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Chen W, Chen L, Cui L, Liu Z, Yuan W. Genome-wide analysis of radish AHL gene family and functional verification of RsAHL14 in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1401414. [PMID: 38872889 PMCID: PMC11169806 DOI: 10.3389/fpls.2024.1401414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/15/2024] [Indexed: 06/15/2024]
Abstract
The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factors involved in plant growth, development, and stress responses. However, AHLs have not been systematically analyzed in radish (Raphanus sativus). Therefore, we performed genome-wide identification and expression pattern, gene structure, and function verifications of radish AHLs. We identified 52 radish AHLs (RsAHL1-RsAHL52), which were unevenly distributed across nine chromosomes. Phylogenetic analysis showed that the RsAHLs were divided into two clades (A and B) and subdivided into three types (I, II, and III). Collinearity analysis revealed that the 52 RsAHLs produced 49 repeat events. Tissue expression profiles revealed differential expression of RsAHLs across different tissues, with higher expression observed in flower organs, particularly petals and anthers. qRT-PCR results indicated that RsAHLs responded to abscisic acid, methyl jasmonate, and abiotic stress (low and high temperatures and drought). Additionally, RsAHL14 induced a dwarf phenotype in tomato plants, and RsAHL14-overexpression tomato plants presented significantly decreased expression levels of the gibberellin (GA) synthetic genes ent-Copalyl diphosphatase, GA3ox-3/-4/-5, and GA20ox-1/-2/-3, but significantly increased expression of the degradation gene GA2ox-1/-3. Thus, RsAHL14 might affect plant growth by regulating GA content. Collectively, our study comprehensively identified RsAHLs in radish and provided a reference for further research on these genes.
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Affiliation(s)
| | | | | | | | - Weiling Yuan
- Hubei Key Laboratory of Vegetable Germplasm Innovation and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
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2
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Inta W, Traiperm P, Ruchisansakun S, Janssens SB, Viboonjun U, Swangpol SC. Evolution and Classification of Musaceae Based on Male Floral Morphology. PLANTS (BASEL, SWITZERLAND) 2023; 12:1602. [PMID: 37111826 PMCID: PMC10144554 DOI: 10.3390/plants12081602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/02/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Classification of the banana family (Musaceae) into three genera, Musa, Ensete and Musella, and infrageneric ranking are still ambiguous. Within the genus Musa, five formerly separated sections were recently merged into sections Musa and Callimusa based on seed morphology, molecular data and chromosome numbers. Nevertheless, other key morphological characters of the genera, sections, and species have not been clearly defined. This research aims to investigate male floral morphology, classify members of the banana family based on overall similarity of morphological traits using 59 banana accessions of 21 taxa and make inferences of the evolutionary relationships of 57 taxa based on ITS, trnL-F, rps16 and atpB-rbcL sequences from 67 Genbank and 10 newly collected banana accessions. Fifteen quantitative characters were examined using principal component analysis and canonical discriminant analysis and 22 qualitative characters were analyzed by the Unweighted Pair Group Method with an Arithmetic Mean (UPGMA). The results showed that fused tepal morphology, median inner tepal shape and length of style supported the three clades of Musa, Ensete and Musella, while shapes of median inner tepal and stigma classified the two Musa sections. In conclusion, a combination of morphological characters of male flowers and molecular phylogenetics well support the taxonomic arrangement within the banana family and the Musa genus and assist in selection of characters to construct an identification key of Musaceae.
