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Mérai Z, Graeber K, Xu F, Donà M, Lalatović K, Wilhelmsson PKI, Fernandez-Pozo N, Rensing SA, Leubner-Metzger G, Mittelsten Scheid O, Dolan L. Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum. Curr Biol 2024; 34:2893-2906.e3. [PMID: 38876102 DOI: 10.1016/j.cub.2024.05.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/18/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.
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Affiliation(s)
- Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Kai Graeber
- Department of Biological Sciences, Royal Holloway University of London, Egham, SRY TW20 0EX, UK
| | - Fei Xu
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Katarina Lalatović
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany; Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), 29010 Málaga, Spain
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, SRY TW20 0EX, UK; Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, 78371 Olomouc, Czech Republic
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Liam Dolan
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
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2
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Chandler JO, Wilhelmsson PKI, Fernandez-Pozo N, Graeber K, Arshad W, Pérez M, Steinbrecher T, Ullrich KK, Nguyen TP, Mérai Z, Mummenhoff K, Theißen G, Strnad M, Scheid OM, Schranz ME, Petřík I, Tarkowská D, Novák O, Rensing SA, Leubner-Metzger G. The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures. THE PLANT CELL 2024; 36:2465-2490. [PMID: 38513609 PMCID: PMC11218780 DOI: 10.1093/plcell/koae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
Plants in habitats with unpredictable conditions often have diversified bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological 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 by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as in seed and pericarp hormone contents, identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting abscisic acid (ABA) sensitivity. This involved expression of morph-specific transcription factors, hypoxia response, and cell wall remodeling genes, as well as altered ABA metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures.
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Affiliation(s)
- Jake O Chandler
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-CSIC-UMA), Málaga 29010, Spain
| | - Kai Graeber
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Waheed Arshad
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
| | - Thu-Phuong Nguyen
- Biosystematics Group, Wageningen University, PB Wageningen 6708, The Netherlands
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Osnabrück 49076, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Department of Genetics, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, PB Wageningen 6708, The Netherlands
| | - Ivan Petřík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg 35043, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg 79104, Germany
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc 78371, Czech Republic
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3
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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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4
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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5
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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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6
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Gramzow L, Sharma R, Theißen G. Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3281. [PMID: 37765445 PMCID: PMC10536770 DOI: 10.3390/plants12183281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.
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Affiliation(s)
- Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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7
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Mérai Z, Xu F, Musilek A, Ackerl F, Khalil S, Soto-Jiménez LM, Lalatović K, Klose C, Tarkowská D, Turečková V, Strnad M, Mittelsten Scheid O. Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum. PLANT PHYSIOLOGY 2023; 192:1584-1602. [PMID: 36861637 PMCID: PMC10231562 DOI: 10.1093/plphys/kiad138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 06/01/2023]
Abstract
The view on the role of light during seed germination stems mainly from studies with Arabidopsis (Arabidopsis thaliana), where light is required to initiate this process. In contrast, white light is a strong inhibitor of germination in other plants, exemplified by accessions of Aethionema arabicum, another member of Brassicaceae. Their seeds respond to light with gene expression changes of key regulators converse to that of Arabidopsis, resulting in opposite hormone regulation and prevention of germination. However, the photoreceptors involved in this process in A. arabicum remain unknown. Here, we screened a mutant collection of A. arabicum and identified koy-1, a mutant that lost light inhibition of germination due to a deletion in the promoter of HEME OXYGENASE 1, the gene for a key enzyme in the biosynthesis of the phytochrome chromophore. koy-1 seeds were unresponsive to red- and far-red light and hyposensitive under white light. Comparison of hormone and gene expression between wild type and koy-1 revealed that very low light fluence stimulates germination, while high irradiance of red and far-red light is inhibitory, indicating a dual role of phytochromes in light-regulated seed germination. The mutation also affects the ratio between the 2 fruit morphs of A. arabicum, suggesting that light reception via phytochromes can fine-tune several parameters of propagation in adaptation to conditions in the habitat.
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Affiliation(s)
- Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Fei Xu
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Andreas Musilek
- Technical University of Vienna, TRIGA Center Atominstitut, Vienna 1020, Austria
| | - Florian Ackerl
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Sarhan Khalil
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Luz Mayela Soto-Jiménez
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Katarina Lalatović
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Cornelia Klose
- Institute of Biology II, University of Freiburg, Freiburg D-79104, Germany
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-78371, Czech Republic
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
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8
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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9
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Walden N, Schranz ME. Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae. Genome Biol Evol 2023; 15:7059155. [PMID: 36848527 PMCID: PMC10016055 DOI: 10.1093/gbe/evad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/27/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023] Open
Abstract
Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences spanning the entire phylogenetic space. Then, we evaluated the resulting gene sets regarding gene number, functional annotation, and gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs when compared with other gene sets, including the Angiosperms353 set and a Brassicaceae-specific target enrichment gene set. However, the synteny data set comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction, and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae which predating the Brassicaceae lineage diversification ∼25 million years ago.
