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Ojosnegros S, Alvarez JM, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis. PLANTA 2024; 260:111. [PMID: 39356333 PMCID: PMC11447071 DOI: 10.1007/s00425-024-04540-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 09/21/2024] [Indexed: 10/03/2024]
Abstract
MAIN CONCLUSION A novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches. The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein-protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein-protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | - Luis G Quintanilla
- Global Change Research Institute, 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
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain.
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Edwards‐Calma K, Jiménez L, Zenil‐Ferguson R, Heyduk K, Thomas MK, Tribble CM. Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11598. [PMID: 38912653 PMCID: PMC11192160 DOI: 10.1002/aps3.11598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 06/25/2024]
Abstract
Premise Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability. Methods We used fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land-use change. Results Of all native species, Doryopteris angelica had the lowest percentage of occurrences of naturalized species in its suitable area while D. decora had the highest. However, all Doryopteris spp. had a higher percentage overlap, while Pellaea ternifolia had a lower percentage overlap, than expected by chance. Doryopteris decora and D. decipiens had the lowest proportions (<20%) of suitable area covering native habitat. Discussion Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.
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Affiliation(s)
| | - Laura Jiménez
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻi 96822USA
- Centro de Modelamiento MatemáticoUniversidad de ChileSantiagoChile
| | | | - Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻi 96822USA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrs06269ConnecticutUSA
| | - Miles K. Thomas
- Herbarium Pacificum, Bernice Pauahi Bishop MuseumHonoluluHawaiʻi 96813USA
| | - Carrie M. Tribble
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻi 96822USA
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Wefferling KM, Castro M, Castro S, Holmlund H, Loureiro J, Rothfels CJ, Schuettpelz E. Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts. AMERICAN JOURNAL OF BOTANY 2024; 111:e16305. [PMID: 38517199 DOI: 10.1002/ajb2.16305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
PREMISE The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity. METHODS We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches. RESULTS We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California. CONCLUSIONS Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.
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Affiliation(s)
- Keir M Wefferling
- Department of Biology, Gary A. Fewless Herbarium, Cofrin Center for Biodiversity, University of Wisconsin-Green Bay, Green Bay, 54311, Wisconsin, USA
| | - Mariana Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Helen Holmlund
- Natural Science Division, Pepperdine University, Malibu, 90263, California, USA
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Carl J Rothfels
- Department of Biology, Ecology Center, and Intermountain Herbarium, Utah State University, Logan, 84322, Utah, USA
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20560, DC, USA
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Tani E, Xanthopoulou A, Bazakos C. Editorial: Advances on genomics and genetics of horticultural crops and their contribution to breeding efforts - volume II. FRONTIERS IN PLANT SCIENCE 2024; 15:1385217. [PMID: 38476687 PMCID: PMC10927967 DOI: 10.3389/fpls.2024.1385217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Affiliation(s)
- Eleni Tani
- Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Merino G, Ramírez-Barahona S, Olson ME, Núñez-Farfán J, García-Oliva F, Eguiarte LE. Distribution and morphological variation of tree ferns (Cyatheaceae) along an elevation gradient. PLoS One 2023; 18:e0291945. [PMID: 37756353 PMCID: PMC10530041 DOI: 10.1371/journal.pone.0291945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Knowing how species and communities respond to environmental change is fundamental in the context of climate change. The search for patterns of abundance and phenotypic variation along altitudinal gradients can provide evidence on adaptive limits. We evaluated the species abundance and the variation in morphometric and stomatal characters in five tree ferns species (Cyathea fulva, C. divergens, C. myosuroides, Alsophila firma and Gymnosphaera salvinii) distributed along an elevation gradient in a well-preserved Mexican cloud forest. Variation at the community and species level was assessed using exploratory and multivariate data analysis methods. We wanted to explore if the species abundance is environmentally determined, to determine the degree of variation along the elevation gradient, to test for differences between zones and associations with elevation, humidity and soil nutrients, and to assess contribution of the intra- and interspecific variation to the community response to elevation and soil nutrients. The studied fern community showed strong species turnover along the elevation gradient, with some influence of soil nutrient concentration, supporting environmental determinism. All measured characters displayed variation along the gradient. Stomatal characters (size and density) had significantly less variation than morphometric characters (trunk diameter, stipe length and blade length), but stomatal density also shows interesting intraspecific patterns. In general, patterns within the fern community suggest a strong influence of species identity, especially of species inhabiting the lower edge of the cloud forest, which showed the clearest morphometric and stomatal patterns, associated to contrasting environments rather than to changes in elevation. The coincidence between morphometric and stomatal patterns in this area suggest hydraulic adjustments in response to contrasting environments. Our results provide evidence that tree ferns species respond to environmental changes through adjustments of morphometric plasticity and stomatal density, which is relevant to predict possible responses to variation in environmental conditions resulting from climate change.