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Affiliation(s)
- Wandee Inta
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Paweena Traiperm
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Saroj Ruchisansakun
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Steven B. Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
- Department of Biology, KU Leuven, 3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, 3001 Leuven, Belgium
| | - Unchera Viboonjun
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sasivimon C. Swangpol
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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3
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Zhao H, Liao H, Li S, Zhang R, Dai J, Ma P, Wang T, Wang M, Yuan Y, Fu X, Cheng J, Duan X, Xie Y, Zhang P, Kong H, Shan H. Delphinieae flowers originated from the rewiring of interactions between duplicated and diversified floral organ identity and symmetry genes. THE PLANT CELL 2023; 35:994-1012. [PMID: 36560915 PMCID: PMC10015166 DOI: 10.1093/plcell/koac368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Species of the tribe Delphinieae (Ranunculaceae) have long been the focus of morphological, ecological, and evolutionary studies due to their highly specialized, nearly zygomorphic (bilaterally symmetrical) spiral flowers with nested petal and sepal spurs and reduced petals. The mechanisms underlying the development and evolution of Delphinieae flowers, however, remain unclear. Here, by conducting extensive phylogenetic, comparative transcriptomic, expression, and functional studies, we clarified the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae. We found that duplication and/or diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes was tightly associated with the origination of Delphinieae flowers. Specifically, an AGL6-lineage member (such as the Delphinium ajacis AGL6-1a) represses sepal spur formation and petal development in the lateral and ventral parts of the flower while determining petal identity redundantly with AGL6-1b. By contrast, two CYC2-like genes, CYC2b and CYC2a, define the dorsal and lateral-ventral identities of the flower, respectively, and form complex regulatory links with AP3-3, AGL6-1a, and DIV1. Therefore, duplication and diversification of floral symmetry genes, as well as co-option of the duplicated copies into the preexisting floral regulatory network, have been key for the origin of Delphinieae flowers.
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Affiliation(s)
- Huiqi Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Hong Liao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuixian Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Dai
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Pengrui Ma
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tianpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meimei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Yi Yuan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jie Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yanru Xie
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Advances in Research on the Regulation of Floral Development by CYC-like Genes. Curr Issues Mol Biol 2023; 45:2035-2059. [PMID: 36975501 PMCID: PMC10047570 DOI: 10.3390/cimb45030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.
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Damerval C, Claudot C, Le Guilloux M, Conde e Silva N, Brunaud V, Soubigou-Taconnat L, Caius J, Delannoy E, Nadot S, Jabbour F, Deveaux Y. Evolutionary analyses and expression patterns of TCP genes in Ranunculales. FRONTIERS IN PLANT SCIENCE 2022; 13:1055196. [PMID: 36531353 PMCID: PMC9752903 DOI: 10.3389/fpls.2022.1055196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
TCP transcription factors play a role in a large number of developmental processes and are at the crossroads of numerous hormonal biosynthetic and signaling pathways. The complete repertoire of TCP genes has already been characterized in several plant species, but not in any species of early diverging eudicots. We focused on the order Ranunculales because of its phylogenetic position as sister group to all other eudicots and its important morphological diversity. Results show that all the TCP genes expressed in the floral transcriptome of Nigella damascena (Ranunculaceae) are the orthologs of the TCP genes previously identified from the fully sequenced genome of Aquilegia coerulea. Phylogenetic analyses combined with the identification of conserved amino acid motifs suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. We highlight independent duplications in core eudicots and Ranunculales within the class I and class II subfamilies, resulting in different numbers of paralogs within the main subclasses of TCP genes. This has most probably major consequences on the functional diversification of these genes in different plant clades. The expression patterns of TCP genes in Nigella damascena were consistent with the general suggestion that CIN and class I TCP genes may have redundant roles or take part in same pathways, while CYC/TB1 genes have more specific actions. Our findings open the way for future studies at the tissue level, and for investigating redundancy and subfunctionalisation in TCP genes and their role in the evolution of morphological novelties.
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Affiliation(s)
- Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Carmine Claudot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - José Caius
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
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6
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Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
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Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
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7
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Lightweight Challenge-Response Authentication in SDN-Based UAVs Using Elliptic Curve Cryptography. ELECTRONICS 2022. [DOI: 10.3390/electronics11071026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Unmanned aerial vehicles (UAVs) (also known as drones) are aircraft that do not require the presence of a human pilot to fly. UAVs can be controlled remotely by a human operator or autonomously by onboard computer systems. UAVs have many military uses, including battlefield surveillance, effective target tracking and engagement in air-to-ground warfare, and situational awareness in challenging circumstances. They also offer a distinct advantage in various applications such as forest fire monitoring and surveillance. Surveillance systems are developed using advanced technologies in the modern era of communications and networks. As a result, UAVs require enhancements to control and manage systems efficiently. Network security is a critical concern with respect to UAVs due to the risk of surveillance information theft and physical misuse. Although several new tools have been introduced to secure networks, attackers can use more advanced methods to get into a UAV network and create problems that pose an organizational threat to the entire system. Security mechanisms also reduce the performance of systems because some restrictive measures prevent users from accessing specific resources, but a few techniques and tools have overcome the problem of performance reduction in various scenarios. There are many types of attacks, i.e., denial of service attacks (DOS), distributed denial of service attacks (DDOS), address resolution protocol (ARP) spoofing, sniffing, etc., that make it challenging to maintain a UAV network. This research paper proposes a lightweight challenge-response authentication that can overcome the previously mentioned problems. As security is provided by utilizing a minimum number of bits in memory, this technique offers the same security features while using fewer network resources, low computing resources, and low power consumption.
