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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Arshad W, Steinbrecher T, Wilhelmsson PK, Fernandez-Pozo N, Pérez M, Mérai Z, Rensing SA, Chandler JO, Leubner-Metzger G. Aethionema arabicum dimorphic seed trait resetting during transition to seedlings. FRONTIERS IN PLANT SCIENCE 2024; 15:1358312. [PMID: 38525145 PMCID: PMC10957558 DOI: 10.3389/fpls.2024.1358312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M- seeds, and IND fruits. The dimorphic seedlings derived from M+ and M- seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M- seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.
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Affiliation(s)
- Waheed Arshad
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Tina Steinbrecher
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | | | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Department Plant Breeding and Physiology, Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-CSIC-UMA), Málaga, Spain
| | - Marta Pérez
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Jake O. Chandler
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Gerhard Leubner-Metzger
- Seed Biology and Technology Group, Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
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Mohammed S, Bhattacharya S, Gesing MA, Klupsch K, Theißen G, Mummenhoff K, Müller C. Morphologically and physiologically diverse fruits of two Lepidium species differ in allocation of glucosinolates into immature and mature seed and pericarp. PLoS One 2020; 15:e0227528. [PMID: 32841235 PMCID: PMC7447065 DOI: 10.1371/journal.pone.0227528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/11/2020] [Indexed: 11/18/2022] Open
Abstract
The morphology and physiology of diaspores play crucial roles in determining the fate of seeds in unpredictable habitats. In some genera of the Brassicaceae different types of diaspores can be found. Lepidium appelianum produces non-dormant seeds within indehiscent fruits while in L. campestre dormant seeds are released from dehiscent fruits. We investigated whether the allocation of relevant defence compounds into different tissues in different Lepidium species may be related to the diverse dispersal strategy (indehiscent and dehiscent) and seed physiology (non-dormant and dormant). Total glucosinolate concentration and composition were analysed in immature and mature seeds and pericarps of L. appelianum and L. campestre using high-performance liquid chromatography. Moreover, for comparison, transgenic RNAi L. campestre lines were used that produce indehiscent fruits due to silencing of LcINDEHISCENCE, the INDEHISCENCE ortholog of L. campestre. Total glucosinolate concentrations were lower in immature compared to mature seeds in all studied Lepidium species and transgenic lines. In contrast, indehiscent fruits of L. appelianum maintained their total glucosinolate concentration in mature pericarps compared to immature ones, while in dehiscent L. campestre and in indehiscent RNAi-LcIND L. campestre a significant decrease in total glucosinolate concentrations from immature to mature pericarps could be detected. Indole glucosinolates were detected in lower abundance than the other glucosinolate classes (aliphatic and aromatic). Relatively high concentrations of 4-methoxyindol-3-ylmethyl glucosinolate were found in mature seeds of L. appelianum compared to other tissues, while no indole glucosinolates were detected in mature diaspores of L. campestre. The diaspores of the latter species may rather depend on aliphatic and aromatic glucosinolates for long-term protection. The allocation patterns of glucosinolates correlate with the morpho-physiologically distinct fruits of L. appelianum and L. campestre and may be explained by the distinct dispersal strategies and the dormancy status of both species.
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Affiliation(s)
- Said Mohammed
- Department of Biology, Botany, University of Osnabrück, Osnabrück, Germany
- Department of Biology, Debre Birhan University, Debre Birhan, Ethiopia
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, Osnabrück, Germany
| | | | - Katharina Klupsch
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Osnabrück, Germany
| | - Caroline Müller
- Faculty of Biology, Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
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Bhattacharya S, Sperber K, Özüdoğru B, Leubner-Metzger G, Mummenhoff K. Naturally-primed life strategy plasticity of dimorphic Aethionema arabicum facilitates optimal habitat colonization. Sci Rep 2019; 9:16108. [PMID: 31695083 PMCID: PMC6834856 DOI: 10.1038/s41598-019-52520-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/09/2019] [Indexed: 11/21/2022] Open
Abstract
Plasticity in plant dispersal traits can maximise the ability of a plant species to survive in stressful environments during colonization. Aethionema arabicum (Brassicaceae) is a dimorphic annual species that is hypothesized to survive stressful conditions during colonization due to adaptive plasticity in life-phase (vegetative vs sexual) and fruit morph (dehiscent [DEH] vs indehiscent fruits [IND]). We tested for adaptive plasticity in life-phase and fruit morphs along laboratory environmental stress gradients found in the natural habitats of Ae. arabicum. We considered optimal environmental conditions (750-2000 m above sea level) to be those that resulted in the following fitness parameters: higher biomass and a higher total number of fruits compared to stressful habitats. We found evidence of plasticity in life-phase and fruit-morph along a stressful environmental gradient. High hydrothermal stress proportionally increased the number of dehiscent morphs and non-dormant seeds germinating in autumn. This offsets natural phenology towards dry and cold winter (less hydrothermal stress), yielding fewer fruits that dehisce in the next generation. We conclude that the plastic responses of Ae. arabicum to natural stress gradients constitute a strategy of long-term adaptive benefits and favouring potential pathways of colonisation of the optimal habitat.
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Affiliation(s)
- Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany.
| | - Katja Sperber
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe, Ankara, 06800, Turkey
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, United Kingdom
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
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