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Marchetti F, Distéfano AM, Cainzos M, Setzes N, Cascallares M, López GA, Zabaleta E, Carolina Pagnussat G. Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways. ANNALS OF BOTANY 2024; 134:367-384. [PMID: 38953500 PMCID: PMC11341678 DOI: 10.1093/aob/mcae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
This review summarizes recent progress in our current understanding of the mechanisms underlying the cell death pathways in bryophytes, focusing on conserved pathways and particularities in comparison to angiosperms. Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It is part of specific developmental programmes and maintains homeostasis of the organism in response to unfavourable environments. Bryophytes could provide valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to those present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programmes, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective.
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Affiliation(s)
- Fernanda Marchetti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Ayelén Mariana Distéfano
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Maximiliano Cainzos
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Nicolás Setzes
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Milagros Cascallares
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriel Alejandro López
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
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Kang P, Yoo YH, Kim DI, Yim JH, Lee H. De Novo Transcriptome Assembly and Comparative Analysis of Differentially Expressed Genes Involved in Cold Acclimation and Freezing Tolerance of the Arctic Moss Aulacomnium turgidum (Wahlenb.) Schwaegr. PLANTS (BASEL, SWITZERLAND) 2023; 12:1250. [PMID: 36986936 PMCID: PMC10054522 DOI: 10.3390/plants12061250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Cold acclimation refers to a phenomenon in which plants become more tolerant to freezing after exposure to non-lethal low temperatures. Aulacomnium turgidum (Wahlenb.) Schwaegr is a moss found in the Arctic that can be used to study the freezing tolerance of bryophytes. To improve our understanding of the cold acclimation effect on the freezing tolerance of A. turgidum, we compared the electrolyte leakage of protonema grown at 25 °C (non-acclimation; NA) and at 4 °C (cold acclimation; CA). Freezing damage was significantly lower in CA plants frozen at -12 °C (CA-12) than in NA plants frozen at -12 °C (NA-12). During recovery at 25 °C, CA-12 demonstrated a more rapid and greater level of the maximum photochemical efficiency of photosystem II than NA-12, indicating a greater recovery capacity for CA-12 compared to NA-12. For the comparative analysis of the transcriptome between NA-12 and CA-12, six cDNA libraries were constructed in triplicate, and RNA-seq reads were assembled into 45,796 unigenes. The differential gene expression analysis showed that a significant number of AP2 transcription factor genes and pentatricopeptide repeat protein-coding genes related to abiotic stress and the sugar metabolism pathway were upregulated in CA-12. Furthermore, starch and maltose concentrations increased in CA-12, suggesting that cold acclimation increases freezing tolerance and protects photosynthetic efficiency through the accumulation of starch and maltose in A. turgidum. A de novo assembled transcriptome can be used to explore genetic sources in non-model organisms.
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Affiliation(s)
- Pilsung Kang
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; (P.K.); (Y.-H.Y.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Yo-Han Yoo
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; (P.K.); (Y.-H.Y.)
| | - Dong-Il Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Joung Han Yim
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; (P.K.); (Y.-H.Y.)
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; (P.K.); (Y.-H.Y.)
- Polar Science, University of Science and Technology, Incheon 21990, Republic of Korea
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3
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Woudenberg S, Renema J, Tomescu AMF, De Rybel B, Weijers D. Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants. PLANT PHYSIOLOGY 2022; 190:85-99. [PMID: 35904762 PMCID: PMC9434249 DOI: 10.1093/plphys/kiac304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/08/2022] [Indexed: 05/31/2023]
Abstract
The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.
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Affiliation(s)
| | | | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University–Humboldt, Arcata, California 95521, USA
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Sorojsrisom ES, Haller BC, Ambrose BA, Eaton DAR. Selection on the gametophyte: Modeling alternation of generations in plants. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11472. [PMID: 35495198 PMCID: PMC9039789 DOI: 10.1002/aps3.11472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/14/2022] [Indexed: 05/12/2023]
Abstract
PREMISE The degree of gametophyte dependence on the sporophyte life stage is a major feature that differentiates the life cycles of land plants, yet the evolutionary consequences of this difference remain poorly understood. Most evolutionary models assume organisms are either haploid or diploid for their entire lifespan, which is not appropriate for simulating plant life cycles. Here, we introduce shadie (Simulating Haploid-Diploid Evolution), a new, simple Python program for implementing simulations with biphasic life cycles and analyzing their results, using SLiM 3 as a simulation back end. METHODS We implemented evolutionary simulations under three realistic plant life cycle models supported in shadie, using either standardized or biologically realistic parameter settings to test how variation in plant life cycles and sexual systems affects patterns of genome diversity. RESULTS The dynamics of single beneficial mutation fixation did not vary dramatically between different models, but the patterns of spatial variation did differ, demonstrating that different life histories and model parameters affect both genetic diversity and linkage disequilibrium. The rate of linkage disequilibrium decay away from selected sites varied depending on model parameters such as cloning and selfing rates, through their impact on effective population sizes. DISCUSSION Evolutionary simulations are an exciting, underutilized approach in evolutionary research and education. shadie can aid plant researchers in developing null hypotheses, examining theory, and designing empirical studies, in order to investigate the role of the gametophyte life stage, and the effects of variation in plant life cycles, on plant genome evolution.