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Yu Q, Tian X, Lin C, Specht CD, Liao J. Expression and Function Studies of CYC/ TB1-Like Genes in the Asymmetric Flower Canna (Cannaceae, Zingiberales). FRONTIERS IN PLANT SCIENCE 2020; 11:580576. [PMID: 33343594 PMCID: PMC7746682 DOI: 10.3389/fpls.2020.580576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
The asymmetric flower, lacking any plane of symmetry, is rare among angiosperms. Canna indica L. has conspicuously asymmetric flowers resulting from the presence of a half-fertile stamen, while the other androecial members develop as petaloid staminodes or abort early during development. The molecular basis of the asymmetric distribution of fertility and petaloidy in the androecial whorls remains unknown. Ontogenetic studies have shown that Canna flowers are borne on monochasial (cincinnus) partial florescences within a racemose inflorescence, with floral asymmetry likely corresponding to the inflorescence architecture. Given the hypothesized role of CYC/TB1 genes in establishing floral symmetry in response to the influence of the underlying inflorescence architecture, the spatiotemporal expression patterns of three Canna CYC/TB1 homologs (CiTBL1a, CiTBL1b-1, and CiTBL1b-2) were analyzed during inflorescence and floral development using RNA in situ hybridization and qRT-PCR. In the young inflorescence, both CiTBL1a and CiTBL1b-1 were found to be expressed in the bracts and at the base of the lateral florescence branches, whereas transcripts of CiTBL1b-2 were mainly detected in flower primordia and inflorescence primordia. During early flower development, expression of CiTBL1a and CiTBL1b-1 were both restricted to the developing sepals and petals. In later flower development, expression of CiTBL1a was reduced to a very low level while CiTBL1b-1 was detected with extremely high expression levels in the petaloid androecial structures including the petaloid staminodes, the labellum, and the petaloid appendage of the fertile stamen. In contrast, expression of CiTBL1b-2 was strongest in the fertile stamen throughout flower development, from early initiation of the stamen primordium to maturity of the ½ anther. Heterologous overexpression of CiTBL genes in Arabidopsis led to dwarf plants with smaller petals and fewer stamens, and altered the symmetry of mature flowers. These data provide evidence for the involvement of CYC/TB1 homologs in the development of the asymmetric Cannaceae flower.
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Affiliation(s)
- Qianxia Yu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China
- Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xueyi Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Canjia Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China
- Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology/Economic Botany/Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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9
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Wessinger CA, Hileman LC. Parallelism in Flower Evolution and Development. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways.
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Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
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Zhao Y, Broholm SK, Wang F, Rijpkema AS, Lan T, Albert VA, Teeri TH, Elomaa P. TCP and MADS-Box Transcription Factor Networks Regulate Heteromorphic Flower Type Identity in Gerbera hybrida. PLANT PHYSIOLOGY 2020; 184:1455-1468. [PMID: 32900982 PMCID: PMC7608168 DOI: 10.1104/pp.20.00702] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/25/2020] [Indexed: 05/19/2023]
Abstract
The large sunflower family, Asteraceae, is characterized by compressed, flower-like inflorescences that may bear phenotypically distinct flower types. The CYCLOIDEA (CYC)/TEOSINTE BRANCHED1-like transcription factors (TFs) belonging to the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) protein family are known to regulate bilateral symmetry in single flowers. In Asteraceae, they function at the inflorescence level, and were recruited to define differential flower type identities. Here, we identified upstream regulators of GhCYC3, a gene that specifies ray flower identity at the flower head margin in the model plant Gerbera hybrida We discovered a previously unidentified expression domain and functional role for the paralogous CINCINNATA-like TCP proteins. They function upstream of GhCYC3 and affect the developmental delay of marginal ray primordia during their early ontogeny. At the level of single flowers, the Asteraceae CYC genes show a unique function in regulating the elongation of showy ventral ligules that play a major role in pollinator attraction. We discovered that during ligule development, the E class MADS-box TF GRCD5 activates GhCYC3 expression. We propose that the C class MADS-box TF GAGA1 contributes to stamen development upstream of GhCYC3 Our data demonstrate how interactions among and between the conserved floral regulators, TCP and MADS-box TFs, contribute to the evolution of the elaborate inflorescence architecture of Asteraceae.
