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Ramirez‐Castillo R, Palma‐Rojas C, Seguel PJ, Grusz AL, Araya‐Jaime C. Unfurling an improved method for visualizing mitotic chromosomes in ferns. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11588. [PMID: 39184202 PMCID: PMC11342230 DOI: 10.1002/aps3.11588] [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: 09/05/2023] [Revised: 01/09/2024] [Accepted: 02/05/2024] [Indexed: 08/27/2024]
Abstract
Premise Cytotaxonomy employs chromosome visualization to study organismal relationships and evolution. Despite the critical value of cytogenetic data, cytotypes are lacking for many plant groups. Here, we present an improved approach for visualizing mitotic chromosomes in ferns, a key lineage of land plants, using the dividing cells of unfurling croziers (fiddleheads). Methods and Results Our modified mitotic chromosome preparation incorporates a brief pectinase-cellulase pretreatment, as well as colchicine fixation and the Feulgen reaction to improve the staining and separation of mitotic chromosomes. To demonstrate this easy and efficient assessment, we determined the sporophytic (2n) chromosome number for three fern species: Cheilanthes mollis (2n = 60), Cheilanthes hypoleuca (2n = 120), and Nephrolepis cordifolia (2n = 82). Conclusions The new method presented here improves visualizations of mitotic chromosomes from the dividing nuclei of young fern croziers. Fiddleheads are widely accessible in nature and in living collections worldwide, and this modified approach increases their suitability for fern cytotaxonomic studies.
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Affiliation(s)
| | | | - Pedro Jara Seguel
- Núcleo de Estudios Ambientales, Facultad de Recursos NaturalesUniversidad Católica de TemucoTemucoChile
| | - Amanda L. Grusz
- University of Minnesota DuluthDuluth55812MinnesotaUSA
- National Museum of Natural HistorySmithsonian InstitutionWashington, D.C.20013USA
| | - Cristian Araya‐Jaime
- Departamento de BiologíaUniversidad de La SerenaLa SerenaChile
- Instituto Multidisciplinario de Investigación y Posgrado Universidad de La SerenaLa SerenaChile
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2
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Zhang R, Zhang J, Xu YX, Sun JM, Dai SJ, Shen H, Yan YH. Dynamic evolution of MADS-box genes in extant ferns via large-scale phylogenomic analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1410554. [PMID: 38974983 PMCID: PMC11224435 DOI: 10.3389/fpls.2024.1410554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 07/09/2024]
Abstract
Introduction Several studies of MADS-box transcription factors in flowering plants have been conducted, and these studies have indicated that they have conserved functions in floral organ development; MIKC-type MADS-box genes has been proved to be expanded in ferns, however, few systematic studies of these transcription factors have been conducted in non-seed plants. Although ferns and seed plants are sister groups, they exhibit substantial morphological differences. Methods Here, we clarified the evolution of MADS-box genes across 71 extant fern species using available transcriptome, genome, and gene expression data. Results We obtained a total of 2,512 MADS-box sequences, ranging from 9 to 89 per species. The most recent common ancestor (MRCA) of ferns contained approximately three type I genes and at least 5-6 type II MADS-box genes. The domains, motifs, expression of type I and type II proteins, and the structure of the both type genes were conserved in ferns as to other land plants. Within type II genes, MIKC*-type proteins are involved in gametophyte development in ferns; MIKCC-type proteins have broader expression patterns in ferns than in seed plants, and these protein sequences are likely conserved in extant seed plants and ferns because of their diverse roles in diploid sporophyte development. More than 90% of MADS-box genes are type II genes, and MIKCC genes, especially CRM1 and CRM6-like genes, have undergone a large expansion in leptosporangiate ferns; the diverse expression patterns of these genes might be related to the fuctional diversification and increased complexity of the plant body plan. Tandem duplication of CRM1 and CRM6-like genes has contributed to the expansion of MIKCC genes. Conclusion or Discussion This study provides new insights into the diversity, evolution, and functions of MADS-box genes in extant ferns.
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Affiliation(s)
- Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiao Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yue-Xia Xu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jun-Mei Sun
- School of Science, Qiongtai Normal University, Haikou, Hainan, China
| | - Shao-Jun Dai
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yue-Hong Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
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3
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Li C, Wickell D, Kuo LY, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, Shu S, Plott C, Barry K, Rajasekar S, Grimwood J, Han X, Sun S, Hou Z, He W, Dai G, Sun C, Schmutz J, Leebens-Mack JH, Li FW, Wang L. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proc Natl Acad Sci U S A 2024; 121:e2312607121. [PMID: 38236735 PMCID: PMC10823260 DOI: 10.1073/pnas.2312607121] [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: 07/31/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.