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Affiliation(s)
- Elissa S. Sorojsrisom
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam Ave., Schermerhorn Ext.New York10027USA
- New York Botanical Garden2900 Southern Blvd.BronxNew York10458USA
| | - Benjamin C. Haller
- Department of Computational BiologyCornell University, IthacaNew York14853USA
| | | | - Deren A. R. Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam Ave., Schermerhorn Ext.New York10027USA
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Meissner ST. Plant sexual reproduction: perhaps the current plant two-sex model should be replaced with three- and four-sex models? PLANT REPRODUCTION 2021; 34:175-189. [PMID: 34213647 PMCID: PMC8360875 DOI: 10.1007/s00497-021-00420-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The two-sex model makes the assumption that there are only two sexual reproductive states: male and female. However, in land plants (embryophytes) the application of this model to the alternation of generations life cycle requires the subtle redefinition of several common terms related to sexual reproduction, which seems to obscure aspects of one or the other plant generation: For instance, the homosporous sporophytic plant is treated as being asexual, and the gametophytes of angiosperms treated like mere gametes. In contrast, the proposal is made that the sporophytes of homosporous plants are indeed sexual reproductive organisms, as are the gametophytes of heterosporous plants. This view requires the expansion of the number of sexual reproductive states we accept for these plant species; therefore, a three-sex model for homosporous plants and a four-sex model for heterosporous plants are described and then contrasted with the current two-sex model. These new models allow the use of sexual reproductive terms in a manner largely similar to that seen in animals, and may better accommodate the plant alternation of generations life cycle than does the current plant two-sex model. These new models may also help stimulate new lines of research, and examples of how they might alter our view of events in the flower, and may lead to new questions about sexual determination and differentiation, are presented. Thus it is suggested that land plant species have more than merely two sexual reproductive states and that recognition of this may promote our study and understanding of them.
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Affiliation(s)
- Scott T Meissner
- Institute of Biology, University of the Philippines Diliman, 1101, Quezon City, NCR, Philippines.
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De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel. Genes (Basel) 2021; 12:genes12071017. [PMID: 34208974 PMCID: PMC8304985 DOI: 10.3390/genes12071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.
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High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae. Mol Phylogenet Evol 2020; 154:106965. [PMID: 32956800 DOI: 10.1016/j.ympev.2020.106965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.
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Youngstrom CE, Geadelmann LF, Irish EE, Cheng CL. A fern WUSCHEL-RELATED HOMEOBOX gene functions in both gametophyte and sporophyte generations. BMC PLANT BIOLOGY 2019; 19:416. [PMID: 31601197 PMCID: PMC6788082 DOI: 10.1186/s12870-019-1991-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/27/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Post-embryonic growth of land plants originates from meristems. Genetic networks in meristems maintain the stem cells and direct acquisition of cell fates. WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors involved in meristem networks have only been functionally characterized in two evolutionarily distant taxa, mosses and seed plants. This report characterizes a WOX gene in a fern, which is located phylogenetically between the two taxa. RESULTS CrWOXB transcripts were detected in proliferating tissues, including gametophyte and sporophyte meristems of Ceratopteris richardii. In addition, CrWOXB is expressed in archegonia but not the antheridia of gametophytes. Suppression of CrWOXB expression in wild-type RN3 plants by RNAi produced abnormal morphologies of gametophytes and sporophytes. The gametophytes of RNAi lines produced fewer cells, and fewer female gametes compared to wild-type. In the sporophyte generation, RNAi lines produced fewer leaves, pinnae, roots and lateral roots compared to wild-type sporophytes. CONCLUSIONS Our results suggest that CrWOXB functions to promote cell divisions and organ development in the gametophyte and sporophyte generations, respectively. CrWOXB is the first intermediate-clade WOX gene shown to function in both generations in land plants.