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Affiliation(s)
- Yafei Zhao
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Suvi K Broholm
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Feng Wang
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Anneke S Rijpkema
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260
| | - Teemu H Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Paula Elomaa
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
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11
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Pabón-Mora N, Madrigal Y, Alzate JF, Ambrose BA, Ferrándiz C, Wanke S, Neinhuis C, González F. Evolution of Class II TCP genes in perianth bearing Piperales and their contribution to the bilateral calyx in Aristolochia. THE NEW PHYTOLOGIST 2020; 228:752-769. [PMID: 32491205 DOI: 10.1111/nph.16719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/20/2020] [Indexed: 05/21/2023]
Abstract
Controlled spatiotemporal cell division and expansion are responsible for floral bilateral symmetry. Genetic studies have pointed to class II TCP genes as major regulators of cell division and floral patterning in model core eudicots. Here we study their evolution in perianth-bearing Piperales and their expression in Aristolochia, a rare occurrence of bilateral perianth outside eudicots and monocots. The evolution of class II TCP genes reveals single-copy CYCLOIDEA-like genes and three paralogs of CINCINNATA (CIN) in early diverging angiosperms. All class II TCP genes have independently duplicated in Aristolochia subgenus Siphisia. Also CIN2 genes duplicated before the diversification of Saruma and Asarum. Sequence analysis shows that CIN1 and CIN3 share motifs with Cyclin proteins and CIN2 genes have lost the miRNA319a binding site. Expression analyses of all paralogs of class II TCP genes in Aristolochia fimbriata point to a role of CYC and CIN genes in maintaining differential perianth expansion during mid- and late flower developmental stages by promoting cell division in the distal and ventral portion of the limb. It is likely that class II TCP genes also contribute to cell division in the leaf, the gynoecium and the ovules in A. fimbriata.
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Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | | | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, 46022, Spain
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Christoph Neinhuis
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Favio González
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
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12
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Presence/absence of a CACTA transposon in the CYC2c gene of two genotypes of Helianthus × multiflorus cv. “Meteor” characterized by a radiate inflorescence with different shape of disk flower corollas. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Yang Y, Sun M, Yuan C, Han Y, Zheng T, Cheng T, Wang J, Zhang Q. Interactions between WUSCHEL- and CYC2-like Transcription Factors in Regulating the Development of Reproductive Organs in Chrysanthemum morifolium. Int J Mol Sci 2019; 20:ijms20061276. [PMID: 30875718 PMCID: PMC6471657 DOI: 10.3390/ijms20061276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
Chrysanthemum morifolium is a gynomonoecious plant that bears both female zygomorphic ray florets and bisexual actinomorphic disc florets in the inflorescence. This sexual system is quite prevalent in Asteraceae, but poorly understood. CYCLOIDEA (CYC) 2 subclade transcription factors, key regulators of flower symmetry and floret identity in Asteraceae, have also been speculated to function in reproductive organs and could be an entry point for studying gynomonoecy. However, the molecular mechanism is still unclear. On the other hand, the Arabidopsis WUSCHEL (WUS) transcription factor has been proven to play a vital role in the development of reproductive organs. Here, a WUS homologue (CmWUS) in C. morifolium was isolated and characterized. Overexpression of CmWUS in A. thaliana led to shorter siliques and fewer stamens, which was similar to CYC2-like genes reported before. In addition, both CmWUS and CmCYC2 were highly expressed in flower buds during floral organ differentiation and in the reproductive organs at later development stages, indicating their involvement in the development of reproductive organs. Moreover, CmWUS could directly interact with CmCYC2d. Thus, our data suggest a collaboration between CmWUS and CmCYC2 in the regulation of reproductive organ development in chrysanthemum and will contribute to a further understanding of the gynomonoecious sexual system in Asteraceae.
