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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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Fujiwara T, Liu H, Meza-Torres EI, Morero RE, Vega AJ, Liang Z, Ebihara A, Leitch IJ, Schneider H. Evolution of genome space occupation in ferns: linking genome diversity and species richness. ANNALS OF BOTANY 2023; 131:59-70. [PMID: 34259813 PMCID: PMC9904345 DOI: 10.1093/aob/mcab094] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/10/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species-rich lineage of land plants, are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number. METHODS We conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation. KEY RESULTS The measurements of DNA C-values for 233 species more than doubled the taxon coverage from ~2.2 % in previous studies to 5.3 % of extant diversity. The dataset not only documented substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also supported the predicted correlation between species diversity and the dynamics of genome evolution. CONCLUSIONS Our results demonstrated substantial genome disparity among different groups of ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.
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Affiliation(s)
- Tao Fujiwara
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, Japan
| | - Hongmei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Esteban I Meza-Torres
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Rita E Morero
- Instituto Multidiscipinario de Biologia Vegetal, Universidad Nacional de Cordoba, Consejo Nacional de Investigaciones Científicas y Tecnicas, Cordoba, Argentina
| | - Alvaro J Vega
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Zhenlong Liang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Sciences, Tsukuba, Japan
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Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species of Tmesipteris (Psilotaceae). Int J Mol Sci 2023; 24:ijms24032708. [PMID: 36769031 PMCID: PMC9916801 DOI: 10.3390/ijms24032708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Giant genomes are rare across the plant kingdom and their study has focused almost exclusively on angiosperms and gymnosperms. The scarce genetic data that are available for ferns, however, indicate differences in their genome organization and a lower dynamism compared to other plant groups. Tmesipteris is a small genus of mainly epiphytic ferns that occur in Oceania and several Pacific Islands. So far, only two species with giant genomes have been reported in the genus, T. tannensis (1C = 73.19 Gbp) and T. obliqua (1C = 147.29 Gbp). Low-coverage genome skimming sequence data were generated in these two species and analyzed using the RepeatExplorer2 pipeline to identify and quantify the repetitive DNA fraction of these genomes. We found that both species share a similar genomic composition, with high repeat diversity compared to taxa with small (1C < 10 Gbp) genomes. We also found that, in general, characterized repetitive elements have relatively high heterogeneity scores, indicating ancient diverging evolutionary trajectories. Our results suggest that a whole genome multiplication event, accumulation of repetitive elements, and recent activation of those repeats have all played a role in shaping these genomes. It will be informative to compare these data in the future with data from the giant genome of the angiosperm Paris japonica, to determine if the structures observed here are an emergent property of massive genomic inflation or derived from lineage specific processes.
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Vanneste S, Beeckman T. Pericyclic versus Endodermal Lateral Roots: Which Came First? TRENDS IN PLANT SCIENCE 2020; 25:727-729. [PMID: 32507522 DOI: 10.1016/j.tplants.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Digging into the limited literature on lateral root (LR) formation in early vascular plants, we came to the novel conclusion that the pericycle, rather than the endodermis as commonly assumed, represents the ancestral tissue that was evolutionarily recruited to form LRs.
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Affiliation(s)
- Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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5
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Lehtonen S, Poczai P, Sablok G, Hyvönen J, Karger DN, Flores J. Exploring the phylogeny of the marattialean ferns. Cladistics 2020; 36:569-593. [DOI: 10.1111/cla.12419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 01/21/2023] Open
Affiliation(s)
- Samuli Lehtonen
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Dirk N. Karger
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
| | - Jorge Flores
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
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Liu H, Schneider H, Yu Y, Fuijwara T, Khine PK. Towards the conservation of the Mesozoic relict fern Christensenia: a fern species with extremely small populations in China. JOURNAL OF PLANT RESEARCH 2019; 132:601-616. [PMID: 31446516 DOI: 10.1007/s10265-019-01131-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/07/2019] [Indexed: 05/14/2023]
Abstract
The Chinese occurrences of the marattioid fern genus Christensenia have been considered as requiring protection because of its extreme rarity and very small population size. Here, we explored different biological aspects to enable protection of these rare ferns, well known as Mesozoic living fossils. Firstly, we documented the cytology of the Chinese occurrences for the first time. This is the second tetraploid record of Christensenia worth for further studies to confirm its taxonomic status. Secondly, we obtained the first complete plastid genome of this genus, which confirmed the proposed conservatism of the plastid genome structure in marattioid ferns. By comparing the chloroplast genome with other marattioids, we identified several candidate regions to develop highly variable markers to investigate the intra-species diversity of marattioid ferns. Thirdly, phylogenetic analyses of rbcL sequences implied that there are at least two distinct species of Christensenia. Finally, we re-assessed the conservation status of Christensenia in the context of its local and global distribution by assessing specimen information extracted from publications and digitized voucher information. This assessment confirmed the need to obtain more accurate information about the distribution of this genus to assess the status incorporating the disjunct distribution from southern China and India in the North towards the Solomon Islands in the South.