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Affiliation(s)
| | - Lander F. Geadelmann
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
| | - Erin E. Irish
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
| | - Chi-Lien Cheng
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, Iowa 52242 USA
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Lipinska AP, Serrano-Serrano ML, Cormier A, Peters AF, Kogame K, Cock JM, Coelho SM. Rapid turnover of life-cycle-related genes in the brown algae. Genome Biol 2019; 20:35. [PMID: 30764885 PMCID: PMC6374913 DOI: 10.1186/s13059-019-1630-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations. RESULTS We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression. CONCLUSION Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.
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Affiliation(s)
- Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - Alexandre Cormier
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | | | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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11
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Histology versus phylogeny: Viewing plant embryogenesis from an evo-devo perspective. Curr Top Dev Biol 2019; 131:545-564. [DOI: 10.1016/bs.ctdb.2018.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Abstract
With the origin of pollination in ancient seed plants, the male gametophyte ("pollen") began to evolve a new and unique life history stage, the progamic phase, a post-pollination period in which pollen sexual maturation occurs in interaction with sporophyte-derived tissues. Pollen performance traits mediate the timing of the fertilization process, often in competition with other pollen, via the speed of pollen germination, sperm development, and pollen tube growth. Studies of pollen development rarely address the issue of performance or its evolution, which involves linking variation in developmental rates to relative fitness within populations or to adaptations on a macroevolutionary scale. Modifications to the pollen tube pathway and changes in the intensity of pollen competition affect the direction and strength of selection on pollen performance. Hence, pollen developmental evolution is always contextual-it involves both the population biology of pollen reaching stigmas and the co-evolution of sporophytic traits, such as the pollen tube pathway and mating system. For most species, performance evolution generally reflects a wandering history of periods of directional selection and relaxed selection, channeled by developmental limitations, a pattern that favors the accumulation of diversity and redundancy in developmental mechanisms and the genetic machinery. Developmental biologists are focused on finding universal mechanisms that underlie pollen function, and these are largely mechanisms that have evolved through their effects on performance. Here, we suggest ways in which studies of pollen performance or function could progress by cross-fertilization between the "evo" and "devo" fields.
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Affiliation(s)
- Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States.
| | - John B Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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Wilhelmsson PKI, Mühlich C, Ullrich KK, Rensing SA. Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae. Genome Biol Evol 2018; 9:3384-3397. [PMID: 29216360 PMCID: PMC5737466 DOI: 10.1093/gbe/evx258] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants—Embryophyta—with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition.
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Affiliation(s)
| | - Cornelia Mühlich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
| | | | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
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Dangwal M, Das S. Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function. J Mol Evol 2018; 86:511-530. [PMID: 30206666 DOI: 10.1007/s00239-018-9863-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Abstract
Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity. Plants at the "transition zone", between aquatic and terrestrial ecosystem, are also the most vulnerable because of climate change and may contain clues for successful mitigation of the challenges of climate change. Identification and comparative analyses of such genetic elements and gene families are few in mosses, liverworts, hornworts and lycophytes. Ovate family proteins (OFPs) are plant-specific transcriptional repressors and are acknowledged for their roles in important growth and developmental processes in land plants, and information about the functional aspects of OFPs in early land plants is fragmentary. As a first step towards addressing this gap, a comprehensive in silico analysis was carried out utilizing publicly available genome sequences of Marchantia polymorpha (Mp), Physcomitrella patens (Pp), Selaginella moellendorffii (Sm) and Sphagnum fallax (Sf). Our analysis led to the identification of 4 MpOFPs, 19 PpOFPs, 6 SmOFPs and 3 SfOFPs. Cross-genera analysis revealed a drastic change in the structure and physiochemical properties in OFPs suggesting functional diversification and genomic plasticity during the evolutionary course. Knowledge gained from this comparative analysis will form the framework towards deciphering and dissection of their developmental and adaptive role/s in early land plants and could provide insights into evolutionary strategies adapted by land plants.