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Affiliation(s)
- Yi 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, Engineering Research Center of Landscape Environment of Ministry of Education, 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.
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, 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.
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, 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.
| | - Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, 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.
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, 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, Engineering Research Center of Landscape Environment of Ministry of Education, 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, Engineering Research Center of Landscape Environment of Ministry of Education, 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, Engineering Research Center of Landscape Environment of Ministry of Education, 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.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
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14
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Damerval C, Citerne H, Conde e Silva N, Deveaux Y, Delannoy E, Joets J, Simonnet F, Staedler Y, Schönenberger J, Yansouni J, Le Guilloux M, Sauquet H, Nadot S. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:18. [PMID: 30740117 PMCID: PMC6357683 DOI: 10.3389/fpls.2019.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.
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Affiliation(s)
- Catherine Damerval
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hélène Citerne
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Deveaux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Simonnet
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yannick Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Sophie Nadot
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
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15
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Plus ça change, plus c'est la même chose: The developmental evolution of flowers. Curr Top Dev Biol 2019; 131:211-238. [DOI: 10.1016/bs.ctdb.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Liu J, Li CQ, Dong Y, Yang X, Wang YZ. Dosage imbalance of B- and C-class genes causes petaloid-stamen relating to F 1 hybrid variation. BMC PLANT BIOLOGY 2018; 18:341. [PMID: 30526487 PMCID: PMC6286610 DOI: 10.1186/s12870-018-1562-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Great advances have been achieved in our understanding of flower development and evolution since the establishment of the ABC model. However, it remains a challenge to define the exact context of organ identity in the component interactions of the ABC model. RESULTS Through hybridization, we detected a homeotic mutant in Petrocosmea (Gesneriaceae) uniquely displayed by the 'petaloid-stamen' in the third whorl with petal identity. Comparative Real-time PCR analyses demonstrate that both two B-class genes DEF2 and GLO are excessively expressed while the transcripts of the C-class gene PLE are reduced in the third floral whorl in the mutant compared to that in the wild-type F1 hybrids. Further allele-specific expression (ASE) analyses indicate that an allele-specific change in PgPLE might be responsible for up-regulation of both B-class genes and down-regulation of the C-class gene in the petaloid-stamen mutants. CONCLUSIONS Our findings suggest that the petaloid-stamen is consequent upon an evident dosage imbalance between B- and C-class products that is probably triggered by a cis-regulatory change. In addition, the genetic pathway for the floral organ identity might be in parallel with that for the floral symmetry. The extreme variation in hybrids further suggests that interspecific hybridization may represent a major factor for evolutionary innovation and diversification in plants.
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Affiliation(s)
- Jing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chao-Qun Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yang Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Xia Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Yin-Zheng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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17
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Lu R, Xu W, Lu Q, Li P, Losh J, Hina F, Li E, Qiu Y. Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae. PLANT DIVERSITY 2018; 40:253-264. [PMID: 30740572 PMCID: PMC6317509 DOI: 10.1016/j.pld.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/21/2023]
Abstract
The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)-Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered C roomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (EST-SSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
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Affiliation(s)
- Ruisen Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wuqin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qixiang Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jocelyn Losh
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Faiza Hina
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Enxiang Li
- College of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Corresponding author.
