1
|
Cannon AE, Vanegas DC, Sabharwal T, Salmi ML, Wang J, Clark G, McLamore ES, Roux SJ. Polarized distribution of extracellular nucleotides promotes gravity-directed polarization of development in spores of Ceratopteris richardii. FRONTIERS IN PLANT SCIENCE 2023; 14:1265458. [PMID: 37854113 PMCID: PMC10579945 DOI: 10.3389/fpls.2023.1265458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023]
Abstract
Gravity directs the polarization of Ceratopteris fern spores. This process begins with the uptake of calcium through channels at the bottom of the spore, a step necessary for the gravity response. Data showing that extracellular ATP (eATP) regulates calcium channels led to the hypothesis that extracellular nucleotides could play a role in the gravity-directed polarization of Ceratopteris spores. In animal and plant cells ATP can be released from mechanosensitive channels. This report tests the hypothesis that the polarized release of ATP from spores could be activated by gravity, preferentially along the bottom of the spore, leading to an asymmetrical accumulation of eATP. In order to carry out this test, an ATP biosensor was used to measure the [eATP] at the bottom and top of germinating spores during gravity-directed polarization. The [eATP] along the bottom of the spore averaged 7-fold higher than the concentration at the top. All treatments that disrupted eATP signaling resulted in a statistically significant decrease in the gravity response. In order to investigate the source of ATP release, spores were treated with Brefeldin A (BFA) and gadolinium trichloride (GdCl3). These treatments resulted in a significant decrease in gravity-directed polarization. An ATP biosensor was also used to measure ATP release after treatment with both BFA and GdCl3. Both of these treatments caused a significant decrease in [ATP] measured around spores. These results support the hypothesis that ATP could be released from mechanosensitive channels and secretory vesicles during the gravity-directed polarization of Ceratopteris spores.
Collapse
Affiliation(s)
- Ashley E. Cannon
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Diana C. Vanegas
- Agricultural and Biological Engineering Department, The University of Florida, Gainesville, FL, United States
| | - Tanya Sabharwal
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Mari L. Salmi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Jeffrey Wang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Greg Clark
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Eric S. McLamore
- Agricultural and Biological Engineering Department, The University of Florida, Gainesville, FL, United States
| | - Stanley J. Roux
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
2
|
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.
Collapse
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.)
| |
Collapse
|
3
|
Cannon AE, Sabharwal T, Salmi ML, Chittari GK, Annamalai V, Leggett L, Morris H, Slife C, Clark G, Roux SJ. Two distinct light-induced reactions are needed to promote germination in spores of Ceratopteris richardii. FRONTIERS IN PLANT SCIENCE 2023; 14:1150199. [PMID: 37332704 PMCID: PMC10272463 DOI: 10.3389/fpls.2023.1150199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Germination of Ceratopteris richardii spores is initiated by light and terminates 3-4 days later with the emergence of a rhizoid. Early studies documented that the photoreceptor for initiating this response is phytochrome. However, completion of germination requires additional light input. If no further light stimulus is given after phytochrome photoactivation, the spores do not germinate. Here we show that a crucial second light reaction is required, and its function is to activate and sustain photosynthesis. Even in the presence of light, blocking photosynthesis with DCMU after phytochrome photoactivation blocks germination. In addition, RT-PCR showed that transcripts for different phytochromes are expressed in spores in darkness, and the photoactivation of these phytochromes results in the increased transcription of messages encoding chlorophyll a/b binding proteins. The lack of chlorophyll-binding protein transcripts in unirradiated spores and their slow accumulation makes it unlikely that photosynthesis is required for the initial light reaction. This conclusion is supported by the observation that the transient presence of DCMU, only during the initial light reaction, had no effect on germination. Additionally, the [ATP] in Ceratopteris richardii spores increased coincidentally with the length of light treatment during germination. Overall, these results support the conclusion that two distinct light reactions are required for the germination of Ceratopteris richardii spores.