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Affiliation(s)
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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Perroud PF, Haas FB, Hiss M, Ullrich KK, Alboresi A, Amirebrahimi M, Barry K, Bassi R, Bonhomme S, Chen H, Coates JC, Fujita T, Guyon-Debast A, Lang D, Lin J, Lipzen A, Nogué F, Oliver MJ, Ponce de León I, Quatrano RS, Rameau C, Reiss B, Reski R, Ricca M, Saidi Y, Sun N, Szövényi P, Sreedasyam A, Grimwood J, Stacey G, Schmutz J, Rensing SA. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:168-182. [PMID: 29681058 DOI: 10.1111/tpj.13940] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Alessandro Alboresi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mojgan Amirebrahimi
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Haodong Chen
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Daniel Lang
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Junyan Lin
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Melvin J Oliver
- USDA-ARS-MWA, Plant Genetics Research Unit, University of Missouri, Columbia, MO, 652117, USA
| | - Inés Ponce de León
- Department of Molecular Biology, Clemente Estable Biological Research Institute, Avenida Italia 3318, CP 11600, Montevideo, Uruguay
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, One Brookings Drive, St Louis, MO, 63130, USA
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Mariana Ricca
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Younousse Saidi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ning Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Avinash Sreedasyam
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
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Abstract
500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs. Many such plant-typical features have been studied in flowering plants, but their evolutionary origins were long clouded. With the sequencing of a moss genome a decade ago, inference of ancestral land plant states using comparative genomics, phylogenomics and evolutionary developmental approaches began in earnest. In the past few years, the ever increasing availability of genomic and transcriptomic data of organisms representing the earliest common ancestors of the plant tree of life has much informed our understanding of the conquest of land by plants.
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Affiliation(s)
- Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.
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18
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Grosche C, Genau AC, Rensing SA. Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1621. [PMID: 30459800 PMCID: PMC6232258 DOI: 10.3389/fpls.2018.01621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/18/2018] [Indexed: 05/08/2023]
Abstract
Arbuscular mycorrhiza is one of the most common plant symbiotic interactions observed today. Due to their nearly ubiquitous occurrence and their beneficial impact on both partners it was suggested that this mutualistic interaction was crucial for plants to colonize the terrestrial habitat approximately 500 Ma ago. On the plant side the association is established via the common symbiotic pathway (CSP). This pathway allows the recognition of the fungal symbiotic partner, subsequent signaling to the nucleus, and initiation of the symbiotic program with respect to specific gene expression and cellular re-organization. The downstream part of the CSP is a regulatory network that coordinates the transcription of genes necessary to establish the symbiosis, comprising multiple GRAS transcription factors (TFs). These regulate their own expression as an intricate transcriptional network. Deduced from non-host genome data the loss of genes encoding CSP components coincides with the loss of the interaction itself. Here, we analyzed bryophyte species with special emphasis on the moss Physcomitrella patens, supposed to be a non-host, for the composition of the GRAS regulatory network components. We show lineage specific losses and expansions of several of these factors in bryophytes, potentially coinciding with the proposed host/non-host status of the lineages. We evaluate losses and expansions and infer clade-specific evolution of GRAS TFs.
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Affiliation(s)
- Christopher Grosche
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- *Correspondence: Stefan A. Rensing,
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19
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Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell 2017; 171:287-304.e15. [PMID: 28985561 DOI: 10.1016/j.cell.2017.09.030] [Citation(s) in RCA: 721] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 04/21/2017] [Accepted: 09/18/2017] [Indexed: 02/01/2023]
Abstract
The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia.
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Shiori Sugamata Aki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Felix Althoff
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mario A Arteaga-Vazquez
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | | | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Liam Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Juan Caballero-Perez
- National Laboratory of Genomics for Biodiversity, CINVESTAV-IPN, Km 9.6 Lib. Norte Carr. Irapuato-León, 36821, Irapuato, Guanajuato, México
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Shota Chiyoda
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mansi Chovatia
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kevin M Davies
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11-600, Palmerston North, New Zealand
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ana E Dorantes-Acosta
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | - D Magnus Eklund
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Stevie N Florent
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | | | - Asao Fujiyama
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Bence Galik
- Bioinformatics & Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), UMR232, Université de Montpellier, Montpellier 34394, France
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Takahiro Hamada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | | | - Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Hirakawa
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Qidong Jia
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mitsuru Kakita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Takehiko Kanazawa
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Bank Organization, Tohoku University, Aoba, Sendai 980-8573, Japan
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Plant and Soil Sciences, University of Kentucky, 321 Plant Science Building, 1405 Veterans Dr., Lexington, KY 40546, USA
| | - Megan Kennedy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Keita Kinose
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yuji Kohara
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Eri Koide
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Komatsu
- Department of Bioproduction Technology, Junior College of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Sarah Kopischke
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Minoru Kubo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Erika Lindquist
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna M Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chia-Wei Lu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Efraín De Luna
- Instituto de Ecología, AC., Red de Biodiversidad y Sistemática, Xalapa, Veracruz, 91000, México
| | | | - Naoki Minamino
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Miya Mizutani
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Isabel Monte
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Rebecca Mosher
- The School of Plant Sciences, The University of Arizona, Tuscon, AZ, USA
| | - Hideki Nagasaki
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan; Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Kazuhiko Nishitani
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Masaki Okumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Jeremy Phillips
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Anke Reinders
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Ryosuke Sano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Shinichiro Sawa
- Graduate school of Science and Technology, Kumamoto University, Kurokami 2-39-1, Kumamoto 860-8555, Japan
| | - Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Roberto Solano
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Alexander Spunde
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | | | - Daisuke Takezawa
- Graduate School of Science and Engineering and Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan
| | - Hirokazu Tomogane
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Takashi Ueda
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Ryusuke Yokoyama
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | | | - Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Sabine Zachgo
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
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20
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Macaisne N, Liu F, Scornet D, Peters AF, Lipinska A, Perrineau MM, Henry A, Strittmatter M, Coelho SM, Cock JM. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development 2017; 144:409-418. [PMID: 28049657 DOI: 10.1242/dev.141523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/12/2016] [Indexed: 01/09/2023]
Abstract
The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.