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Affiliation(s)
- Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - David Wickell
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Mellissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ85721
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Weijun He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Yanji133000, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing100048, China
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing100700, China
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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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Yu JG, Tang JY, Wei R, Lan MF, Xiang RC, Zhang XC, Xiang QP. The first homosporous lycophyte genome revealed the association between the recent dynamic accumulation of LTR-RTs and genome size variation. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01366-0. [PMID: 37380791 DOI: 10.1007/s11103-023-01366-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
The contrasting genome size between homosporous and heterosporous plants is fascinating. Different from the heterosporous seed plants and mainly homosporous ferns, the lycophytes are either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). Many lycophytes are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer's disease. For the seed-free vascular plants, several high-quality genomes of heterosporous Selaginella, homosporous ferns (maidenhair fern, monkey spider tree fern), and heterosporous ferns (Azolla) have been published and provided important insights into the origin and evolution of early land plants. However, the homosporous lycophyte genome has not been decoded. Here, we assembled the first homosporous lycophyte genome and conducted comparative genomic analyses by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size of Lycopodium clavatum is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is long terminal repeat (LTR). This study disclosed a high birth rate and a low death rate of the LTR-RTs in homosporous lycophytes, but the opposite occurs in heterosporous lycophytes. we propose that the recent activity of LTR-RT is responsible for the immense genome size variation between homosporous and heterosporous lycophytes. By combing Ks analysis with a phylogenetic approach, we discovered two whole genome duplications (WGD). Morover, we identified all the five recognized key enzymes for the HupA biosynthetic pathway in the L. clavatum genome, but found this pathway incomplete in other major lineages of land plants. Overall, this study is of great importance for the medicinal utilization of lycophytes and the decoded genome data will be a key cornerstone to elucidate the evolution and biology of early vascular land plants.
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Affiliation(s)
- Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
| | - Mei-Fang Lan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Rui-Chen Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
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6
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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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7
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Chen H, Fang Y, Zwaenepoel A, Huang S, Van de Peer Y, Li Z. Revisiting ancient polyploidy in leptosporangiate ferns. THE NEW PHYTOLOGIST 2023; 237:1405-1417. [PMID: 36349406 PMCID: PMC7614084 DOI: 10.1111/nph.18607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/30/2022] [Indexed: 05/31/2023]
Abstract
Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.
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Affiliation(s)
- Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Yuhan Fang
- Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sanwen Huang
- Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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8
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. NATURE PLANTS 2022; 8:1038-1051. [PMID: 36050461 PMCID: PMC9477723 DOI: 10.1038/s41477-022-01226-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
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Affiliation(s)
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Rijan R Dhakal
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Clemens Rössner
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Annette Becker
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shengchun Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
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9
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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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10
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Zhong Y, Liu Y, Wu W, Chen J, Sun C, Liu H, Shu J, Ebihara A, Yan Y, Zhou R, Schneider H. Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides. Genome Biol Evol 2022; 14:evac127. [PMID: 35946426 PMCID: PMC9387920 DOI: 10.1093/gbe/evac127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongmei Liu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
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11
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Wang FG, Wang AH, Bai CK, Jin DM, Nie LY, Harris AJ, Che L, Wang JJ, Li SY, Xu L, Shen H, Gu YF, Shang H, Duan L, Zhang XC, Chen HF, Yan YH. Genome size evolution of the extant lycophytes and ferns. PLANT DIVERSITY 2022; 44:141-152. [PMID: 35505989 PMCID: PMC9043363 DOI: 10.1016/j.pld.2021.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 05/11/2023]
Abstract
Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.
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Affiliation(s)
- Fa-Guo Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ai-Hua Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, 530001, China
| | - Cheng-Ke Bai
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Dong-Mei Jin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Li-Yun Nie
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Le Che
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Juan-Juan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shi-Yu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lei Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu-Feng Gu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, 518114, Shenzhen, China
- Life Science and Technology College, Harbin Normal University, Harbin, 150025, China
| | - Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Corresponding author.
| | - Yue-Hong Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, 518114, Shenzhen, China
- Corresponding author. The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, 518114, Shenzhen, Guangdong, China.
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12
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Kinosian SP, Rowe CA, Wolf PG. Why Do Heterosporous Plants Have So Few Chromosomes? FRONTIERS IN PLANT SCIENCE 2022; 13:807302. [PMID: 35251082 PMCID: PMC8888854 DOI: 10.3389/fpls.2022.807302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The mechanisms controlling chromosome number, size, and shape, and the relationship of these traits to genome size, remain some of the least understood aspects of genome evolution. Across vascular plants, there is a striking disparity in chromosome number between homosporous and heterosporous lineages. Homosporous plants (comprising most ferns and some lycophytes) have high chromosome numbers compared to heterosporous lineages (some ferns and lycophytes and all seed plants). Many studies have investigated why homosporous plants have so many chromosomes. However, homospory is the ancestral condition from which heterospory has been derived several times. Following this phylogenetic perspective, a more appropriate question to ask is why heterosporous plants have so few chromosomes. Here, we review life history differences between heterosporous and homosporous plants, previous work on chromosome number and genome size in each lineage, known mechanisms of genome downsizing and chromosomal rearrangements, and conclude with future prospects for comparative research.
