance breeding of D. catenatum.
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12
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He S, Ma R, Liu Z, Zhang D, Wang S, Guo Y, Chen M. Overexpression of BnaAGL11, a MADS-Box Transcription Factor, Regulates Leaf Morphogenesis and Senescence in Brassica napus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3420-3434. [PMID: 35261232 DOI: 10.1021/acs.jafc.1c07622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Previous studies have reported that SEEDSTICK/AGAMOUS-LIKE 11 (AtSTK/AtAGL11), a MADS-box transcription factor, plays important roles in many biological processes in Arabidopsis thaliana. However, the function of BnaAGL11, an AtAGL11 homologous gene from Brassica napus, in leaf development remains unknown. Here, we found that the ectopic expression of any copy of Bna.C09.AGL11, Bna.A03.AGL11, and Bna.A09.AGL11 in A. thaliana led to smaller and curly leaves and promoted leaf senescence. Consistently, the overexpression of Bna.C09.AGL11 in B. napus also caused smaller and curly leaves and accelerated leaf senescence. Furthermore, we demonstrated that Bna.C09.AGL11 controlled leaf morphogenesis by indirectly downregulating the genes of Bna.A01.DWF4 and Bna.C07.PGX3 and promoted leaf senescence by indirectly upregulating the genes of Bna.A04.ABI5, Bna.A05.ABI5, Bna.C04.ABI5-1, and Bna.C01.SEN4 and directly activating the transcription of Bna.C04.ABI5-2 and Bna.C03.SEN4 genes. Our results provide new insights into the underlying regulatory mechanism of BnaAGL11 during leaf development in B. napus.
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Affiliation(s)
- Shuangcheng He
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Rong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zijin Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Da Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shixiang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mingxun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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13
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Di Marzo M, Viana VE, Banfi C, Cassina V, Corti R, Herrera-Ubaldo H, Babolin N, Guazzotti A, Kiegle E, Gregis V, de Folter S, Sampedro J, Mantegazza F, Colombo L, Ezquer I. Cell wall modifications by α-XYLOSIDASE1 are required for control of seed and fruit size in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1499-1515. [PMID: 34849721 DOI: 10.1093/jxb/erab514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Cell wall modifications are of pivotal importance during plant development. Among cell wall components, xyloglucans are the major hemicellulose polysaccharide in primary cell walls of dicots and non-graminaceous monocots. They can connect the cellulose microfibril surface to affect cell wall mechanical properties. Changes in xyloglucan structure are known to play an important role in regulating cell growth. Therefore, the degradation of xyloglucan is an important modification that alters the cell wall. The α-XYLOSIDASE1 (XYL1) gene encodes the only α-xylosidase acting on xyloglucans in Arabidopsis thaliana. Here, we showed that mutation of XYL1 strongly influences seed size, seed germination, and fruit elongation. We found that the expression of XYL1 is directly regulated in developing seeds and fruit by the MADS-box transcription factor SEEDSTICK. We demonstrated that XYL1 complements the stk smaller seed phenotype. Finally, by atomic force microscopy, we investigated the role of XYL1 activity in maintaining cell stiffness and growth, confirming the importance of cell wall modulation in shaping organs.
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Affiliation(s)
- Maurizio Di Marzo
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Vívian Ebeling Viana
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
- Plant Genomics and Breeding Center, Federal University of Pelotas, Capão do Leão-RS, Brazil
| | - Camilla Banfi
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Valeria Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milan-Bicocca, Monza, Italy
| | - Roberta Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milan-Bicocca, Monza, Italy
- Department of Materials Science, University of Milan-Bicocca, Milan, Italy
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36824 Irapuato, Guanajuato, México
| | - Nicola Babolin
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Andrea Guazzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Edward Kiegle
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Veronica Gregis
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36824 Irapuato, Guanajuato, México
| | - Javier Sampedro
- Universidad de Santiago de Compostela, Departamento de Fisiología Vegetal, Facultad de Biología, Rúa Lope Gómez de Marzoa, s/n. Campus sur, 15782 Santiago de Compostela, A Coruña, Spain
| | - Francesco Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milan-Bicocca, Monza, Italy
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
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14
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Abstract
Flowering plants produce flowers and one of the most complex floral structures is the pistil or the gynoecium. All the floral organs differentiate from the floral meristem. Various reviews exist on molecular mechanisms controlling reproductive development, but most focus on a short time window and there has been no recent review on the complete developmental time frame of gynoecium and fruit formation. Here, we highlight recent discoveries, including the players, interactions and mechanisms that govern gynoecium and fruit development in Arabidopsis. We also present the currently known gene regulatory networks from gynoecium initiation until fruit maturation.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, México
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15
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Paolo D, Orozco-Arroyo G, Rotasperti L, Masiero S, Colombo L, de Folter S, Ambrose BA, Caporali E, Ezquer I, Mizzotti C. Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development. Genes (Basel) 2021; 12:1189. [PMID: 34440362 PMCID: PMC8393894 DOI: 10.3390/genes12081189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.