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Affiliation(s)
- Nicolas Macaisne
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Fuli Liu
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | | | - Agnieszka Lipinska
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Marie-Mathilde Perrineau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Antoine Henry
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Martina Strittmatter
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
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21
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Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD. A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants. MOLECULAR PLANT 2016; 9:205-220. [PMID: 26687813 DOI: 10.1016/j.molp.2015.12.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 05/08/2023]
Abstract
Identifying the genetic mechanisms that underpin the evolution of new organ and tissue systems is an aim of evolutionary developmental biology. Comparative functional genetic studies between angiosperms and bryophytes can define those genetic changes that were responsible for developmental innovations. Here, we report the generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte Physcomitrella patens, including detailed sporophyte developmental progression. We identified a comprehensive set of sporophyte-specific transcription factors, and found that many of these genes have homologs in angiosperms that function in developmental processes such as flowering and shoot branching. Deletion of the PpTCP5 transcription factor results in development of supernumerary sporangia attached to a single seta, suggesting that it negatively regulates branching in the moss sporophyte. Given that TCP genes repress branching in angiosperms, we suggest that this activity is ancient. Finally, comparison of P. patens and Arabidopsis thaliana transcriptomes led us to the identification of a conserved core of transcription factors expressed in tip-growing cells. We identified modifications in the expression patterns of these genes that could account for developmental differences between P. patens tip-growing cells and A. thaliana pollen tubes and root hairs.
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Affiliation(s)
- Carlos Ortiz-Ramírez
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | | | - Anna Thamm
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Mingyi Wang
- Division of Plant Biology, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - José A Feijó
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal; Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Building, College Park, MD 20742-5815, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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22
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Johnson MG, Shaw AJ. Genetic diversity, sexual condition, and microhabitat preference determine mating patterns inSphagnum(Sphagnaceae) peat-mosses. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12497] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Matthew G. Johnson
- Biology Department; Duke University; 130 Science Drive Box 90338 Durham NC 27708 USA
| | - A. Jonathan Shaw
- Biology Department; Duke University; 130 Science Drive Box 90338 Durham NC 27708 USA
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23
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Frank MH, Scanlon MJ. Transcriptomic evidence for the evolution of shoot meristem function in sporophyte-dominant land plants through concerted selection of ancestral gametophytic and sporophytic genetic programs. Mol Biol Evol 2014; 32:355-67. [PMID: 25371433 DOI: 10.1093/molbev/msu303] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Alternation of generations, in which the haploid and diploid stages of the life cycle are each represented by multicellular forms that differ in their morphology, is a defining feature of the land plants (embryophytes). Anciently derived lineages of embryophytes grow predominately in the haploid gametophytic generation from apical cells that give rise to the photosynthetic body of the plant. More recently evolved plant lineages have multicellular shoot apical meristems (SAMs), and photosynthetic shoot development is restricted to the sporophyte generation. The molecular genetic basis for this evolutionary shift from gametophyte-dominant to sporophyte-dominant life cycles remains a major question in the study of land plant evolution. We used laser microdissection and next generation RNA sequencing to address whether angiosperm meristem patterning genes expressed in the sporophytic SAM of Zea mays are expressed in the gametophytic apical cells, or in the determinate sporophytes, of the model bryophytes Marchantia polymorpha and Physcomitrella patens. A wealth of upregulated genes involved in stem cell maintenance and organogenesis are identified in the maize SAM and in both the gametophytic apical cell and sporophyte of moss, but not in Marchantia. Significantly, meiosis-specific genetic programs are expressed in bryophyte sporophytes, long before the onset of sporogenesis. Our data suggest that this upregulated accumulation of meiotic gene transcripts suppresses indeterminate cell fate in the Physcomitrella sporophyte, and overrides the observed accumulation of meristem patterning genes. A model for the evolution of indeterminate growth in the sporophytic generation through the concerted selection of ancestral meristem gene programs from gametophyte-dominant lineages is proposed.