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Affiliation(s)
- Sylvia P. Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Carol A. Rowe
- Earth System Science Center, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Paul G. Wolf
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
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13
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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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14
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Mossion V, Dauphin B, Grant J, Kessler M, Zemp N, Croll D. Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure. Mol Ecol Resour 2021; 22:254-271. [PMID: 34310066 PMCID: PMC9291227 DOI: 10.1111/1755-0998.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/02/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high‐quality transcripts with an average length of 1,333 bp based on deep RNA‐sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome‐wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High‐quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.
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Affiliation(s)
- Vinciane Mossion
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Benjamin Dauphin
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland.,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Jason Grant
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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15
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Román-Palacios C, Medina CA, Zhan SH, Barker MS. Animal chromosome counts reveal a similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants. J Evol Biol 2021; 34:1333-1339. [PMID: 34101952 DOI: 10.1111/jeb.13884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms that underlie chromosome evolution could provide insights into the processes underpinning the origin, persistence and evolutionary tempo of lineages. Here, we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ~15,000 species. We found remarkable a similarity in the distribution of chromosome counts between animals and flowering plants. Nevertheless, the similarity in the distribution of chromosome numbers between animals and plants is likely to be explained by different drivers. For instance, we found that while animals and flowering plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. By leveraging the largest data set of chromosome counts for animals, we describe a previously undocumented pattern across the Tree of Life-animals and flowering plants show remarkably similar distributions of haploid chromosome numbers.
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Affiliation(s)
| | - Cesar A Medina
- Department of Neuroscience, University of Arizona, Tucson, AZ, USA
| | - Shing H Zhan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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16
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Li Z, McKibben MTW, Finch GS, Blischak PD, Sutherland BL, Barker MS. Patterns and Processes of Diploidization in Land Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:387-410. [PMID: 33684297 DOI: 10.1146/annurev-arplant-050718-100344] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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17
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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18
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Huang CH, Qi X, Chen D, Qi J, Ma H. Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:433-455. [PMID: 31628713 DOI: 10.1111/jipb.12877] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/17/2019] [Indexed: 05/07/2023]
Abstract
Ferns, the second largest group of vascular plants, originated ~400 million years ago (Mya). They became dominant in the ancient Earth landscape before the angiosperms and are still important in current ecosystems. Many ferns have exceptionally high chromosome numbers, possibly resulting from whole-genome duplications (WGDs). However, WGDs have not been investigated molecularly across fern diversity. Here we detected and dated fern WGDs using a phylogenomic approach and by calculating synonymous substitution rates (Ks). We also investigated a possible correlation between proposed WGDs and shifts in species diversification rates. We identified 19 WGDs: three ancient events along the fern phylogenetic backbone that are shared by 66%-97% of extant ferns, with additional lineage-specific WGDs for eight orders, providing strong evidence for recurring genome duplications across fern evolutionary history. We also observed similar Ks peak values for more than half of these WGDs, with multiple WGDs occurring close to the Cretaceous (~145-66 Mya). Despite the repeated WGD events, the biodiversity of ferns declined during the Cretaceous, implying that other factors probably contributed to the floristic turnover from ferns to angiosperms. This study provides molecular evidence for recurring WGDs in ferns and offers important clues to the genomic evolutionary history of ferns.
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Affiliation(s)
- Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Duoyuan Chen
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Polyploidy in gymnosperms - Insights into the genomic and evolutionary consequences of polyploidy in Ephedra. Mol Phylogenet Evol 2020; 147:106786. [PMID: 32135310 DOI: 10.1016/j.ympev.2020.106786] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 10/24/2022]
Abstract
While polyploidization is recognized as a major evolutionary driver for ferns and angiosperms, little is known about its impact in gymnosperms, where polyploidy is much less frequent. We explore Ephedra to evaluate (i) the extent of genome size diversity in the genus and the influence polyploidy has had on the evolution of nuclear DNA contents, and (ii) identify where shifts in genome size and polyploidy have occurred both temporally and spatially. A phylogenetic framework of all Ephedra species together with genome sizes and karyotypes for 87% and 67% of them respectively, were used to explore ploidy evolution and its global distribution patterns. Polyploidy was shown to be extremely common, with 41 species (83%) being polyploid (up to 8×) or having polyploid cytotypes - the highest frequency and level reported for any gymnosperm. Genome size was also diverse, with values ranging ~5-fold (8.09-38.34 pg/1C) - the largest range for any gymnosperm family - and increasing in proportion to ploidy level (i.e. no genome downsizing). Our findings provide novel data which support the view that gymnosperms have a more conserved mode of genomic evolution compared with angiosperms.
