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Ojosnegros S, Alvarez JM, Grossmann J, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns. Int J Mol Sci 2023; 24:12429. [PMID: 37569809 PMCID: PMC10419320 DOI: 10.3390/ijms241512429] [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: 06/23/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Ferns and lycophytes have received scant molecular attention in comparison to angiosperms. The advent of high-throughput technologies allowed an advance towards a greater knowledge of their elusive genomes. In this work, proteomic analyses of heart-shaped gametophytes of two ferns were performed: the apomictic Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. In total, a set of 218 proteins shared by these two gametophytes were analyzed using the STRING database, and their proteome associated with metabolism, genetic information processing, and responses to abiotic stress is discussed. Specifically, we report proteins involved in the metabolism of carbohydrates, lipids, and nucleotides, the biosynthesis of amino acids and secondary compounds, energy, oxide-reduction, transcription, translation, protein folding, sorting and degradation, and responses to abiotic stresses. The interactome of this set of proteins represents a total network composed of 218 nodes and 1792 interactions, obtained mostly from databases and text mining. The interactions among the identified proteins of the ferns D. affinis and D. oreades, together with the description of their biological functions, might contribute to a better understanding of the function and development of ferns as well as fill knowledge gaps in plant evolution.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain; (S.O.); (J.M.A.)
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain; (S.O.); (J.M.A.)
| | - Jonas Grossmann
- Functional Genomic Center Zurich, University and ETH Zurich, 8092 Zurich, Switzerland;
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland; (V.G.); (U.G.)
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos, 28933 Móstoles, Spain;
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland; (V.G.); (U.G.)
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain; (S.O.); (J.M.A.)
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2
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Aragón-Raygoza A, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem. FRONTIERS IN PLANT SCIENCE 2022; 13:924660. [PMID: 36035690 PMCID: PMC9413220 DOI: 10.3389/fpls.2022.924660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, United States
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
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3
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Spotting the Targets of the Apospory Controller TGS1 in Paspalum notatum. PLANTS 2022; 11:plants11151929. [PMID: 35893633 PMCID: PMC9332697 DOI: 10.3390/plants11151929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Sexuality and apomixis are interconnected plant reproductive routes possibly behaving as polyphenic traits under the influence of the environment. In the subtropical grass Paspalum notatum, one of the controllers of apospory, a main component of gametophytic apomixis reproduction, is TRIMETHYLGUANOSINE SYNTHASE 1 (TGS1), a multifunctional gene previously associated with RNA cleavage regulation (including mRNA splicing as well as rRNA and miRNA processing), transcriptional modulation and the establishment of heterochromatin. In particular, the downregulation of TGS1 induces a sexuality decline and the emergence of aposporous-like embryo sacs. The present work was aimed at identifying TGS1 target RNAs expressed during reproductive development of Paspalum notatum. First, we mined available RNA databases originated from spikelets of sexual and apomictic plants, which naturally display a contrasting TGS1 representation, to identify differentially expressed mRNA splice variants and miRNAs. Then, the role of TGS1 in the generation of these particular molecules was investigated in antisense tgs1 sexual lines. We found that CHLOROPHYLL A-B BINDING PROTEIN 1B-21 (LHC Ib-21, a component of the chloroplast light harvesting complex), QUI-GON JINN (QGJ, encoding a MAP3K previously associated with apomixis) and miR2275 (a meiotic 24-nt phasi-RNAs producer) are directly or indirectly targeted by TGS1. Our results point to a coordinated control exercised by signal transduction and siRNA machineries to induce the transition from sexuality to apomixis.
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4
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Kinosian SP, Wolf PG. The biology of C. richardii as a tool to understand plant evolution. eLife 2022; 11:75019. [PMID: 35311640 PMCID: PMC8979586 DOI: 10.7554/elife.75019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/18/2022] [Indexed: 12/12/2022] Open
Abstract
The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.
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Affiliation(s)
- Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Chicago, United States
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama, Huntsville, United States
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Fernández H, Grossmann J, Gagliardini V, Feito I, Rivera A, Rodríguez L, Quintanilla LG, Quesada V, Cañal MJ, Grossniklaus U. Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:718932. [PMID: 34868105 PMCID: PMC8633544 DOI: 10.3389/fpls.2021.718932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA3 and GA4, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA4, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA3 and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.
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Affiliation(s)
- Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomics Center, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Móstoles, Spain
| | - Víctor Quesada
- Department of Biochemistry and Molecular Biology, Institute of Oncology of the Principality of Asturias, Oviedo University, Móstoles, Spain
| | - Mª Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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7
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Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
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8
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Hornych O, Testo WL, Sessa EB, Watkins JE, Campany CE, Pittermann J, Ekrt L. Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns. THE NEW PHYTOLOGIST 2021; 229:607-619. [PMID: 32740926 PMCID: PMC7754499 DOI: 10.1111/nph.16836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 05/23/2023]
Abstract
Sex expression of homosporous ferns is controlled by multiple factors, one being the antheridiogen system. Antheridiogens are pheromones released by sexually mature female fern gametophytes, turning nearby asexual gametophytes precociously male. Nevertheless, not all species respond. It is still unknown how many fern species use antheridiogens, how the antheridiogen system evolved, and whether it is affected by polyploidy and/or apomixis. We tested the response of 68 fern species to antheridiogens in cultivation. These results were combined with a comprehensive review of literature to form the largest dataset of antheridiogen interactions to date. Analyzed species also were coded as apomictic or sexual and diploid or polyploid. Our final dataset contains a total of 498 interactions involving 208 species (c. 2% of all ferns). About 65% of studied species respond to antheridiogen. Multiple antheridiogen types were delimited and their evolution is discussed. Antheridiogen responsiveness was not significantly affected by apomixis or polyploidy. Antheridiogens are widely used by ferns to direct sex expression. The antheridiogen system likely evolved multiple times and provides homosporous ferns with the benefits often associated with heterospory, such as increased rates of outcrossing. Despite expectations, antheridiogens may be beneficial to polyploids and apomicts.