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Affiliation(s)
- Nora Walden
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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10
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Fernandez-Pozo N. PEATmoss: A Gene Expression Atlas for Bryophytes. Methods Mol Biol 2023; 2703:91-107. [PMID: 37646940 DOI: 10.1007/978-1-0716-3389-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany.
- Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Algarrobo-Costa, Málaga, Spain.
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Gramzow L, Klupsch K, Fernández-Pozo N, Hölzer M, Marz M, Rensing SA, Theißen G. Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae). BMC PLANT BIOLOGY 2022; 22:340. [PMID: 35836106 PMCID: PMC9281134 DOI: 10.1186/s12870-022-03631-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/03/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. RESULTS We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. CONCLUSIONS Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.
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Affiliation(s)
- Lydia Gramzow
- Matthias Schleiden Institute / Genetics, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Katharina Klupsch
- Matthias Schleiden Institute / Genetics, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Noé Fernández-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, 35043, Marburg, Germany
- Departamento de Fruticultura Subtropical y Mediterránea, IHSM - CSIC - UMA, Málaga, 29010, Spain
| | - Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
- Present Address: Methodology and Research Infrastructure/Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, 35043, Marburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79108, Freiburg, Germany
| | - Günter Theißen
- Matthias Schleiden Institute / Genetics, Friedrich Schiller University Jena, 07743, Jena, Germany.
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Fernandez-Pozo N, Bombarely A. EasyGDB: a low-maintenance and highly customizable system to develop genomics portals. Bioinformatics 2022; 38:4048-4050. [PMID: 35748710 PMCID: PMC9364376 DOI: 10.1093/bioinformatics/btac412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects. AVAILABILITY AND IMPLEMENTATION The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb.
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Affiliation(s)
| | - Aureliano Bombarely
- Department of Bioscience, Universita degli Studi di Milano, Milan 20133, Italy,Departamento de Biotecnología y Mejora Vegetal de Especies Cultivadas, Biología Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Valencia 46022, Spain
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13
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Xu T, Yang X, Jia Y, Li Z, Tang G, Li X, Wang B, Wang T, Lin J, Guo L, Ye K. A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:607-620. [PMID: 35092713 DOI: 10.1111/tpj.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Tun Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xiaofei Yang
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanyan Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Zihang Li
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Guangbo Tang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiujuan Li
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Tingjie Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Li Guo
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
- Faculty of Science, Leiden University, Leiden, The Netherlands
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Arshad W, Lenser T, Wilhelmsson PKI, Chandler JO, Steinbrecher T, Marone F, Pérez M, Collinson ME, Stuppy W, Rensing SA, Theißen G, Leubner-Metzger G. A tale of two morphs: developmental patterns and mechanisms of seed coat differentiation in the dimorphic diaspore model Aethionema arabicum (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:166-181. [PMID: 33945185 DOI: 10.1111/tpj.15283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
The developmental transition from a fertilized ovule to a dispersed diaspore (seed or fruit) involves complex differentiation processes of the ovule's integuments leading to the diversity in mature seed coat structures in angiosperms. In this study, comparative imaging and transcriptome analysis were combined to investigate the morph-specific developmental differences during outer seed coat differentiation and mucilage production in Aethionema arabicum, the Brassicaceae model for diaspore dimorphism. One of the intriguing adaptations of this species is the production and dispersal of morphologically distinct, mucilaginous and non-mucilaginous diaspores from the same plant (dimorphism). The dehiscent fruit morph programme producing multiple mucilaginous seed diaspores was used as the default trait combination, similar to Arabidopsis thaliana, and was compared with the indehiscent fruit morph programme leading to non-mucilaginous diaspores. Synchrotron-based radiation X-ray tomographic microscopy revealed a co-ordinated framework of morph-specific early changes in internal anatomy of developing A. arabicum gynoecia including seed abortion in the indehiscent programme and mucilage production by the mucilaginous seed coat. The associated comparative analysis of the gene expression patterns revealed that the unique seed coat dimorphism of Ae. arabicum provides an excellent model system for comparative study of the control of epidermal cell differentiation and mucilage biosynthesis by the mucilage transcription factor cascade and their downstream cell wall and mucilage remodelling genes. Elucidating the underlying molecular framework of the dimorphic diaspore syndrome is key to understanding differential regulation of bet-hedging survival strategies in challenging environments, timely in the face of global climatic change.
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Affiliation(s)
- Waheed Arshad
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Teresa Lenser
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Per K I Wilhelmsson
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, D-35043, Germany
| | - Jake O Chandler
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen, CH-5232, Switzerland
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Margaret E Collinson
- Department of Earth Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Wolfgang Stuppy
- Botanischer Garten der Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, D-44780, Germany
- The Royal Botanic Gardens, Kew, Wellcome Trust Millennium Building, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, D-35043, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
- Laboratory of Growth Regulators, Palacký University, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, CZ-78371, Czech Republic
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