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20
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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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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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22
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Abstract
Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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Zhang R, Wang FG, Zhang J, Shang H, Liu L, Wang H, Zhao GH, Shen H, Yan YH. Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates. Int J Mol Sci 2019; 20:ijms20081926. [PMID: 31010109 PMCID: PMC6515051 DOI: 10.3390/ijms20081926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/14/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous–Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, Ceratopteris thalictroides, for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site (Ks) between paralogs; Ks age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a Ks peak value of approximately 1.2 was obtained for both samples; however, the Ks frequency distributions varied significantly. Importantly, we dated the WGD event at 51–53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as C. thalictroides, which exhibits higher temperature tolerance.
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Affiliation(s)
- Rui Zhang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Fa-Guo Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Jiao Zhang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Li Liu
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Hao Wang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Guo-Hua Zhao
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Hui Shen
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
| | - Yue-Hong Yan
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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Grossmann J, Fernández H, Chaubey PM, Valdés AE, Gagliardini V, Cañal MJ, Russo G, Grossniklaus U. Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp. affinis. FRONTIERS IN PLANT SCIENCE 2017; 8:336. [PMID: 28382042 PMCID: PMC5360702 DOI: 10.3389/fpls.2017.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 05/19/2023]
Abstract
Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a "species-specific transcriptome database" (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non-model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.
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Affiliation(s)
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology (BOS), Oviedo UniversityOviedo, Spain
- *Correspondence: Helena Fernández
| | - Pururawa M. Chaubey
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
| | - Ana E. Valdés
- Physiological Botany, Uppsala BioCenter, Uppsala UniversityUppsala, Sweden
- Linnean Centre for Plant BiologyUppsala, Sweden
| | - Valeria Gagliardini
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
| | - María J. Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology (BOS), Oviedo UniversityOviedo, Spain
| | | | - Ueli Grossniklaus
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
- Ueli Grossniklaus
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26
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Zhang Z, He Z, Xu S, Li X, Guo W, Yang Y, Zhong C, Zhou R, Shi S. Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Sci Rep 2016; 6:35634. [PMID: 27782130 PMCID: PMC5080628 DOI: 10.1038/srep35634] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 10/03/2016] [Indexed: 12/26/2022] Open
Abstract
The mangrove fern genus Acrostichum grows in the extremely unstable marine intertidal zone under harsh conditions, such as high salt concentrations, tidal rhythms and long-term climate changes. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species of Acrostichum, A. aureum and A. speciosum, as well as a species in the sister genus, Ceratopteris thalictroides. We obtained 47,517, 36,420 and 60,823 unigenes for the three ferns, of which 24.39-45.63% were annotated using public databases. The estimated divergence time revealed that Acrostichum adapted to the coastal region during the late Cretaceous, whereas the two mangrove ferns from the Indo West-Pacific (IWP) area diverged more recently. Two methods (the modified branch-site model and the Kh method) were used to identify several positively selected genes, which may contribute to differential adaptation of the two Acrostichum species to different light and salt conditions. Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone.
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Affiliation(s)
- Zhang Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
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27
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Grusz AL, Rothfels CJ, Schuettpelz E. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. BMC Genomics 2016; 17:692. [PMID: 27577050 PMCID: PMC5006594 DOI: 10.1186/s12864-016-3034-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/22/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. RESULTS We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. CONCLUSIONS Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.
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Affiliation(s)
- Amanda L. Grusz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
- Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, MN 55812 USA
| | - Carl J. Rothfels
- Department of Integrative Biology, University of California Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720-2466 USA
| | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
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28
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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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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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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31
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Soltis DE, Misra BB, Shan S, Chen S, Soltis PS. Polyploidy and the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:896-907. [PMID: 26993527 DOI: 10.1016/j.bbapap.2016.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/23/2022]
Abstract
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
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32
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Röser M. Mitosis and Interphase of the Highly Polyploid Palm Voanioalagerardii (2n = 606 ± 3). Cytogenet Genome Res 2015; 147:70-9. [PMID: 26594788 DOI: 10.1159/000441677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2015] [Indexed: 11/19/2022] Open
Abstract
The endemic, highly polyploid, monotypic Madagascan palm genus Voanioala (2n ≈ 606) was studied with regard to mitotic stages and interphase. Features of the cell cycle, morphology and sizes of metaphase chromosomes, fluorochrome banding patterns, and silver staining of NORs of such an extremely high polyploid organism are reported for the first time. On a whole, karyokinesis appears to be stable and efficient. A comparison with closely related palm taxa reveals that V. gerardii is 38-ploid, and comparison with the closely related genera Butia, Cocos (coconut) and Jubaea shows that Voanioala has lost ∼ 35% of its DNA amount subsequent to polyploidization and has suppressed between 74 and 88% of the original nucleolar organizers. About 10 active NORs are present in the nuclei. An auto- or allopolyploid origin of Voanioala is discussed with respect to currently available nuclear gene data. The biogeographic relations to Jubaeopsis, a closely related, monotypic, apparently likewise relict palm genus from eastern mainland South Africa are discussed. From a cytogenetic point of view, a common polyploid ancestor of both genera is most likely, but the available molecular phylogenetic data are not univocal.