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24
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Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol 2014; 6:1238-52. [PMID: 24879432 PMCID: PMC4041004 DOI: 10.1093/gbe/evu099] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandInstitute of Systematic Botany, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandMTA-ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Hungary
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Zsófia Hock
- Institute of Systematic Botany, University of Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), SingaporeThe Santa Fe Institute, Santa Fe NM
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25
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O’Donoghue MT, Chater C, Wallace S, Gray JE, Beerling DJ, Fleming AJ. Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3567-81. [PMID: 23888066 PMCID: PMC3745722 DOI: 10.1093/jxb/ert190] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Bryophytes, the most basal of the extant land plants, diverged at least 450 million years ago. A major feature of these plants is the biphasic alternation of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. These dramatic differences in form and function occur in a constant genetic background, raising the question of whether the switch from gametophyte-to-sporophyte development reflects major changes in the spectrum of genes being expressed or alternatively whether only limited changes in gene expression occur and the differences in plant form are due to differences in how the gene products are put together. This study performed replicated microarray analyses of RNA from several thousand dissected and developmentally staged sporophytes of the moss Physcomitrella patens, allowing analysis of the transcriptomes of the sporophyte and early gametophyte, as well as the early stages of moss sporophyte development. The data indicate that more significant changes in transcript profile occur during the switch from gametophyte to sporophyte than recently reported, with over 12% of the entire transcriptome of P. patens being altered during this major developmental transition. Analysis of the types of genes contributing to these differences supports the view of the early sporophyte being energetically and nutritionally dependent on the gametophyte, provides a profile of homologues to genes involved in angiosperm stomatal development and physiology which suggests a deeply conserved mechanism of stomatal control, and identifies a novel series of transcription factors associated with moss sporophyte development.
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Affiliation(s)
| | - Caspar Chater
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Simon Wallace
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Julie E. Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew J. Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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26
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McDaniel SF, Neubig KM, Payton AC, Quatrano RS, Cove DJ. Recent gene-capture on the UV sex chromosomes of the moss Ceratodon purpureus. Evolution 2013; 67:2811-22. [PMID: 24094335 DOI: 10.1111/evo.12165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/02/2013] [Indexed: 01/12/2023]
Abstract
Sex chromosomes evolve from ordinary autosomes through the expansion and subsequent degeneration of a region of suppressed recombination that is inherited through one sex. Here we investigate the relative timing of these processes in the UV sex chromosomes of the moss Ceratodon purpureus using molecular population genetic analyses of eight newly discovered sex-linked loci. In this system, recombination is suppressed on both the female-transmitted (U) sex chromosome and the male-transmitted (V) chromosome. Genes on both chromosomes therefore should show the deleterious effects of suppressed recombination and sex-limited transmission, while purifying selection should maintain homologs of genes essential for both sexes on both sex chromosomes. Based on analyses of eight sex-linked loci, we show that the nonrecombining portions of the U and V chromosomes expanded in at least two events (~0.6-1.3 MYA and ~2.8-3.5 MYA), after the divergence of C. purpureus from its dioecious sister species, Trichodon cylindricus and Cheilothela chloropus. Both U- and V-linked copies showed reduced nucleotide diversity and limited population structure, compared to autosomal loci, suggesting that the sex chromosomes experienced more recent selective sweeps that the autosomes. Collectively these results highlight the dynamic nature of gene composition and molecular evolution on nonrecombining portions of the U and V sex chromosomes.
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Affiliation(s)
- Stuart F McDaniel
- Biology Department, University of Florida, Gainesville, Florida, 32611.