Collapse
|
4
|
Ojosnegros S, Alvarez JM, Grossmann J, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades. Int J Mol Sci 2022; 23:ijms232214027. [PMID: 36430514 PMCID: PMC9693225 DOI: 10.3390/ijms232214027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Ferns are a diverse evolutionary lineage, sister to the seed plants, which is of great ecological importance and has a high biotechnological potential. Fern gametophytes represent one of the simplest autotrophic, multicellular plant forms and show several experimental advantages, including a simple and space-efficient in vitro culture system. However, the molecular basis of fern growth and development has hardly been studied. Here, we report on a proteomic study that identified 417 proteins shared by gametophytes of the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. Most proteins are predicted to localize to the cytoplasm, the chloroplast, or the nucleus, and are linked to enzymatic, binding, and structural activities. A subset of 145 proteins are involved in growth, reproduction, phytohormone signaling and biosynthesis, and gene expression, including homologs of SHEPHERD (SHD), HEAT SHOCK PROTEIN 90-5 (CR88), TRP4, BOBBER 1 (BOB1), FLAVONE 3'-O-METHYLTRANSFERASE 1 (OMT1), ZEAXANTHIN EPOXIDASE (ABA1), GLUTAMATE DESCARBOXYLASE 1 (GAD), and dsRNA-BINDING DOMAIN-LIKE SUPERFAMILY PROTEIN (HLY1). Nearly 25% of the annotated proteins are associated with responses to biotic and abiotic stimuli. As for biotic stress, the proteins PROTEIN SGT1 HOMOLOG B (SGT1B), SUPPRESSOR OF SA INSENSITIVE2 (SSI2), PHOSPHOLIPASE D ALPHA 1 (PLDALPHA1), SERINE/THREONINE-PROTEIN KINASE SRK2E (OST1), ACYL CARRIER PROTEIN 4 (ACP4), and NONHOST RESISTANCE TO P. S. PHASEOLICOLA1 (GLPK) are worth mentioning. Regarding abiotic stimuli, we found proteins associated with oxidative stress: SUPEROXIDE DISMUTASE[CU-ZN] 1 (CSD1), and GLUTATHIONE S-TRANSFERASE U19 (GSTU19), light intensity SERINE HYDROXYMETHYLTRANSFERASE 1 (SHM1) and UBIQUITIN-CONJUGATING ENZYME E2 35 (UBC35), salt and heavy metal stress included MITOCHONDRIAL PHOSPHATE CARRIER PROTEIN 3 (PHT3;1), as well as drought and thermotolerance: LEA7, DEAD-BOX ATP-DEPENDENT RNA HELICASE 38 (LOS4), and abundant heat-shock proteins and other chaperones. In addition, we identified interactomes using the STRING platform, revealing protein-protein associations obtained from co-expression, co-occurrence, text mining, homology, databases, and experimental datasets. By focusing on ferns, this proteomic study increases our knowledge on plant development and evolution, and may inspire future applications in crop species.
Collapse
Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomic Center Zurich, University and ETH Zurich, 8092 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - 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, 8006 Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
- Correspondence: ; Tel.: +34-985-104-811
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Geng Y, Yan A, Zhou Y. Positional cues and cell division dynamics drive meristem development and archegonium formation in Ceratopteris gametophytes. Commun Biol 2022; 5:650. [PMID: 35778477 PMCID: PMC9249879 DOI: 10.1038/s42003-022-03627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Fern gametophytes are autotrophic and independent of sporophytes, and they develop pluripotent meristems that drive prothallus development and sexual reproduction. To reveal cellular dynamics during meristem development in fern gametophytes, we performed long-term time-lapse imaging and determined the real-time lineage, identity and division activity of each single cell from meristem initiation to establishment in gametophytes of the fern Ceratopteris richardii. Our results demonstrate that in Ceratopteris gametophytes, only a few cell lineages originated from the marginal layer contribute to meristem initiation and proliferation, and the meristem lacks a distinguishable central zone or apical cell with low division activity. Within the meristem, cell division is independent of cell lineages and cells at the marginal layer are more actively dividing than inner cells. Furthermore, the meristem triggers differentiation of adjacent cells into egg-producing archegonia in a position-dependent manner. These findings advance the understanding of diversified meristem and gametophyte development in land plants. Time-lapse imaging of the fern Ceratopteris richardii during meristem initiation and proliferation provides insights into the lineage, identity and division activity of each cell throughout the growth of gametophytes.
Collapse
Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
7
|
Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
Collapse
Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
8
|
Sun J, Li GS. Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides. AMERICAN JOURNAL OF BOTANY 2020; 107:1470-1480. [PMID: 33216953 DOI: 10.1002/ajb2.1570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question. METHODS ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF. RESULTS ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it. CONCLUSIONS Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.
Collapse
Affiliation(s)
- Jun Sun
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou, 416000, China
| | - Gui-Sheng Li
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou, 416000, China
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Giarola V, Jung NU, Singh A, Satpathy P, Bartels D. Analysis of pcC13-62 promoters predicts a link between cis-element variations and desiccation tolerance in Linderniaceae. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3773-3784. [PMID: 29757404 PMCID: PMC6022661 DOI: 10.1093/jxb/ery173] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/09/2018] [Indexed: 05/24/2023]
Abstract
Reproductive structures of plants (e.g. seeds) and vegetative tissues of resurrection plants can tolerate desiccation. Many genes encoding desiccation-related proteins (DRPs) have been identified in the resurrection plant Craterostigma plantagineum, but the function of these genes remains mainly hypothetical. Here, the importance of the DRP gene pcC13-62 for desiccation tolerance is evaluated by analysing its expression in C. plantagineum and in the closely related desiccation-tolerant species Lindernia brevidens and the desiccation-sensitive species Lindernia subracemosa. Quantitative analysis revealed that pcC13-62 transcripts accumulate at a much lower level in desiccation-sensitive species than in desiccation-tolerant species. The study of pcC13-62 promoters from these species demonstrated a correlation between promoter activity and gene expression levels, suggesting transcriptional regulation of gene expression. Comparison of promoter sequences identified a dehydration-responsive element motif in the promoters of tolerant species that is required for dehydration-induced β-glucuronidase (GUS) accumulation. We hypothesize that variations in the regulatory sequences of the pcC13-62 gene occurred to establish pcC13-62 expression in vegetative tissues, which might be required for desiccation tolerance. The pcC13-62 promoters could also be activated by salt stress in Arabidopsis thaliana plants stably transformed with promoter::GUS constructs.