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Affiliation(s)
- Martin Röser
- Institute of Biology, University Halle-Wittenberg, Halle, Germany
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33
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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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Suo J, Zhao Q, Zhang Z, Chen S, Cao J, Liu G, Wei X, Wang T, Yang C, Dai S. Cytological and Proteomic Analyses of Osmunda cinnamomea Germinating Spores Reveal Characteristics of Fern Spore Germination and Rhizoid Tip Growth. Mol Cell Proteomics 2015; 14:2510-34. [PMID: 26091698 DOI: 10.1074/mcp.m114.047225] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 12/29/2022] Open
Abstract
Fern spore is a good single-cell model for studying the sophisticated molecular networks in asymmetric cell division, differentiation, and polar growth. Osmunda cinnamomea L. var. asiatica is one of the oldest fern species with typical separate-growing trophophyll and sporophyll. The chlorophyllous spores generated from sporophyll can germinate without dormancy. In this study, the spore ultrastructure, antioxidant enzyme activities, as well as protein and gene expression patterns were analyzed in the course of spore germination at five typical stages (i.e. mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Proteomic analysis revealed 113 differentially expressed proteins, which were mainly involved in photosynthesis, reserve mobilization, energy supplying, protein synthesis and turnover, reactive oxygen species scavenging, signaling, and cell structure modulation. The presence of multiple proteoforms of 25 differentially expressed proteins implies that post-translational modification may play important roles in spore germination. The dynamic patterns of proteins and their encoding genes exhibited specific characteristics in the processes of cell division and rhizoid tip growth, which include heterotrophic and autotrophic metabolisms, de novo protein synthesis and active protein turnover, reactive oxygen species and hormone (brassinosteroid and ethylene) signaling, and vesicle trafficking and cytoskeleton dynamic. In addition, the function skew of proteins in fern spores highlights the unique and common mechanisms when compared with evolutionarily divergent spermatophyte pollen. These findings provide an improved understanding of the typical single-celled asymmetric division and polar growth during fern spore germination.
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Affiliation(s)
- Jinwei Suo
- From the ‡Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Qi Zhao
- From the ‡Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Zhengxiu Zhang
- From the ‡Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Sixue Chen
- ‖Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32610
| | - Jian'guo Cao
- ¶College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Guanjun Liu
- §State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Xing Wei
- §State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Tai Wang
- **Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuanping Yang
- §State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Shaojun Dai
- From the ‡Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China; §State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin 150040, China;
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35
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Henry TA, Bainard JD, Newmaster SG. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing. Genome 2015; 57:555-66. [PMID: 25727714 DOI: 10.1139/gen-2014-0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.
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Affiliation(s)
- Thomas A Henry
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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36
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Plackett ARG, Di Stilio VS, Langdale JA. Ferns: the missing link in shoot evolution and development. FRONTIERS IN PLANT SCIENCE 2015; 6:972. [PMID: 26594222 PMCID: PMC4635223 DOI: 10.3389/fpls.2015.00972] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/23/2015] [Indexed: 05/02/2023]
Abstract
Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.