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27
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Szövényi P, Ricca M, Hock Z, Shaw JA, Shimizu KK, Wagner A. Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Mol Biol Evol 2013; 30:1929-39. [PMID: 23686659 DOI: 10.1093/molbev/mst095] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The masking hypothesis predicts that selection is more efficient in haploids than in diploids, because dominant alleles can mask the deleterious effects of recessive alleles in diploids. However, gene expression breadth and noise can potentially counteract the effect of masking on the rate at which genes evolve. Land plants are ideal to ask whether masking, expression breadth, or expression noise dominate in their influence on the rate of molecular evolution, because they have a biphasic life cycle in which the duration and complexity of the haploid and diploid phase varies among organisms. Here, we generate and compile genome-wide gene expression, sequence divergence, and polymorphism data for Arabidopsis thaliana and for the moss Funaria hygrometrica to show that the evolutionary rates of haploid- and diploid-specific genes contradict the masking hypothesis. Haploid-specific genes do not evolve more slowly than diploid-specific genes in either organism. Our data suggest that gene expression breadth influence the evolutionary rate of phase-specific genes more strongly than masking. Our observations have implications for the role of haploid life stages in the purging of deleterious mutations, as well as for the evolution of ploidy.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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28
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Wuest SE, Schmid MW, Grossniklaus U. Cell-specific expression profiling of rare cell types as exemplified by its impact on our understanding of female gametophyte development. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:41-9. [PMID: 23276786 DOI: 10.1016/j.pbi.2012.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/03/2012] [Indexed: 05/20/2023]
Abstract
Expression profiling of single cells can yield insights into cell specification, cellular differentiation processes, and cell type-specific responses to environmental stimuli. Recent work has established excellent tools to perform genome-wide expression studies of individual cell types, even if the cells of interest occur at low frequency within an organ. We review the advances and impact of gene expression studies of rare cell types, as exemplified by recently gained insights into the development and function of the angiosperm female gametophyte. The detailed transcriptional characterization of different stages during female gametophyte development has significantly helped to improve our understanding of cellular specification or cell-cell communication processes. Next-generation sequencing approaches--used increasingly for expression profiling--will now allow for comparative approaches that focus on agriculturally, ecologically or evolutionarily relevant aspects of plant reproduction.
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Affiliation(s)
- Samuel E Wuest
- Institute of Evolutionary Biology and Environmental Studies & Zürich-Basel Plant Science Center, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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29
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Fernández-Aparicio M, Huang K, Wafula EK, Honaas LA, Wickett NJ, Timko MP, dePamphilis CW, Yoder JI, Westwood JH. Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development. Mol Biol Rep 2012; 40:3395-407. [DOI: 10.1007/s11033-012-2417-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/18/2012] [Indexed: 12/11/2022]
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30
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Schmidt A, Schmid MW, Grossniklaus U. Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:18-29. [PMID: 22449040 DOI: 10.1111/j.1365-313x.2012.04897.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reproduction is a crucial step in the life cycle of plants. The male and female germline lineages develop in the reproductive organs of the flower, which in higher plants are the anthers and ovules, respectively. Development of the germline lineage initiates from a dedicated sporophytic cell that undergoes meiosis to form spores that subsequently give rise to the gametophytes through mitotic cell divisions. The mature male and female gametophytes harbour the male (sperm cells) and female gametes (egg and central cell), respectively. Those unite during double fertilization to initiate embryo and endosperm development in sexually reproducing higher plants. While cytological changes involved in development of the germline lineages have been well characterized in a number of species, investigation of the transcriptional basis underlying their development and the specification of the gametes proved challenging. This is largely due to the inaccessibility of the cells constituting the germline lineages, which are enclosed by sporophytic tissues. Only recently, these technical limitations could be overcome by combining new methods to isolate the relevant cells with powerful transcriptional profiling methods, such as microarrays or high-throughput sequencing of RNA. This review focuses on these technical advances and the new insights gained from them concerning the transcriptional basis and molecular mechanisms underlying germline development.
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Affiliation(s)
- Anja Schmidt
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, Zürich, Switzerland.