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Affiliation(s)
- Hongmei Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
| | - Ying Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Tao Fuijwara
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
| | - Phyo Kay Khine
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
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7
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Kuo LY, Huang YJ, Chang J, Chiou WL, Huang YM. Evaluating the spore genome sizes of ferns and lycophytes: a flow cytometry approach. THE NEW PHYTOLOGIST 2017; 213:1974-1983. [PMID: 28164337 DOI: 10.1111/nph.14291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/17/2016] [Indexed: 05/23/2023]
Abstract
Ferns and lycophytes produce spores to initiate the gametophyte stage for sexual reproduction. Approximately 10% of these seedless vascular plants are apomictic, and produce genomic unreduced spores. Genome size comparisons between spores and leaves are a reliable, and potentially easier way to determine their reproductive mode compared to traditional approaches. However, estimation of the spore genome sizes of these plants has not been attempted. We attempted to evaluate the spore genome sizes of ferns and lycophytes using flow cytometry, collected spores from selected species representing different spore physical properties and taxonomic groups, and sought to optimize bead-vortexing conditions. By evaluating the spore and sporophyte genome sizes, we examined whether reproductive modes could be ascertained from these flow cytometry results. We proposed two separate sets of optimized bead-vortexing conditions for the nuclear extraction of green and nongreen spores. We further successfully extracted spore nuclei of 19 families covering most orders, and the qualities and quantities of these extractions satisfied the C-value criteria. These evaluated genome sizes further supported the reproductive modes reported previously. In the current study, flow cytometry was used for the first time to evaluate the spore genome sizes of ferns and lycophytes. This use of spore flow cytometry provides a new, efficient approach to ascertaining the reproductive modes of these plants.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Jia Huang
- Department of Forensic Science, Central Police University, Taoyuan City, 33304, Taiwan
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - JenYu Chang
- Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute, Chiayi City, 60044, Taiwan
| | - Wen-Liang Chiou
- Division of Botanical Garden, Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
- Dr. Cecilia Koo Botanic Conservation and Environmental Protection Foundation/Conservation Center, Pingtung County, 90646, Taiwan
| | - Yao-Moan Huang
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
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8
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Puttick MN, Clark J, Donoghue PCJ. Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms. Proc Biol Sci 2017; 282:20152289. [PMID: 26631568 PMCID: PMC4685785 DOI: 10.1098/rspb.2015.2289] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.
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Affiliation(s)
- Mark N Puttick
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James Clark
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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9
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A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
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10
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Baniaga AE, Arrigo N, Barker MS. The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution. Genome Biol Evol 2016; 8:1516-25. [PMID: 27189987 PMCID: PMC4898805 DOI: 10.1093/gbe/evw091] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 02/07/2023] Open
Abstract
The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome.
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Affiliation(s)
| | - Nils Arrigo
- Department of Ecology & Evolutionary Biology, University of Arizona Department of Ecology & Evolution, University of Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona
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11
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Clark J, Hidalgo O, Pellicer J, Liu H, Marquardt J, Robert Y, Christenhusz M, Zhang S, Gibby M, Leitch IJ, Schneider H. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. THE NEW PHYTOLOGIST 2016; 210:1072-82. [PMID: 26756823 DOI: 10.1111/nph.13833] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The genome evolution of ferns has been considered to be relatively static compared with angiosperms. In this study, we analyse genome size data and chromosome numbers in a phylogenetic framework to explore three hypotheses: the correlation of genome size and chromosome number, the origin of modern ferns from ancestors with high chromosome numbers, and the occurrence of several whole-genome duplications during the evolution of ferns. To achieve this, we generated new genome size data, increasing the percentage of fern species with genome sizes estimated to 2.8% of extant diversity, and ensuring a comprehensive phylogenetic coverage including at least three species from each fern order. Genome size was correlated with chromosome number across all ferns despite some substantial variation in both traits. We observed a trend towards conservation of the amount of DNA per chromosome, although Osmundaceae and Psilotaceae have substantially larger chromosomes. Reconstruction of the ancestral genome traits suggested that the earliest ferns were already characterized by possessing high chromosome numbers and that the earliest divergences in ferns were correlated with substantial karyological changes. Evidence for repeated whole-genome duplications was found across the phylogeny. Fern genomes tend to evolve slowly, albeit genome rearrangements occur in some clades.
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Affiliation(s)
- James Clark
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Hongmei Liu
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Jeannine Marquardt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Yannis Robert
- 18, Rue des Capucines, F-97431, La Plaine des Palmistes, La Réunion, France
| | - Maarten Christenhusz
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
- Plant Gateway, 5 Talbot Street, Hertford, Hertfordshire, SG13 7BX, UK
| | - Shouzhou Zhang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Mary Gibby
- Department of Science, Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Life Sciences, Sun Yatsen University, Guangzhou, 510275, Guangdong, China
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12
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Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP. An Exploration into Fern Genome Space. Genome Biol Evol 2015; 7:2533-44. [PMID: 26311176 PMCID: PMC4607520 DOI: 10.1093/gbe/evv163] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
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Affiliation(s)
- Paul G Wolf
- Ecology Center and Department of Biology, Utah State University
| | - Emily B Sessa
- Department of Biology, University of Florida Genetics Institute, University of Florida
| | - Daniel Blaine Marchant
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley
| | - Erin M Sigel
- Department of Biology, Duke University Present address: Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Clayton J Visger
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University
| | - Douglas E Soltis
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Pamela S Soltis
- Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Joshua P Der
- Department of Biological Science, California State University, Fullerton
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13
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Ranker TA, Sundue MA. Why are there so few species of ferns? TRENDS IN PLANT SCIENCE 2015; 20:402-403. [PMID: 25986968 DOI: 10.1016/j.tplants.2015.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 06/04/2023]
Abstract
A recent study has documented a natural hybridization event between two fern lineages that last shared a common ancestor about 60 million years ago. This is one of the deepest hybridization events ever described and has important implications for plant speciation theory.
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Affiliation(s)
- Tom A Ranker
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Michael A Sundue
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA; The Pringle Herbarium, Department of Plant Biology, The University of Vermont, 27 Colchester Ave., Burlington, VT 05405, USA
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14
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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