Collapse
Affiliation(s)
- Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee, Bonn, Germany
| | - Niklas Udo Jung
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee, Bonn, Germany
| | - Aishwarya Singh
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee, Bonn, Germany
| | - Pooja Satpathy
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee, Bonn, Germany
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee, Bonn, Germany
| |
Collapse
|
11
|
Ruiz-Estévez M, Bakkali M, Martín-Blázquez R, Garrido-Ramos MA. Identification and Characterization of TALE Homeobox Genes in the Endangered Fern Vandenboschia speciosa. Genes (Basel) 2017; 8:E275. [PMID: 29039766 PMCID: PMC5664125 DOI: 10.3390/genes8100275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 12/18/2022] Open
Abstract
We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of seven three amino acid loop extension (TALE) homeobox genes (four KNOTTED-like homeobox (KNOX) and three BEL1-like homeobox (BELL) genes) identified after next generation sequencing (NGS) and assembly of the sporophyte and gametophyte transcriptomes of the endangered fern species Vandenboschia speciosa. Among the four KNOX genes, two belonged to the KNOX1 class and the other two belonged to the KNOX2 class. Analysis of the deduced amino acid sequences supported the typical domain structure of both types of TALE proteins, and the homology to TALE proteins of mosses, lycophytes, and seed plant species. The expression analyses demonstrate that these homeodomain proteins appear to have a key role in the establishment and development of the gametophyte and sporophyte phases of V. speciosa lifecycle, as well as in the control of the transition between both phases. Vandenboschia speciosa VsKNAT3 (a KNOX2 class protein) as well as VsBELL4 and VsBELL10 proteins have higher expression levels during the sporophyte program. On the contrary, one V. speciosa KNOX1 protein (VsKNAT6) and one KNOX2 protein (VsKNAT4) seem important during the development of the gametophyte phase. TALE homeobox genes might be among the key regulators in the gametophyte-to-sporophyte developmental transition in regular populations that show alternation of generations, since some of the genes analyzed here (VsKNAT3, VsKNAT6, VsBELL4, and VsBELL6) are upregulated in a non-alternating population in which only independent gametophytes are found (they grow by vegetative reproduction outside of the range of sporophyte distribution). Thus, these four genes might trigger the vegetative propagation of the gametophyte and the repression of the sexual development in populations composed of independent gametophytes. This study represents a comprehensive identification and characterization of TALE homeobox genes in V. speciosa, and gives novel insights about the role of these genes in fern development.
Collapse
Affiliation(s)
- Mercedes Ruiz-Estévez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Mohammed Bakkali
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Rubén Martín-Blázquez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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;
| |
Collapse
|
14
|
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]
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Valledor L, Menéndez V, Canal MJ, Revilla A, Fernández H. Proteomic approaches to sexual development mediated by antheridiogen in the fern Blechnum spicant
L. Proteomics 2014; 14:2061-71. [DOI: 10.1002/pmic.201300166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/11/2014] [Accepted: 07/07/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Luis Valledor
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Virginia Menéndez
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - María Jesús Canal
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Angeles Revilla
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Helena Fernández
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| |
Collapse
|
17
|
Huang Q, Li W, Fan R, Chang Y. New MADS-box gene in fern: cloning and expression analysis of DfMADS1 from Dryopteris fragrans. PLoS One 2014; 9:e86349. [PMID: 24466046 PMCID: PMC3899247 DOI: 10.1371/journal.pone.0086349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 12/06/2013] [Indexed: 11/18/2022] Open
Abstract
MADS genes encode a family of transcription factors, some of which control the identities of floral organs in flowering plants. Most of the MADS-box genes in fern have been cloned and analyzed in model plants, such as Ceratopteris richardii and Ceratopteris pteridoides. In this study, a new MADS-box gene, DfMADS1(GU385475), was cloned from Dryopteris fragrans (L.) Schott to better understand the role of MADS genes in the evolution of floral organs. The full-length DfMADS1 cDNA was 973 bp in length with a 75bp 5′-UTR and a 169bp 3′-UTR. The DfMADS1 protein was predicted to contain a typical MIKC-type domain structure consisting of a MADS domain, a short I region, a K domain, and a C-terminal region. The DfMADS1 protein showed high homology with MADS box proteins from other ferns. Phylogenetic analysis revealed that DfMADS1 belongs to the CRM1-like subfamily. RT-PCR analysis indicated that DfMADS1 is expressed in both the gametophytes and the sporophytes of D. fragrans.