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Affiliation(s)
- Gabriel Merino
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Ciudad Universitaria, Coyoacán, Mexico City, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mark E. Olson
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Núñez-Farfán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Cai Z, Wang X, Xie Z, Wen Z, Yu X, Xu S, Su X, Luo J. Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways. FRONTIERS IN PLANT SCIENCE 2023; 14:1222414. [PMID: 37746005 PMCID: PMC10513451 DOI: 10.3389/fpls.2023.1222414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
Light serves not only as a signaling cue perceived by plant photoreceptors but also as an essential energy source captured by chloroplasts. However, excessive light can impose stress on plants. Fern gametophytes possess the unique ability to survive independently and play a critical role in the alternation of generations. Due to their predominantly shaded distribution under canopies, light availability becomes a limiting factor for gametophyte survival, making it imperative to investigate their response to light. Previous research on fern gametophytes' light response has been limited to the physiological level. In this study, we examined the light response of Adiantum flabellulatum gametophytes under different photosynthetic photon flux density (PPFD) levels and identified their high sensitivity to low light. We thereby determined optimal and stress-inducing light conditions. By employing transcriptome sequencing, weighted gene co-expression network analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified 10,995 differentially expressed genes (DEGs). Notably, 3 PHYBs and 5 Type 1 CRYs (CRY1s) were significantly down-regulated at low PPFD (0.1 μmol m-2 s-1). Furthermore, we annotated 927 DEGs to pathways related to photosynthesis and 210 to the flavonoid biosynthesis pathway involved in photoprotection. Additionally, we predicted 34 transcription factor families and identified a close correlation between mTERFs and photosynthesis, as well as a strong co-expression relationship between MYBs and bHLHs and genes encoding flavonoid synthesis enzymes. This comprehensive analysis enhances our understanding of the light response of fern gametophytes and provides novel insights into the mechanisms governing their responses to light.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xiaochen Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zhenyu Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zhenyi Wen
- College of Ecology and Environment, Hainan University, Haikou, Hainan, China
| | - Xudong Yu
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Shitao Xu
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Xinyu Su
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Krieg CP, Seeger K, Campany C, Watkins JE, McClearn D, McCulloh KA, Sessa EB. Functional traits and trait coordination change over the life of a leaf in a tropical fern species. AMERICAN JOURNAL OF BOTANY 2023; 110:e16151. [PMID: 36879521 DOI: 10.1002/ajb2.16151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Plant ecological strategies are often defined by the integration of underlying traits related to resource acquisition, allocation, and growth. Correlations between key traits across diverse plants suggest that variation in plant ecological strategies is largely driven by a fast-slow continuum of plant economics. However, trait correlations may not be constant through the life of a leaf, and it is still poorly understood how trait function varies over time in long-lived leaves. METHODS Here, we compared trait correlations related to resource acquisition and allocation across three different mature frond age cohorts in a tropical fern species, Saccoloma inaequale. RESULTS Fronds exhibited high initial investments of nitrogen and carbon, but with declining return in photosynthetic capacity after the first year. In the youngest fronds, we found water-use efficiency to be significantly lower than in the oldest mature fronds due to increased transpiration rates. Our data suggest that middle-aged fronds are more efficient relative to younger, less water-use efficient fronds and that older fronds exhibit greater nitrogen investments without higher photosynthetic return. In addition, several trait correlations expected under the leaf economics spectrum (LES) do not hold within this species, and some trait correlations only appear in fronds of a specific developmental age. CONCLUSIONS These findings contextualize the relationship between traits and leaf developmental age with those predicted to underlie plant ecological strategy and the LES and are among the first pieces of evidence for when relative physiological trait efficiency is maximized in a tropical fern species.
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Affiliation(s)
| | - Kate Seeger
- Department of Biology, Macalester College, Saint Paul, MN, 55105, USA
| | - Courtney Campany
- Department of Biology, Shepherd University, Shepherdstown, WV, 25443, USA
| | - James E Watkins
- Department of Biology, Colgate University, Hamilton, NY, 13346, USA
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Mitchell N, Piatczyc NP, Wang DD, Edwards J. High-speed video and plant ultrastructure define mechanisms of gametophyte dispersal. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11463. [PMID: 35495193 PMCID: PMC9039801 DOI: 10.1002/aps3.11463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 05/06/2023]
Abstract
Dispersal of gametophytes is critical for land plant survivorship and reproduction. It defines potential colonization and geographical distribution as well as genetic mixing and evolution. C. T. Ingold's classic works on Spore Discharge in Land Plants and Spore Liberation review mechanisms for spore release and dispersal based on real-time observations, basic histology, and light microscopy. Many mechanisms underlying spore liberation are explosive and have evolved independently multiple times. These mechanisms involve physiological processes such as water gain and loss, coupled with structural features using different plant tissues. Here we review how high-speed video and analyses of ultrastructure have defined new biomechanical mechanisms for the dispersal of gametophytes through the dissemination of haploid diaspores, including spores, pollen, and asexual reproductive propagules. This comparative review highlights the diversity and importance of rapid movements in plants for dispersing gametophytes and considerations for using combinations of high-speed video methods and microscopic techniques to understand these dispersal movements. A deeper understanding of these mechanisms is crucial not only for understanding gametophyte ecology but also for applied engineering and biomimetic applications used in human technologies.
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Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of Wisconsin–Eau ClaireEau Claire54701WisconsinUSA
| | - Nancy P. Piatczyc
- Biology DepartmentWilliams College, WilliamstownMassachusetts01267USA
| | - Darren D. Wang
- Biology DepartmentWilliams College, WilliamstownMassachusetts01267USA
| | - Joan Edwards
- Biology DepartmentWilliams College, WilliamstownMassachusetts01267USA
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