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Affiliation(s)
- Andrew R. G. Plackett
- Department of Plant Sciences, University of OxfordOxford, UK
- *Correspondence: Andrew R. G. Plackett,
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37
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Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Yano K, Matsuoka M. De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB. ACTA ACUST UNITED AC 2014; 56:e5. [DOI: 10.1093/pcp/pcu184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Metcalfe CJ, Casane D. Accommodating the load: The transposable element content of very large genomes. Mob Genet Elements 2014; 3:e24775. [PMID: 24616835 PMCID: PMC3943481 DOI: 10.4161/mge.24775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 01/31/2023] Open
Abstract
Very large genomes, that is, those above 20 Gb, are rare but widely distributed throughout the eukaryotes. They are found within the diatoms, dinoflagellates, metazoans and green plants, but so far have not been found in the excavates. There is a known positive correlation between genome size and the proportion of the genome composed of transposable elements (TEs). Very large genomes may therefore be expected to be almost entirely composed of TEs. Of the large genomes examined, in the angiosperms, gymnosperms and the dinoflagellates only a small portion of the genome was identified as TEs, most of these genomes were unidentified and may be novel or diverse TEs. In the salamanders and lungfish, 25 to 47% of the genome were identifiable retrotransposons, that is, TEs that copy themselves before insertion. However, the predominant class of TEs found in the lungfish was not the same as that found in the salamanders. The little data we have at the moment suggests therefore that the diversity and abundance of TEs is variable between taxa with large genomes, similar to patterns found in taxa with smaller genomes. Based on results from the human genome, we suggest that the ‘missing’ portion of the lungfish and salamander genomes are old, highly divergent, and therefore inactive copies of TEs. The data available indicate that, unlike plants with large genomes, neither the lungfish nor the salamanders show an increased risk of extinction. Based on a slow rate of DNA loss in salamanders it has been suggested that the large salamander genome is the result of run-away genome expansion involving genome size increases via TE proliferation associated with reduced recombination rate. We know of no studies on DNA loss or recombination rates in lungfish genomes, however a similar scenario could describe the process of genome expansion in the lungfish. A series of waves of TE transposition and sequence decay would describe the pattern of TE content seen in both the lungfish and the salamanders. The lungfish and salamanders, therefore, may accommodate their large load of TEs because these TEs have accumulated gradually over a long period of time and have been subject to inactivation and decay.
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Affiliation(s)
- Cushla J Metcalfe
- Instituto de Biociências; Universidade de São Paulo; Cidade Universitária; São Paulo, Brazil
| | - Didier Casane
- Laboratoire Evolution Génomes et Spéciation; UPR9034 CNRS; Gif-sur-Yvette, France ; Université Paris Diderot; Sorbonne Paris Cité, France
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39
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Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG. Between two fern genomes. Gigascience 2014; 3:15. [PMID: 25324969 PMCID: PMC4199785 DOI: 10.1186/2047-217x-3-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/18/2014] [Indexed: 11/10/2022] Open
Abstract
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Joshua P Der
- Department of Biology, Penn State University, 201 Life Science Building, University Park, PA 16801, USA ; Current address: Department of Biological Science, California State University, 800 N. State College Blvd., Fullerton, CA 92831, USA
| | - Aaron M Duffy
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 3529-6720 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, 38 Nishigounaka, Myo-daiji-cho, Okazaki 444-8585, Japan
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Fay-Wei Li
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - D Blaine Marchant
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Carl J Rothfels
- Department of Zoology, University of British Columbia, 2329 W. Mall, WAITING Vancouver, BC V6T 1Z4, Canada ; Current address: University Herbarium and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, Berkeley, CA 94720, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Mari L Salmi
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Erin M Sigel
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Douglas E Soltis
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Dennis W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Paul G Wolf
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
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40
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Crawford DJ, Doyle JJ, Soltis DE, Soltis PS, Wendel JF. Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130341. [PMID: 24958916 PMCID: PMC4071516 DOI: 10.1098/rstb.2013.0341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Daniel J Crawford
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 17 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 17 32611, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Bomfleur B, McLoughlin S, Vajda V. Fossilized Nuclei and Chromosomes Reveal 180 Million Years of Genomic Stasis in Royal Ferns. Science 2014; 343:1376-7. [DOI: 10.1126/science.1249884] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hawkins TJ, Deeks MJ, Wang P, Hussey PJ. The evolution of the actin binding NET superfamily. FRONTIERS IN PLANT SCIENCE 2014; 5:254. [PMID: 24926301 PMCID: PMC4046492 DOI: 10.3389/fpls.2014.00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/19/2014] [Indexed: 05/19/2023]
Abstract
The Arabidopsis Networked (NET) superfamily are plant-specific actin binding proteins which specifically label different membrane compartments and identify specialized sites of interaction between actin and membranes unique to plants. There are 13 members of the superfamily in Arabidopsis, which group into four distinct clades or families. NET homologs are absent from the genomes of metazoa and fungi; furthermore, in plantae, NET sequences are also absent from the genome of mosses and more ancient extant plant clades. A single family of the NET proteins is found encoded in the club moss genome, an extant species of the earliest vascular plants. Gymnosperms have examples from families 4 and 3, with a hybrid form of NET1 and 2 which shows characteristics of both NET1 and NET2. In addition to NET3 and 4 families, the NET1 and pollen-expressed NET2 families are found only as independent sequences in Angiosperms. This is consistent with the divergence of reproductive actin. The four families are conserved across Monocots and Eudicots, with the numbers of members of each clade expanding at this point, due, in part, to regions of genome duplication. Since the emergence of the NET superfamily at the dawn of vascular plants, they have continued to develop and diversify in a manner which has mirrored the divergence and increasing complexity of land-plant species.