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Affiliation(s)
- Dario Paolo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Gregorio Orozco-Arroyo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Lisa Rotasperti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Simona Masiero
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, Mexico;
| | | | - Elisabetta Caporali
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Chiara Mizzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
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16
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Cruz-Valderrama JE, Bernal-Gallardo JJ, Herrera-Ubaldo H, de Folter S. Building a Flower: The Influence of Cell Wall Composition on Flower Development and Reproduction. Genes (Basel) 2021; 12:genes12070978. [PMID: 34206830 PMCID: PMC8304806 DOI: 10.3390/genes12070978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Floral patterning is a complex task. Various organs and tissues must be formed to fulfill reproductive functions. Flower development has been studied, mainly looking for master regulators. However, downstream changes such as the cell wall composition are relevant since they allow cells to divide, differentiate, and grow. In this review, we focus on the main components of the primary cell wall-cellulose, hemicellulose, and pectins-to describe how enzymes involved in the biosynthesis, modifications, and degradation of cell wall components are related to the formation of the floral organs. Additionally, internal and external stimuli participate in the genetic regulation that modulates the activity of cell wall remodeling proteins.
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Paving the Way for Fertilization: The Role of the Transmitting Tract. Int J Mol Sci 2021; 22:ijms22052603. [PMID: 33807566 PMCID: PMC7961442 DOI: 10.3390/ijms22052603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 01/12/2023] Open
Abstract
Angiosperm reproduction relies on the precise growth of the pollen tube through different pistil tissues carrying two sperm cells into the ovules’ embryo sac, where they fuse with the egg and the central cell to accomplish double fertilization and ultimately initiate seed development. A network of intrinsic and tightly regulated communication and signaling cascades, which mediate continuous interactions between the pollen tube and the sporophytic and gametophytic female tissues, ensures the fast and meticulous growth of pollen tubes along the pistil, until it reaches the ovule embryo sac. Most of the pollen tube growth occurs in a specialized tissue—the transmitting tract—connecting the stigma, the style, and the ovary. This tissue is composed of highly secretory cells responsible for producing an extensive extracellular matrix. This multifaceted matrix is proposed to support and provide nutrition and adhesion for pollen tube growth and guidance. Insights pertaining to the mechanisms that underlie these processes remain sparse due to the difficulty of accessing and manipulating the female sporophytic tissues enclosed in the pistil. Here, we summarize the current knowledge on this key step of reproduction in flowering plants with special emphasis on the female transmitting tract tissue.
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Lee HK, Goring DR. Two subgroups of receptor-like kinases promote early compatible pollen responses in the Arabidopsis thaliana pistil. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1198-1211. [PMID: 33097927 DOI: 10.1093/jxb/eraa496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
In flowering plants, cell-cell communication between the compatible pollen grain/growing pollen tube and the pistil is an essential component for successful sexual reproduction. In Arabidopsis thaliana, the later stages of this dialogue are mediated by several peptide ligands and receptors that guide pollen tubes to the ovules for the release of sperm cells. Despite a detailed understanding of these processes, a key gap remains regarding the nature of the regulators that function at the earlier stages which are essential steps leading to fertilization. Here, we report on new functions for A. thaliana Receptor-Like Kinase (RLK) genes belonging to the LRR-II and LRR-VIII-2 RLK subgroups in the female reproductive tract to regulate compatible pollen hydration and the early stages of pollen tube growth. Mutant pistils for the A. thaliana RKF1 gene cluster were observed to support reduced wild-type pollen hydration and, when combined with the SERK1 and SERK3/BAK1 mutations, reduced pollen tube travel distances occurred. As these mutant pistils displayed a wild-type morphology, we propose that the observed altered compatible pollen responses result from an impaired pollen-pistil dialogue at these early stages.