Collapse
Affiliation(s)
- Qingyang Huang
- Laboratory of Plant Research, College of Life sciences, Northeast Agricultural University, Harbin, Heilongjiang Province, P. R. China
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin, Heilongjiang Province, P. R. China
| | - Wenhua Li
- Laboratory of Plant Research, College of Life sciences, Northeast Agricultural University, Harbin, Heilongjiang Province, P. R. China
| | - Ruifeng Fan
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, P. R. China
| | - Ying Chang
- Laboratory of Plant Research, College of Life sciences, Northeast Agricultural University, Harbin, Heilongjiang Province, P. R. China
- * E-mail:
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Zha HG, Liu T, Zhou JJ, Sun H. MS-desi, a desiccation-related protein in the floral nectar of the evergreen velvet bean (Mucuna sempervirens Hemsl): molecular identification and characterization. PLANTA 2013; 238:77-89. [PMID: 23568404 DOI: 10.1007/s00425-013-1876-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/27/2013] [Indexed: 05/11/2023]
Abstract
Plant desiccation-related proteins (DRPs) were first identified as pcC13-62 from the resurrection plant Craterostigma plantagineum and it has been suggested they are involved in plant desiccation tolerance. We identified and characterized a plant DRP, which we called MS-desi, in the floral nectar of a subtropical bean species, Mucuna sempervirens (MS). MS-desi is a major nectar protein (nectarin) of the bean plant and expresses exclusively in the stylopodium, where the nectary is located. The full-length MS-desi gene encodes for a protein of 306 amino acids with a molecular mass of 33,248 Da, and possesses a ferritin-like domain and a signal peptide of 30 amino acids. Structural and phylogenetic analysis demonstrated MS-desi has high similarity to members of the plant DRPs, including pcC 13-62 protein. MS-desi has a similar hydropathy profile to that of pcC13-62 with a grand average of hydropathy index of 0.130 for MS-desi and 0.106 for pcC13-62 protein, which is very different from those of dehydrins and late embryogenesis abundant proteins. The protein's secondary structures, both predicted from the amino acid sequence and directly analysed by far UV circular dichroism, showed that MS-desi is mainly composed of alpha helices and is relatively temperature dependent. The structure change is reversible within a wide range of temperatures. Purified MS-desi and raw MS floral nectar showed dose-dependent citrate synthase inhibition activity, but insensitivity to lactate dehydrogenase, suggesting that, unlike dehydrins, it does not act as a chaperone. The overall results constitute, to our knowledge, the first study on a desiccation-related protein in plant floral nectar.
Collapse
Affiliation(s)
- Hong-Guang Zha
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | | | | | | |
Collapse
|
21
|
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.
Collapse
Affiliation(s)
- Thomas J Bushart
- The University of Texas at Austin, 1 University Station A6700, Austin, Texas 78712, USA
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Gene expression associated with apogamy commitment in Ceratopteris richardii. ACTA ACUST UNITED AC 2012; 25:293-304. [DOI: 10.1007/s00497-012-0198-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/08/2012] [Indexed: 11/26/2022]
|
23
|
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.
Collapse
Affiliation(s)
- Joshua P Der
- Department of Biology and Center for Integrated Biosystems, Utah State University, Logan, UT 84322-5305, USA.
| | | | | | | | | |
Collapse
|
24
|
Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to GxE. Trends Ecol Evol 2009; 24:649-58. [PMID: 19699549 PMCID: PMC2805859 DOI: 10.1016/j.tree.2009.06.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 06/05/2009] [Accepted: 06/08/2009] [Indexed: 12/21/2022]
Abstract
Analyses of gene expression data sets for multiple individuals and species promise to shed light on the mode of evolution of gene expression. However, complementary complexities challenge this goal. Characterization of the genetic variation underlying gene expression can easily be compromised by lack of environmental control. Conversely, the breadth of conclusions from studies of environmental effects has been limited by the use of single strains. Controlled studies have hinted at extensive genexenvironment interaction. Thus, both genetics and environment are key components in models of the evolution of gene expression. We review the literature on the evolution of gene expression in terms of genetics (G), environmental response (E) and GxE interactions to make this conceptual point.