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18
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Fambrini M, Bellanca M, Costa Muñoz M, Usai G, Cavallini A, Pugliesi C. Ligulate inflorescence of Helianthus × multiflorus, cv. Soleil d'Or, correlates with a mis-regulation of a CYCLOIDEA gene characterised by insertion of a transposable element. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:956-967. [PMID: 30022587 DOI: 10.1111/plb.12876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Members of CYCLOIDEA (CYC)/TEOSINTE BRANCHED1 (TB1) transcription factor family are essential to control flower symmetry and inflorescence architecture. In the Helianthus annuus genome, ten CYC/TB1 genes have been identified. Studies performed on mutants recognised HaCYC2c as one of the key players controlling zygomorphism in sunflower. We identified CYC2c genes in the diploid Helianthus decapetalus (HdCYC2c) and in the interspecific hybrid Helianthus × multiflorus (H × mCYC2cA and H × mCYC2cB), a triploid (2n = 3× = 51), originated from unreduced eggs of H. decapetalus fertilised by reduced H. annuus male gametes. Phylogenetic analysis showed that HdCYC2c and H × mCYC2c were placed within a CYC2 subclade together with HaCYC2c but distinct from it. The present data showed that in H. × multiflorus the allele derived from H. annuus is deleted or highly modified. The H. × multiflorus taxon exists as radiate and ligulate inflorescence types. We analysed CYC2c expression in H. decapetalus and in the cultivar 'Soleil d'Or' of H. × multiflorus, a ligulate inflorescence type with actinomorphic corolla of disk flowers transformed into a zygomorphic ray-like corolla. In H. decapetalus, the HdCYC2c gene showed differential expression between developing flower types, being up-regulated in the corolla of ray flowers in comparison to the disk flower corolla. In H. × multiflorus, an insertion of 865 bp, which is part of a CACTA transposable element, was found in the 5'-untranslated region (5'-UTR) of H × mCYC2cB. This insertion could promote, even with epigenetic mechanisms, ectopic expression of the gene throughout the inflorescence, resulting in the observed loss of actinomorphy and originating a ligulate head.
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Affiliation(s)
- M Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Bellanca
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Costa Muñoz
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - G Usai
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - A Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - C Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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Hsin KT, Wang CN. Expression shifts of floral symmetry genes correlate to flower actinomorphy in East Asia endemic Conandron ramondioides (Gesneriaceae). BOTANICAL STUDIES 2018; 59:24. [PMID: 30374786 PMCID: PMC6206312 DOI: 10.1186/s40529-018-0242-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Bilateral symmetry flower (zygomorphy) is the ancestral state for Gesneriaceae species. Yet independent reversions to actinomorphy have been parallelly evolved in several lineages. Conandron ramondioides is a natural radially symmetrical species survived in dense shade mountainous habitats where specialist pollinators are scarce. Whether the mutations in floral symmetry genes such as CYC, RAD and DIV genes, or their expression pattern shifts contribute to the reversion to actinomorphy in C. ramondioides thus facilitating shifts to generalist pollinators remain to be investigated. To address this, we isolated putative orthologues of these genes and relate their expressions to developmental stages of flower actinomorphy. RESULTS Tissue specific RT-PCR found no dorsal identity genes CrCYCs and CrRADs expression in petal and stamen whorls, while the ventral identity gene CrDIV was expressed in all petals. Thus, ventralized actinomorphy is evolved in C. ramondioides. However, CrCYCs still persists their expression in sepal whorl. This is congruent with previous findings that CYC expression in sepals is an ancestral state common to both actinomorphic and zygomorphic core Eudicot species. CONCLUSIONS The loss of dorsal identity genes CrCYCs and CrRADs expression in petal and stamen whorl without mutating these genes specifies that a novel regulation change, possibly on cis-elements of these genes, has evolved to switch zygomorphy to actinomorphy.
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Affiliation(s)
- Kuan-Ting Hsin
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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20
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Zhao Y, Pfannebecker K, Dommes AB, Hidalgo O, Becker A, Elomaa P. Evolutionary diversification of CYC/TB1-like TCP homologs and their recruitment for the control of branching and floral morphology in Papaveraceae (basal eudicots). THE NEW PHYTOLOGIST 2018; 220:317-331. [PMID: 29949661 DOI: 10.1111/nph.15289] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
Angiosperms possess enormous morphological variation in plant architectures and floral forms. Previous studies in Pentapetalae and monocots have demonstrated the involvement of TCP domain CYCLOIDEA/TEOSINTE BRANCHED1-like (CYC/TB1) genes in the control of floral symmetry and shoot branching. However, how TCP/CYC-like (CYL) genes originated, evolved and functionally diversified remain unclear. We conducted a comparative functional study in Ranunculales, the sister lineage to all other eudicots, between Eschscholzia californica and Cysticapnos vesicaria, two species of Papaveraceae with actinomorphic and zygomorphic flowers, respectively. Phylogenetic analysis indicates that CYL genes in Papaveraceae form two paralogous lineages, PapaCYL1 and PapaCYL2. Papaveraceae CYL genes show highly diversified expression patterns as well as functions. Enhanced branching by silencing of EscaCYL1 suggests that the role of CYC/TB1-like genes in branching control is conserved in Papaveraceae. In contrast to the arrest of stamen development in Pentapetalae, PapaCYL genes promote stamen initiation and growth. In addition, we demonstrate that CyveCYLs are involved in perianth development, specifying sepal and petal identity in Cysticapnos by regulating the B-class floral organ identity genes. Our data also suggest the involvement of CyveCYL genes in the regulation of flower symmetry in Cysticapnos. Our work provides evidence of the importance of TCP/CYC-like genes in the promotion of morphological diversity across angiosperms.