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Affiliation(s)
- Hyun Kyung Lee
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Daphne R Goring
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
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19
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Riccini A, Picarella ME, De Angelis F, Mazzucato A. Bulk RNA-Seq analysis to dissect the regulation of stigma position in tomato. PLANT MOLECULAR BIOLOGY 2021; 105:263-285. [PMID: 33104942 DOI: 10.1007/s11103-020-01086-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Transcriptomic analysis of tomato genotypes contrasting for stigma position suggests that stigma insertion occurred by the disruption of a process that finds a parallel in Arabidopsis gynoecium development. Domestication of cultivated tomato (Solanum lycopersicum L.) included the transition from allogamy to autogamy that occurred through the loss of self-incompatibilty and the retraction of the stigma within the antheridial cone. Although the inserted stigma is an established phenotype in modern tomatoes, an exserted stigma is still present in several landraces or vintage varieties. Moreover, exsertion of the stigma is a frequent response to high temperature stress and, being a cause of reduced fertility, a trait of increasing importance. Few QTLs for stigma position have been described and only one of the underlying genes identified. To gain insights on genes involved in stigma position in tomato, a bulk RNA sequencing (RNA-Seq) approach was adopted, using two groups of contrasting genotypes. Phenotypic analysis confirmed the extent and the stability of stigma position in the selected genotypes, whereas they were highly heterogeneous for other reproductive and productive traits. The RNA-Seq analysis yielded 801 differentially expressed genes (DEGs), 566 up-regulated and 235 down-regulated in the genotypes with exserted stigma. Validation by quantitative PCR indicated a high reliability of the RNA-Seq data. Up-regulated DEGs were enriched for genes involved in the cell wall metabolism, lipid transport, auxin response and flavonoid biosynthesis. Down-regulated DEGs were enriched for genes involved in translation. Validation of selected genes on pistil tissue of the 26 single genotypes revealed that differences between bulks could both be due to a general trend of the bulk or to the behaviour of single genotypes. Novel candidate genes potentially involved in the control of stigma position in tomato are discussed.
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Affiliation(s)
- A Riccini
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100, Viterbo, Italy
| | - M E Picarella
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100, Viterbo, Italy
| | - F De Angelis
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100, Viterbo, Italy
| | - A Mazzucato
- Department of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100, Viterbo, Italy.
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20
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Paolo D, Rotasperti L, Schnittger A, Masiero S, Colombo L, Mizzotti C. The Arabidopsis MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of E2Fa. PLANTS 2021; 10:plants10020192. [PMID: 33498552 PMCID: PMC7909557 DOI: 10.3390/plants10020192] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023]
Abstract
Seed size is the result of complex molecular networks controlling the development of the seed coat (of maternal origin) and the two fertilization products, the embryo and the endosperm. In this study we characterized the role of Arabidopsis thaliana MADS-domain transcription factor SEEDSTICK (STK) in seed size control. STK is known to regulate the differentiation of the seed coat as well as the structural and mechanical properties of cell walls in developing seeds. In particular, we further characterized stk mutant seeds. Genetic evidence (reciprocal crosses) of the inheritance of the small-seed phenotype, together with the provided analysis of cell division activity (flow cytometry), demonstrate that STK acts in the earlier phases of seed development as a maternal activator of growth. Moreover, we describe a molecular mechanism underlying this activity by reporting how STK positively regulates cell cycle progression via directly activating the expression of E2Fa, a key regulator of the cell cycle. Altogether, our results unveil a new genetic network active in the maternal control of seed size in Arabidopsis.
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Affiliation(s)
- Dario Paolo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (L.R.); (S.M.); (L.C.)
| | - Lisa Rotasperti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (L.R.); (S.M.); (L.C.)
| | - Arp Schnittger
- Abteilung für Entwicklungsbiologie, Institut für Pflanzenforschung und Mikrobiologie, Universität Hamburg, 22609 Hamburg, Germany;
| | - Simona Masiero
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (L.R.); (S.M.); (L.C.)
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (L.R.); (S.M.); (L.C.)
| | - Chiara Mizzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (L.R.); (S.M.); (L.C.)
- Correspondence: ; Tel.: +39-02-503-14838
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