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31
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Ligrone R, Duckett JG, Renzaglia KS. Major transitions in the evolution of early land plants: a bryological perspective. ANNALS OF BOTANY 2012; 109:851-71. [PMID: 22356739 PMCID: PMC3310499 DOI: 10.1093/aob/mcs017] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/06/2012] [Indexed: 05/02/2023]
Abstract
Background Molecular phylogeny has resolved the liverworts as the earliest-divergent clade of land plants and mosses as the sister group to hornworts plus tracheophytes, with alternative topologies resolving the hornworts as sister to mosses plus tracheophytes less well supported. The tracheophytes plus fossil plants putatively lacking lignified vascular tissue form the polysporangiophyte clade. Scope This paper reviews phylogenetic, developmental, anatomical, genetic and paleontological data with the aim of reconstructing the succession of events that shaped major land plant lineages. Conclusions Fundamental land plant characters primarily evolved in the bryophyte grade, and hence the key to a better understanding of the early evolution of land plants is in bryophytes. The last common ancestor of land plants was probably a leafless axial gametophyte bearing simple unisporangiate sporophytes. Water-conducting tissue, if present, was restricted to the gametophyte and presumably consisted of perforate cells similar to those in the early-divergent bryophytes Haplomitrium and Takakia. Stomata were a sporophyte innovation with the possible ancestral functions of producing a transpiration-driven flow of water and solutes from the parental gametophyte and facilitating spore separation before release. Stomata in mosses, hornworts and polysporangiophytes are viewed as homologous, and hence these three lineages are collectively referred to as the 'stomatophytes'. An indeterminate sporophyte body (the sporophyte shoot) developing from an apical meristem was the key innovation in polysporangiophytes. Poikilohydry is the ancestral condition in land plants; homoiohydry evolved in the sporophyte of polysporangiophytes. Fungal symbiotic associations ancestral to modern arbuscular mycorrhizas evolved in the gametophytic generation before the separation of major present-living lineages. Hydroids are imperforate water-conducting cells specific to advanced mosses. Xylem vascular cells in polysporangiophytes arose either from perforate cells or de novo. Food-conducting cells were a very early innovation in land plant evolution. The inferences presented here await testing by molecular genetics.
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Affiliation(s)
- Roberto Ligrone
- Dipartimento di Scienze ambientali, Seconda Università di Napoli, via Vivaldi 43, Caserta, Italy.
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32
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Pires ND, Dolan L. Morphological evolution in land plants: new designs with old genes. Philos Trans R Soc Lond B Biol Sci 2012; 367:508-18. [PMID: 22232763 PMCID: PMC3248709 DOI: 10.1098/rstb.2011.0252] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The colonization and radiation of multicellular plants on land that started over 470 Ma was one of the defining events in the history of this planet. For the first time, large amounts of primary productivity occurred on the continental surface, paving the way for the evolution of complex terrestrial ecosystems and altering global biogeochemical cycles; increased weathering of continental silicates and organic carbon burial resulted in a 90 per cent reduction in atmospheric carbon dioxide levels. The evolution of plants on land was itself characterized by a series of radical transformations of their body plans that included the formation of three-dimensional tissues, de novo evolution of a multicellular diploid sporophyte generation, evolution of multicellular meristems, and the development of specialized tissues and organ systems such as vasculature, roots, leaves, seeds and flowers. In this review, we discuss the evolution of the genes and developmental mechanisms that drove the explosion of plant morphologies on land. Recent studies indicate that many of the gene families which control development in extant plants were already present in the earliest land plants. This suggests that the evolution of novel morphologies was to a large degree driven by the reassembly and reuse of pre-existing genetic mechanisms.
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Affiliation(s)
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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33
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Rüdinger M, Szövényi P, Rensing SA, Knoop V. Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:370-380. [PMID: 21466601 DOI: 10.1111/j.1365-313x.2011.04600.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The plant-specific pentatricopeptide repeat (PPR) proteins with variable PPR repeat lengths (PLS-type) and protein extensions up to the carboxyterminal DYW domain have received attention as specific recognition factors for the C-to-U type of RNA editing events in plant organelles. Here, we report a DYW-protein knockout in the model plant Physcomitrella patens specifically affecting mitochondrial RNA editing positions cox1eU755SL and rps14eU137SL. Assignment of DYW proteins and RNA editing sites might best be corroborated by data from a taxon with a slightly different, yet similarly manageable low number of editing sites and DYW proteins. To this end we investigated the mitochondrial editing status of the related funariid moss Funaria hygrometrica. We find that: (i) Funaria lacks three mitochondrial RNA editing positions present in Physcomitrella, (ii) that F. hygrometrica cDNA sequence data identify nine DYW proteins as clear orthologues of their P. patens counterparts, and (iii) that the 'missing' 10th DYW protein in F. hygrometrica is responsible for two mitochondrial editing sites in P. patens lacking in F. hygrometrica (nad3eU230SL, nad4eU272SL). Interestingly, the third site of RNA editing missing in F. hygrometrica (rps14eU137SL) is addressed by the DYW protein characterized here and the presence of its orthologue in F. hygrometrica is explained through its simultaneous action on site cox1eU755SL conserved in both mosses.
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Affiliation(s)
- Mareike Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, Bonn, Germany
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