Collapse
Affiliation(s)
- Andrea Hodgins-Davis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
| | | |
Collapse
|
25
|
Salmi ML, Roux SJ. Gene expression changes induced by space flight in single-cells of the fern Ceratopteris richardii. PLANTA 2008; 229:151-9. [PMID: 18807069 DOI: 10.1007/s00425-008-0817-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 09/03/2008] [Indexed: 05/10/2023]
Abstract
This work describes a rare high-throughput evaluation of gene expression changes induced by space flight in a single plant cell. The cell evaluated is the spore of the fern Ceratopteris richardii, which exhibits both perception and response to gravity. cDNA microarray and Q RT-PCR analysis of spores germinating in microgravity onboard NASA space shuttle flight STS-93 revealed changes in the mRNA expression of roughly 5% of genes analyzed. These gene expression changes were compared with gene expression changes that occur during gravity perception and response in animal cells and multicellular plants. Our data contribute to a better understanding of the impact of space flight conditions, including microgravity, on cellular growth and development, and provide insights into the adaptive strategies of individual cells in response to these conditions.
Collapse
Affiliation(s)
- Mari L Salmi
- Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, 1 University Station A6700, Austin, TX 78712-0183, USA
| | | |
Collapse
|
26
|
Johnson GP, Renzaglia KS. Embryology of Ceratopteris richardii (Pteridaceae, tribe Ceratopterideae), with emphasis on placental development. JOURNAL OF PLANT RESEARCH 2008; 121:581-92. [PMID: 18807118 DOI: 10.1007/s10265-008-0187-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 08/15/2008] [Indexed: 05/05/2023]
Abstract
This comprehensive study of early embryology in Ceratopteris richardii combines light microscopy with the first ultrastructural evaluation of any pteridophyte embryo. Emphasis is placed on ontogeny of the foot and placental transfer cells. The embryology of C. richardii shares many similarities with that of other polypodiacious ferns while exhibiting distinctive division patterns. Formative embryonic stages have been reconstructed into three-dimensional models for ease of interpretation. The zygote divides perpendicular to the gametophyte plane and anterioposterior axis. This division establishes a prone embryological habit that maximizes rapid independent establishment of a leaf-root axis in a cordate gametophyte. After the formation of a globular eight-celled stage, initials of the first leaf, and root and shoot apical meristems are defined early by discrete formative divisions. Concomitantly, the foot expands and differentiates to transport nutrients from the gametophyte for the developing embryonic organs. Transfer cell wall ingrowth deposition begins in the gametophyte placental cells before the adjacent sporophyte cells just after the eight-celled stage. These observations provide an anatomical framework for future comparative developmental genetic studies of embryogenesis in free-sporing plants.
Collapse
Affiliation(s)
- Gabriel P Johnson
- Green Plant Morphology Group, Department of Plant Biology, Southern Illinois University, Life Science II Rm 459, 1125 Lincoln Drive, Carbondale, IL 62901, USA.
| | | |
Collapse
|
27
|
Battaglia M, Olvera-Carrillo Y, Garciarrubio A, Campos F, Covarrubias AA. The enigmatic LEA proteins and other hydrophilins. PLANT PHYSIOLOGY 2008. [PMID: 18772351 DOI: 10.1104/pp108120725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Marina Battaglia
- Departamento de Biología Molecular de Plantas , Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, Mexico
| | | | | | | | | |
Collapse
|
28
|
Battaglia M, Olvera-Carrillo Y, Garciarrubio A, Campos F, Covarrubias AA. The enigmatic LEA proteins and other hydrophilins. PLANT PHYSIOLOGY 2008; 148:6-24. [PMID: 18772351 PMCID: PMC2528095 DOI: 10.1104/pp.108.120725] [Citation(s) in RCA: 502] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 07/08/2008] [Indexed: 05/17/2023]
Affiliation(s)
- Marina Battaglia
- Departamento de Biología Molecular de Plantas , Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, Mexico
| | | | | | | | | |
Collapse
|
29
|
Yao J, Chang C, Salmi ML, Hung YS, Loraine A, Roux SJ. Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient. BMC Bioinformatics 2008; 9:288. [PMID: 18564431 PMCID: PMC2459189 DOI: 10.1186/1471-2105-9-288] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 06/18/2008] [Indexed: 11/10/2022] Open
Abstract
Background Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. Results In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. Conclusion This study shows that SCC is an alternative to the Pearson correlation coefficient and the SD-weighted correlation coefficient, and is particularly useful for clustering replicated microarray data. This computational approach should be generally useful for proteomic data or other high-throughput analysis methodology.
Collapse
Affiliation(s)
- Jianchao Yao
- Institute for Cellular and Molecular Biology and Department of Mathematics, University of Texas at Austin, Austin, Texas 78712, USA.