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Affiliation(s)
- Timothy J. Hawkins
- School of Biological and Biomedical Sciences, Durham UniversityDurham, UK
| | - Michael J. Deeks
- College of Life and Environmental Sciences, University of ExeterExeter, UK
| | - Pengwei Wang
- School of Biological and Biomedical Sciences, Durham UniversityDurham, UK
| | - Patrick J. Hussey
- School of Biological and Biomedical Sciences, Durham UniversityDurham, UK
- *Correspondence: Patrick J. Hussey, School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK e-mail:
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Lomax BH, Hilton J, Bateman RM, Upchurch GR, Lake JA, Leitch IJ, Cromwell A, Knight CA. Reconstructing relative genome size of vascular plants through geological time. THE NEW PHYTOLOGIST 2014; 201:636-644. [PMID: 24117890 DOI: 10.1111/nph.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 08/22/2013] [Indexed: 06/02/2023]
Abstract
The strong positive relationship evident between cell and genome size in both animals and plants forms the basis of using the size of stomatal guard cells as a proxy to track changes in plant genome size through geological time. We report for the first time a taxonomic fine-scale investigation into changes in stomatal guard-cell length and use these data to infer changes in genome size through the evolutionary history of land plants. Our data suggest that many of the earliest land plants had exceptionally large genome sizes and that a predicted overall trend of increasing genome size within individual lineages through geological time is not supported. However, maximum genome size steadily increases from the Mississippian (c. 360 million yr ago (Ma)) to the present. We hypothesise that the functional relationship between stomatal size, genome size and atmospheric CO2 may contribute to the dichotomy reported between preferential extinction of neopolyploids and the prevalence of palaeopolyploidy observed in DNA sequence data of extant vascular plants.
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Affiliation(s)
- Barry H Lomax
- Division of Agricultural and Environmental Sciences, The School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Jason Hilton
- School of Geography, Earth and Environmental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Garland R Upchurch
- Department of Biology, Texas State University San Marcos, San Marcos, TX, 78666, USA
| | - Janice A Lake
- Division of Agricultural and Environmental Sciences, The School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Avery Cromwell
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Charles A Knight
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
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Dyer RJ, Pellicer J, Savolainen V, Leitch IJ, Schneider H. Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae). BMC PLANT BIOLOGY 2013; 13:219. [PMID: 24354467 PMCID: PMC3930065 DOI: 10.1186/1471-2229-13-219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/10/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages. RESULTS Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size. CONCLUSIONS Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest.
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Affiliation(s)
- Robert J Dyer
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Vincent Savolainen
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Harald Schneider
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GKS, Korall P, Pryer KM. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 2013; 8:e76957. [PMID: 24116189 PMCID: PMC3792871 DOI: 10.1371/journal.pone.0076957] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.
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Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Dylan O. Burge
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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Leroux O, Eeckhout S, Viane RLL, Popper ZA. Ceratopteris richardii (C-fern): a model for investigating adaptive modification of vascular plant cell walls. FRONTIERS IN PLANT SCIENCE 2013; 4:367. [PMID: 24065974 PMCID: PMC3779834 DOI: 10.3389/fpls.2013.00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/29/2013] [Indexed: 05/22/2023]
Abstract
Plant cell walls are essential for most aspects of plant growth, development, and survival, including cell division, expansive cell growth, cell-cell communication, biomechanical properties, and stress responses. Therefore, characterizing cell wall diversity contributes to our overall understanding of plant evolution and development. Recent biochemical analyses, concomitantly with whole genome sequencing of plants located at pivotal points in plant phylogeny, have helped distinguish between homologous characters and those which might be more derived. Most plant lineages now have at least one fully sequenced representative and although genome sequences for fern species are in progress they are not yet available for this group. Ferns offer key advantages for the study of developmental processes leading to vascularisation and complex organs as well as the specific differences between diploid sporophyte tissues and haploid gametophyte tissues and the interplay between them. Ceratopteris richardii has been well investigated building a body of knowledge which combined with the genomic and biochemical information available for other plants will progress our understanding of wall diversity and its impact on evolution and development.
