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MacKintosh C, Ferrier DEK. Recent advances in understanding the roles of whole genome duplications in evolution. F1000Res 2017; 6:1623. [PMID: 28928963 PMCID: PMC5590085 DOI: 10.12688/f1000research.11792.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2018] [Indexed: 01/21/2023] Open
Abstract
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
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Affiliation(s)
- Carol MacKintosh
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - David E K Ferrier
- The Scottish Oceans Institute, University of St Andrews, Scotland, KY16 8LB, UK
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Global gene expression defines faded whorl specification of double flower domestication in Camellia. Sci Rep 2017; 7:3197. [PMID: 28600507 PMCID: PMC5466612 DOI: 10.1038/s41598-017-03575-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 12/03/2022] Open
Abstract
Double flowers in cultivated camellias are divergent in floral patterns which present a rich resource for demonstrating molecular modifications influenced by the human demands. Despite the key principle of ABCE model in whorl specification, the underlying mechanism of fine-tuning double flower formation remains largely unclear. Here a comprehensive comparative transcriptomics interrogation of gene expression among floral organs of wild type and “formal double” and “anemone double” is presented. Through a combination of transcriptome, small RNA and “degradome” sequencing, we studied the regulatory gene expression network underlying the double flower formation. We obtained the differentially expressed genes between whorls in wild and cultivated Camellia. We showed that the formation of double flowers tends to demolish gene expression canalization of key functions; the faded whorl specification mechanism was fundamental under the diverse patterns of double flowers. Furthermore, we identified conserved miRNA-targets regulations in the control of double flowers, and we found that miR172-AP2, miR156-SPLs were critical regulatory nodes contributing to the diversity of double flower forms. This work highlights the hierarchical patterning of global gene expression in floral development, and supports the roles of “faded ABC model” mechanism and miRNA-targets regulations underlying the double flower domestication.
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Chartier M, Löfstrand S, von Balthazar M, Gerber S, Jabbour F, Sauquet H, Schönenberger J. How (much) do flowers vary? Unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales. Proc Biol Sci 2017; 284:20170066. [PMID: 28381623 PMCID: PMC5394665 DOI: 10.1098/rspb.2017.0066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.
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Affiliation(s)
- Marion Chartier
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Stefan Löfstrand
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Maria von Balthazar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Sylvain Gerber
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Florian Jabbour
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
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Serrano-Serrano ML, Marcionetti A, Perret M, Salamin N. Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600135. [PMID: 28439475 PMCID: PMC5400431 DOI: 10.3732/apps.1600135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15-20% of them annotated using BLAST tools. DISCUSSION This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species.
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Affiliation(s)
- Martha L. Serrano-Serrano
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Anna Marcionetti
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Mathieu Perret
- Conservatoire et Jardin botaniques de la Ville de Genève and Laboratory of Plant Systematics and Biodiversity, University of Geneva, Chemin de l’Impératrice 1, 1292 Chambésy, Geneva, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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Zhou Y, Xu Z, Yong X, Ahmad S, Yang W, Cheng T, Wang J, Zhang Q. SEP-class genes in Prunus mume and their likely role in floral organ development. BMC PLANT BIOLOGY 2017; 17:10. [PMID: 28086797 PMCID: PMC5234111 DOI: 10.1186/s12870-016-0954-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/16/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Flower phylogenetics and genetically controlled development have been revolutionised during the last two decades. However, some of these evolutionary aspects are still debatable. MADS-box genes are known to play essential role in specifying the floral organogenesis and differentiation in numerous model plants like Petunia hybrida, Arabidopsis thaliana and Antirrhinum majus. SEPALLATA (SEP) genes, belonging to the MADS-box gene family, are members of the ABCDE and quartet models of floral organ development and play a vital role in flower development. However, few studies of the genes in Prunus mume have yet been conducted. RESULTS In this study, we cloned four PmSEPs and investigated their phylogenetic relationship with other species. Expression pattern analyses and yeast two-hybrid assays of these four genes indicated their involvement in the floral organogenesis with PmSEP4 specifically related to specification of the prolificated flowers in P. mume. It was observed that the flower meristem was specified by PmSEP1 and PmSEP4, the sepal by PmSEP1 and PmSEP4, petals by PmSEP2 and PmSEP3, stamens by PmSEP2 and PmSEP3 and pistils by PmSEP2 and PmSEP3. CONCLUSION With the above in mind, flower development in P. mume might be due to an expression of SEP genes. Our findings can provide a foundation for further investigations of the transcriptional factors governing flower development, their molecular mechanisms and genetic basis.
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Affiliation(s)
- Yuzhen Zhou
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Zongda Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Xue Yong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Sagheer Ahmad
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Weiru Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Soltis PS, Soltis DE. Ancient WGD events as drivers of key innovations in angiosperms. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:159-65. [PMID: 27064530 DOI: 10.1016/j.pbi.2016.03.015] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), is a ubiquitous feature of plant genomes, contributing to variation in both genome size and gene content. Although polyploidy has occurred in all major clades of land plants, it is most frequent in angiosperms. Following a WGD in the common ancestor of all extant angiosperms, a complex pattern of both ancient and recent polyploidy is evident across angiosperm phylogeny. In several cases, ancient WGDs are associated with increased rates of species diversification. For example, a WGD in the common ancestor of Asteraceae, the largest family of angiosperms with ∼25000 species, is statistically linked to a shift in species diversification; several other old WGDs are followed by increased diversification after a 'lag' of up to three nodes. WGD may thus lead to a genomic combination that generates evolutionary novelty and may serve as a catalyst for diversification. In this paper, we explore possible links between WGD, the origin of novelty, and key innovations and propose a research path forward.
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Affiliation(s)
- Pamela S Soltis
- University of Florida, Florida Museum of Natural History, USA; University of Florida, Genetics Institute, USA.
| | - Douglas E Soltis
- University of Florida, Florida Museum of Natural History, USA; University of Florida, Genetics Institute, USA; Department of Biology, University of Florida, Gainesville, FL, USA
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