| | | | | | | | | | | |
Collapse
|
30
|
Sperm cell architecture, insemination, and fertilization in the model fern, Ceratopteris richardii. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s00497-008-0068-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
31
|
Becker JD, Feijó JA. How many genes are needed to make a pollen tube? Lessons from transcriptomics. ANNALS OF BOTANY 2007; 100:1117-23. [PMID: 17951360 PMCID: PMC2759250 DOI: 10.1093/aob/mcm208] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 03/09/2007] [Accepted: 07/02/2007] [Indexed: 05/23/2023]
Abstract
BACKGROUND Pollen is the male gametophyte of higher plants. Upon pollination, it germinates and develops into a fast-growing cytoplasmic extension, the pollen tube, which ultimately delivers the sperm into the ovary. The biological relevance of its role, and the uniqueness of this kind of cellular organization, have made pollen the focus of many approaches, and it stands today as one of the best-known models in plant cell biology. In contrast, the genetic background of its development has been until recently largely unknown. Some genes involved have been described and a few functional mutants have been characterized, but only to a limited extent and allowing only a limited understanding of the regulatory mechanisms. Yet, being a relatively simple organ (2 or 3 cells), pollen stands as an excellent target for molecular-biology-based approaches. RECENT PROGRESS Recent studies on Arabidopsis thaliana have characterized the transcriptional profile of pollen grains and microgametogenesis in comparison to sporophytic tissues. They underline the unique characteristics of pollen, not only in terms of a strongly reduced set of genes being expressed, but also in terms of the functions of the proteins encoded and the pathways they are involved in. These approaches have expanded the number of genes with known expression in pollen from a few hundred to nearly eight thousand. While for the first time allowing systems and/or gene-family approaches, this information also expands dramatically the possibility of hypothesis-driven experimentation based on specific gene function predictions. Recent studies reveal this to be the case in, for example, transcriptional regulation, cell-cycle progression and gene-silencing mechanisms in mature pollen.
Collapse
Affiliation(s)
- Jörg D. Becker
- Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de Ciência, PT-2780–156 Oeiras, Portugal
| | - José A. Feijó
- Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de Ciência, PT-2780–156 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, Dept. Biologia Vegetal, Campo Grande, C2, PT-1749-016 Lisboa, Portugal
| |
Collapse
|
32
|
Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI. An optimized procedure greatly improves EST vector contamination removal. BMC Genomics 2007; 8:416. [PMID: 17997864 PMCID: PMC2194723 DOI: 10.1186/1471-2164-8-416] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 11/13/2007] [Indexed: 11/21/2022] Open
Abstract
Background The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious concern to researchers. Removal of vector contamination is one of the most significant operations to obtain accurate sequence data containing only a cDNA insert from the basecalls output by an automatic DNA sequencer. Popular bioinformatics programs to accomplish vector trimming include LUCY, cross_match and SeqClean. Results In a recent study, where the program SeqClean was used to remove vector contamination from our test set of EST data compiled through various library construction systems, however, a significant number of errors remained after preliminary trimming. These errors were later almost completely corrected by simply using a re-linearized form of the cloning vector to compare against the target ESTs. The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. Using SeqClean with a re-linearized form of the cloning vector significantly surpassed the other two programs in all tested conditions, while the performance of the other two programs was not influenced by the modified procedure. Vector contamination in dbEST was also investigated in this study: 2203 out of the 48212 ESTs sampled from dbEST (2007-04-18 freeze) were found to match sequences in UNIVEC. Conclusion Vector contamination remains a serious concern to the data quality in the public sequence database nowadays. Based on the results presented here, we feel that our modified procedure with SeqClean should be recommended to all researchers for the task of vector removal from EST or genomic sequences.
Collapse
Affiliation(s)
- Yi-An Chen
- Bioinformatics Core Laboratory, Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
| | | | | | | | | |
Collapse
|
33
|
Affiliation(s)
- Travis A Clark
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | | |
Collapse
|
34
|
Goepfert S, Poirier Y. Beta-oxidation in fatty acid degradation and beyond. CURRENT OPINION IN PLANT BIOLOGY 2007; 10:245-51. [PMID: 17434787 DOI: 10.1016/j.pbi.2007.04.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 04/03/2007] [Indexed: 05/14/2023]
Abstract
The degradation of fatty acids in plants occurs primarily in the peroxisomes through the beta-oxidation cycle. Enzymes that are involved in various aspects of beta-oxidation have been identified recently and shown to act biochemically on a diversity of fatty acids and derivatives. Analysis of several mutants has revealed essential roles for beta-oxidation in the breakdown of reserve triacylglycerols, seed development, seed germination and post-germinative growth before the establishment of photosynthesis. Beta-oxidation has also a considerable importance during the vegetative and reproductive growth phases, and plays a role in plant responses to stress, particularly in the synthesis of jasmonic acid.