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Affiliation(s)
- Olivier Leroux
- Botany and Plant Science and The Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of IrelandGalway, Ireland
- Department of Biology, Research Group Pteridology, Ghent UniversityGhent, Belgium
| | - Sharon Eeckhout
- Department of Biology, Research Group Pteridology, Ghent UniversityGhent, Belgium
| | - Ronald L. L. Viane
- Department of Biology, Research Group Pteridology, Ghent UniversityGhent, Belgium
| | - Zoë A. Popper
- Botany and Plant Science and The Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of IrelandGalway, Ireland
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Bushart TJ, Cannon AE, Ul Haque A, San Miguel P, Mostajeran K, Clark GB, Porterfield DM, Roux SJ. RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): evidence for modulation by calcium pumps and apyrase activity. AMERICAN JOURNAL OF BOTANY 2013; 100:161-74. [PMID: 23048014 DOI: 10.3732/ajb.1200292] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Gravity regulates the magnitude and direction of a trans-cell calcium current in germinating spores of Ceratopteris richardii. Blocking this current with nifedipine blocks the spore's downward polarity alignment, a polarization that is fixed by gravity ∼10 h after light induces the spores to germinate. RNA-seq analysis at 10 h was used to identify genes potentially important for the gravity response. The data set will be valuable for other developmental and phylogenetic studies. METHODS De novo Newbler assembly of 958 527 reads from Roche 454 sequencing was executed. The sequences were identified and analyzed using in silico methods. The roles of endomembrane Ca(2+)-ATPase pumps and apyrases in the gravity response were further tested using pharmacological agents. KEY RESULTS Transcripts related to calcium signaling and ethylene biosynthesis were identified as notable constituents of the transcriptome. Inhibiting the activity of endomembrane Ca(2+)-ATPase pumps with 2,5-di-(t-butyl)-1,4-hydroquinone diminished the trans-cell current, but increased the orientation of the polar axis to gravity. The effects of applied nucleotides and purinoceptor antagonists gave novel evidence implicating extracellular nucleotides as regulators of the gravity response in these fern spores. CONCLUSIONS In addition to revealing general features of the transcriptome of germinating spores, the results highlight a number of calcium-responsive and light-receptive transcripts. Pharmacologic assays indicate endomembrane Ca(2+)-ATPases and extracellular nucleotides may play regulatory roles in the gravity response of Ceratopteris spores.
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Affiliation(s)
- Thomas J Bushart
- The University of Texas at Austin, 1 University Station A6700, Austin, Texas 78712, USA
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Leitch AR, Leitch IJ. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. THE NEW PHYTOLOGIST 2012; 194:629-646. [PMID: 22432525 DOI: 10.1111/j.1469-8137.2012.04105.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The large-scale replacement of gymnosperms by angiosperms in many ecological niches over time and the huge disparity in species numbers have led scientists to explore factors (e.g. polyploidy, developmental systems, floral evolution) that may have contributed to the astonishing rise of angiosperm diversity. Here, we explore genomic and ecological factors influencing seed plant genomes. This is timely given the recent surge in genomic data. We compare and contrast the genomic structure and evolution of angiosperms and gymnosperms and find that angiosperm genomes are more dynamic and diverse, particularly amongst the herbaceous species. Gymnosperms typically have reduced frequencies of a number of processes (e.g. polyploidy) that have shaped the genomes of other vascular plants and have alternative mechanisms to suppress genome dynamism (e.g. epigenetics and activity of transposable elements). Furthermore, the presence of several characters in angiosperms (e.g. herbaceous habit, short minimum generation time) has enabled them to exploit new niches and to be viable with small population sizes, where the power of genetic drift can outweigh that of selection. Together these processes have led to increased rates of genetic divergence and faster fixation times of variation in many angiosperms compared with gymnosperms.
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Affiliation(s)
- A R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, UK
| | - I J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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Yatabe Y, Yamamoto K, Tsutsumi C, Shinohara W, Murakami N, Kato M. Fertility and precocity of Osmunda x intermedia offspring in culture. JOURNAL OF PLANT RESEARCH 2011; 124:265-268. [PMID: 20839027 DOI: 10.1007/s10265-010-0374-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/17/2010] [Indexed: 05/27/2023]
Abstract
The feasibility of later-generation hybrid production in ferns has not been previously studied, although it is a significant factor in relation to reproductive isolation. Osmunda x intermedia, a hybrid between O. japonica and O. lancea, is semifertile and has moderate spore germination rates. Under the artificial conditions of this study, F2 and F3 offspring were formed. Some of the F2 offspring showed precocity, and some of the F3 offspring also showed precocity. This fertility suggests that introgressive hybridization might be ongoing in nature. This also indicates a currently unknown genetic control over the timing of fertile frond production in Osmunda.
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Affiliation(s)
- Yoko Yatabe
- Botanical Gardens, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo 112-0001, Japan.
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50
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Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 2011; 12:99. [PMID: 21303537 PMCID: PMC3042945 DOI: 10.1186/1471-2164-12-99] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 02/08/2011] [Indexed: 11/23/2022] Open
Abstract
Background Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies. Results 681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements. Conclusions This study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant.
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Affiliation(s)
- Joshua P Der
- Department of Biology and Center for Integrated Biosystems, Utah State University, Logan, UT 84322-5305, USA.
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