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Affiliation(s)
- Ondřej Hornych
- Department of BotanyFaculty of ScienceUniversity of South BohemiaBranišovská 1760České BudějoviceCZ37005Czech Republic
| | - Weston L. Testo
- Department of BiologyUniversity of FloridaBox 118525GainesvilleFL32611USA
| | - Emily B. Sessa
- Department of BiologyUniversity of FloridaBox 118525GainesvilleFL32611USA
| | - James E. Watkins
- Department of BiologyColgate University13 Oak Drive HamiltonHamiltonNY13346USA
| | | | - Jarmila Pittermann
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCA95060USA
| | - Libor Ekrt
- Department of BotanyFaculty of ScienceUniversity of South BohemiaBranišovská 1760České BudějoviceCZ37005Czech Republic
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9
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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10
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Wyder S, Rivera A, Valdés AE, Cañal MJ, Gagliardini V, Fernández H, Grossniklaus U. Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:302-311. [PMID: 32000107 DOI: 10.1016/j.plaphy.2020.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 05/01/2023]
Abstract
Apomixis was originally defined as the replacement of sexual reproduction by an asexual process that does not involve fertilization but, in angiosperms, it is often used in the more restricted sense of asexual reproduction through seeds. In ferns, apomixis combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells of the prothallium (apogamy). The genes that control the onset of apogamy in ferns are largely unknown. In this study, we describe the gametophyte transcriptome of the apogamous fern Dryopteris affinis ssp. affinis using an RNA-Seq approach to compare the gene expression profiles of one- and two-dimensional gametophytes, the latter containing apogamic centers. After collapsing highly similar de novo transcripts, we obtained 166,191 unigenes, of which 30% could be annotated using public databases. Multiple quality metrics indicate a good quality of the de novo transcriptome with a low level of fragmentation. Our data show a total of 10,679 genes (6% of all genes) to be differentially expressed between gametophytes of filamentous (one-dimensional) and prothallial (two-dimensional) architecture. 6,110 genes were up-regulated in two-dimensional relative to one-dimensional gametophytes, some of which are implicated in the regulation of meristem growth, auxin signaling, reproduction, and sucrose metabolism. 4,570 genes were down-regulated in two-dimensional versus one-dimensional gametophytes, which are enriched in stimulus and defense genes, as well as genes involved in epigenetic gene regulation and ubiquitin degradation. Our results provide insights into free-living gametophyte development, focusing on the filamentous-to-prothallus growth transition, and provide a useful resource for further investigations of asexual reproduction.
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Affiliation(s)
- Stefan Wyder
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Ana E Valdés
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - María Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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11
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Motte H, Parizot B, Fang T, Beeckman T. The evolutionary trajectory of root stem cells. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:23-30. [PMID: 31707318 DOI: 10.1016/j.pbi.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.
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Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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Chen X, Chen Z, Huang W, Fu H, Wang Q, Wang Y, Cao J. Proteomic analysis of gametophytic sex expression in the fern Ceratopteris thalictroides. PLoS One 2019; 14:e0221470. [PMID: 31425560 PMCID: PMC6699692 DOI: 10.1371/journal.pone.0221470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/08/2019] [Indexed: 01/25/2023] Open
Abstract
Ceratopteris thalictroides, a model fern, has two kinds of gametophytes with different sex expression: male and hermaphrodite. Hermaphroditic gametophytes have one or several archegonia beneath the growing point and a few antheridia at the base or margin. Male gametophytes show a spoon-like shape with much longer than the width and produce many antheridia at the margin and surface. The results of chlorophyll fluorescence detection showed that the photochemical efficiency of hermaphrodites was higher than that of males. By using two-dimensional electrophoresis and mass spectrometry, the differentially abundant proteins in hermaphroditic and male gametophytes were identified. A total of 1136 ± 55 protein spots were detected in Coomassie-stained gels of proteins from hermaphroditic gametophytes, and 1130 ± 65 spots were detected in gels of proteins from male gametophytes. After annotation, 33 spots representing differentially abundant proteins were identified. Among these, proteins involved in photosynthesis and chaperone proteins were over-represented in hermaphrodites, whereas several proteins involved in metabolism were increased in male gametophytes in order to maintain their development under relatively nutritionally deficient conditions. Furthermore, the differentially abundant cytoskeletal proteins detected in this study, such as centrin and actin, may be involved in the formation of sexual organs and are directly related to sex expression. These differentially abundant proteins are important for maintaining the development of gametophytes of different sexes in C. thalictroides.
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Affiliation(s)
- Xuefei Chen
- College of Life Science, East China Normal University, Shanghai, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Zhiyi Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Wujie Huang
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Huanhuan Fu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Quanxi Wang
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Youfang Wang
- College of Life Science, East China Normal University, Shanghai, China
- * E-mail: (YW); (JC)
| | - Jianguo Cao
- College of Life Science, Shanghai Normal University, Shanghai, China
- * E-mail: (YW); (JC)
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