Collapse
Affiliation(s)
- Simon Goepfert
- Department of Plant Molecular Biology, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | |
Collapse
|
35
|
Salmi ML, Morris KE, Roux SJ, Porterfield DM. Nitric oxide and cGMP signaling in calcium-dependent development of cell polarity in Ceratopteris richardii. PLANT PHYSIOLOGY 2007; 144:94-104. [PMID: 17351052 PMCID: PMC1913794 DOI: 10.1104/pp.107.096131] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Single-celled spores of the fern Ceratopteris richardii undergo gravity-directed cell polarity development that is driven by polar calcium currents. Here we present results that establish a role for nitric oxide (NO)/cGMP signaling in transducing the stimulus of gravity to directed polarization of the spores. Application of specific NO donors and scavengers inhibited the calcium-dependent gravity response in a dose-dependent manner. The effects of NO donor exposure were antagonized by application of NO scavenger compounds. Similarly, the guanylate cyclase inhibitors 6-anilino-5,8-quinolinedione and 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin, and the phosphodiesterase inhibitor Viagra, which modulate NO-dependent cGMP levels in the cells, disrupted gravity-directed cell polarity in a dose-dependent manner. Viagra effects were antagonized by application of NO scavengers, consistent with the postulate that NO and cGMP are linked in the signaling pathway. To identify other components of the signaling system we analyzed gene expression changes induced by Viagra treatment using microarrays and quantitative real-time reverse transcription-polymerase chain reaction. Preliminary microarray analysis revealed several genes whose expression was significantly altered by Viagra treatment. Three of these genes had strong sequence similarity to key signal transduction or stress response genes and quantitative real-time reverse transcription-polymerase chain reaction was used to more rigorously quantify the effects of Viagra on their expression in spores and to test how closely these effects could be mimicked by treatment with dibutyryl cGMP. Taken together our results implicate NO and cGMP as downstream effectors that help link the gravity stimulus to polarized growth in C. richardii spores. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers BE 640669 to BE 643506, BQ 086920 to BQ 087668, and CV 734654 to CV 736151.
Collapse
Affiliation(s)
- Mari L Salmi
- Section of Molecular Cell and Developmental Biology, University of Texas, Austin, TX 78712, USA
| | | | | | | |
Collapse
|
36
|
Wada M. The fern as a model system to study photomorphogenesis. JOURNAL OF PLANT RESEARCH 2007; 120:3-16. [PMID: 17252173 DOI: 10.1007/s10265-006-0064-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 10/17/2006] [Indexed: 05/13/2023]
Abstract
The fern gametophyte is a good model system for studying cell biological, physiological, and photobiological aspects of the fundamental processes of plant development and physiological phenomena, because of its autotrophic characteristics and its simple structure. The cells, moreover, are not surrounded by tissue, so observation and manipulation of the cells are very easy. Here I summarize a part of my knowledge of fern systems, which I have studied for nearly 40 years.
Collapse
Affiliation(s)
- Masamitsu Wada
- Division of Photobiology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.
| |
Collapse
|
37
|
Bushart TJ, Roux SJ. Conserved features of germination and polarized cell growth: a few insights from a pollen-fern spore comparison. ANNALS OF BOTANY 2007; 99:9-17. [PMID: 16867999 PMCID: PMC2802967 DOI: 10.1093/aob/mcl159] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 06/12/2006] [Indexed: 05/11/2023]
Abstract
BACKGROUND The germination of both pollen and fern spores results in the emergence of a cell-pollen tube from pollen, rhizoid from spore-that grows in a polar fashion, primarily at its apical end. In both of these tip-growing cells, the delivery of secretory vesicles to the growing end is guided in part by a calcium gradient, with calcium entering at the tip where it is most highly concentrated. The similarities between the two systems extend beyond tip-focused calcium gradients to encompass signalling pathways and elements including calmodulin, nitric oxide, annexins and Rop-GTPases. SCOPE AND AIMS This review is limited to those pathways and elements that function similarly in fern and pollen systems based on currently available evidence. The aim is to illustrate the common mechanisms by which tip growth occurs, facilitate further investigations into this area, and examine the implications for the evolutionarily conserved control of tip growth. CONCLUSIONS The interplay of calcium, nitric oxide and other effectors in both pollen and fern spores suggests certain signalling pathways became important regulators of germination and growth early in the evolution of land plants. Both large- and small-scale comparative genomic methods have shown to be promising in their ability to find new and relevant comparisons for further research. Cross-species comparisons may serve to speed up this process by highlighting both basic pathways and system-specific deviations.
Collapse
Affiliation(s)
| | - Stanley J. Roux
- Molecular Cell and Developmental Biology, University of Texas, Austin, TX 78751, USA
| |
Collapse
|
38
|
Nakazato T, Jung MK, Housworth EA, Rieseberg LH, Gastony GJ. Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii. Genetics 2006; 173:1585-97. [PMID: 16648591 PMCID: PMC1526675 DOI: 10.1534/genetics.106.055624] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 04/18/2006] [Indexed: 11/18/2022] Open
Abstract
Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (approximately 76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).
Collapse
Affiliation(s)
- Takuya Nakazato
- Department of Biology, Indiana University, Bloomington, Indiana 47405-7005, USA.
| | | | | | | | | |
Collapse
|
39
|
Zhang Q, Zhang J, Yang D, Li Y, Li S, Zhu Y. Characterisation and immunolocalisation of a pollen-specific calmodulin-binding protein from rice. FUNCTIONAL PLANT BIOLOGY : FPB 2006; 33:555-562. [PMID: 32689263 DOI: 10.1071/fp05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 03/10/2006] [Indexed: 06/11/2023]
Abstract
A novel calmodulin (CaM)-binding protein of rice (Oryza sativa pollen CaM-binding protein, OsPCBP) was isolated. It contains six tetratrcopeptide repeats (TPRs) with a molecular mass of ~76.7 kDa. Database searches show that OsPCBP is conserved in monocots and dicots. The results from CaM-agarose pull-down assays show that OsPCBP binds to CaM in a Ca2+-dependent manner and its CaM-binding domain (CBD) is located in a segment VSKGWRLLALVLSAQQRY. Northern blot and reverse transcription-polymerase chain reaction (RT-PCR) analysis have demonstrated that OsPCBP is a pollen-specific and late-expressed gene. Immunolocalisation showed that OsPCBP was localised in the amyloplast and intine during the late stage of pollen development. However, upon pollen hydration, there was some leakage of protein and the distribution of OsPCBP in the intine varied with the duration of hydration. After pollen germination, much OsPCBP was observed in the pollen tube wall. These results indicate the relationship of OsPCBP with starch accumulation and its involvement in pollen germination.
Collapse
Affiliation(s)
- Qiusheng Zhang
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Jingjing Zhang
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Daichang Yang
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Yangsheng Li
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Shaoqing Li
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Yingguo Zhu
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| |
Collapse
|
40
|
Cantero A, Barthakur S, Bushart TJ, Chou S, Morgan RO, Fernandez MP, Clark GB, Roux SJ. Expression profiling of the Arabidopsis annexin gene family during germination, de-etiolation and abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2006; 44:13-24. [PMID: 16531057 DOI: 10.1016/j.plaphy.2006.02.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Indexed: 05/07/2023]
Abstract
Annexins are a multigene family in most plant species and are suggested to play a role in a wide variety of essential cellular processes. In Arabidopsis thaliana there are eight different annexins (AnnAt1-8), which range from 29% to 83% in deduced amino acid sequence identity. As a first step toward clarifying the individual functions of these annexins, in this study we have used quantitative real time reverse transcription PCR to assess their differential expression in different tissues or after different stimuli. We determined which annexins are expressed during germination and early seedling growth by assaying annexin expression levels in dry and germinating seeds and in 7-day-old light-grown seedlings. Our results indicate that transcripts for all eight annexins are present in germinating seeds and that transcript levels for all the annexins increase by 7 days of normal growth. We assayed transcript levels in dark grown roots, cotyledons, and hypocotyls and found that the relative abundance of each annexin varied in these dark-grown tissues. We also examined the effects of red and far red light treatments on annexin expression in 5.5-day-old etiolated seedlings. Light treatments significantly altered transcript levels in hypocotyls and cotyledons for only two members of the gene family. Finally, we monitored annexin expression changes in response to a variety of abiotic stresses. We found that the expression of most of the Arabidopsis annexin genes is differentially regulated by exposure to salt, drought, and high- and low-temperature conditions, indicating a likely role for members of this gene family in stress responses.
Collapse
Affiliation(s)
- A Cantero
- Department of Molecular Cell and Developmental Biology, University of Texas, Austin, TX 78713, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Rathinasabapathi B. Ferns represent an untapped biodiversity for improving crops for environmental stress tolerance. THE NEW PHYTOLOGIST 2006; 172:385-90. [PMID: 17083670 DOI: 10.1111/j.1469-8137.2006.01889.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
|
42
|
Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Res 2005; 33:6469-85. [PMID: 16287898 PMCID: PMC1283539 DOI: 10.1093/nar/gki953] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 09/22/2005] [Accepted: 10/19/2005] [Indexed: 01/26/2023] Open
Abstract
To test the inferences of spotted microarray technology against a biochemically well-studied process, we performed transcriptional profiling of conidial germination in the filamentous fungus, Neurospora crassa. We first constructed a 70 base oligomer microarray that assays 3366 predicted genes. To estimate the relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout a time course using a Bayesian analysis of gene expression level. Remarkable consistency of mRNA profiles with previously published northern data was observed. Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. A functional classification database was employed to characterize the global picture of gene expression. Consensus motif searches identified a putative regulatory component associated with genes involved in ribosomal biogenesis. Our transcriptional profiling data correlate well with biochemical and physiological processes associated with conidial germination and will facilitate functional predictions of novel genes in N.crassa and other filamentous ascomycete species. Furthermore, our dataset on conidial germination allowed comparisons to transcriptional mechanisms associated with germination processes of diverse propagules, such as teliospores of the phytopathogenic fungus Ustilago maydis and spores of the social amoeba Dictyostelium discoideum.
Collapse
Affiliation(s)
- Takao Kasuga
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Jeffrey P. Townsend
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT 06269, USA
| | - Chaoguang Tian
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Luz B. Gilbert
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Gertrud Mannhaupt
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthD-85764 Neuherberg, Germany
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| |
Collapse
|