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Affiliation(s)
- Yafei Zhao
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Kai Pfannebecker
- Institute of Botany, University of Giessen, Giessen, 35392, Germany
| | | | - Oriane Hidalgo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
| | - Annette Becker
- Institute of Botany, University of Giessen, Giessen, 35392, Germany
| | - Paula Elomaa
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
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21
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Su S, Shao X, Zhu C, Xu J, Lu H, Tang Y, Jiao K, Guo W, Xiao W, Liu Z, Luo D, Huang X. Transcriptome-Wide Analysis Reveals the Origin of Peloria in Chinese Cymbidium (Cymbidium sinense). PLANT & CELL PHYSIOLOGY 2018; 59:2064-2074. [PMID: 29986119 DOI: 10.1093/pcp/pcy130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/28/2018] [Indexed: 05/29/2023]
Abstract
An orchid flower exhibits a zygomorphic corolla with a well-differentiated labellum. In Cymbidium sinense, many varieties with peloric or pseudopeloric flowers have been bred during centuries of domestication. However, little is known about the molecular basis controlling orchid floral zygomorphy and the origin of these varieties. Here, we studied the floral morphogenesis of C. sinense and transcriptome-wide enriched differentially expressed genes among different varieties. The floral zygomorphy of C. sinense is established in the early developmental process. Out of 27 MIKCC-MADS factors, we found two homeotic MADS genes whose expression was down-regulated in peloric varieties but up-regulated in pseudopeloric varieties. CsAP3-2 expressed in the inner floral organs co-operates with a labellum-specific factor CsAGL6-2, asymmetrically promoting the differentiation of inner tepals. Interestingly, we detected exon deletions on CsAP3-2 in peloric varieties, indicating that loss of B-function results in the origin of peloria. Additional petaloid structures developed when we ectopically expressed these genes in Arabidopsis, suggesting their roles in floral morphogenesis. These findings indicate that the interplay among MADS factors would be crucial for orchid floral zygomorphy, and mutations in these factors may have maintained during artificial selection.
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Affiliation(s)
- Shihao Su
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Xiaoyu Shao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Changfa Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiayin Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hanbin Lu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Yuhuan Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Keyuan Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wuxiu Guo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhongjian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Da Luo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xia Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Hsu HJ, He CW, Kuo WH, Hsin KT, Lu JY, Pan ZJ, Wang CN. Genetic Analysis of Floral Symmetry Transition in African Violet Suggests the Involvement of Trans-acting Factor for CYCLOIDEA Expression Shifts. FRONTIERS IN PLANT SCIENCE 2018; 9:1008. [PMID: 30158940 PMCID: PMC6104639 DOI: 10.3389/fpls.2018.01008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2018] [Indexed: 05/29/2023]
Abstract
With the growing demand for its ornamental uses, the African violet (Saintpaulia ionantha) has been popular owing to its variations in color, shape and its rapid responses to artificial selection. Wild type African violet (WT) is characterized by flowers with bilateral symmetry yet reversals showing radially symmetrical flowers such as dorsalized actinomorphic (DA) and ventralized actinomorphic (VA) peloria are common. Genetic crosses among WT, DA, and VA revealed that these floral symmetry transitions are likely to be controlled by three alleles at a single locus in which the levels of dominance are in a hierarchical fashion. To investigate whether the floral symmetry gene was responsible for these reversals, orthologs of CYCLOIDEA (CYC) were isolated and their expressions correlated to floral symmetry transitions. Quantitative RT-PCR and in situ results indicated that dorsal-specific CYCs expression in WT S. ionantha (SiCYC and SiCYC1B) shifted in DA with a heterotopically extended expression to all petals, but in VA, SiCYC1s' dorsally specific expressions were greatly reduced. Selection signature analysis revealed that the major high-expressed copy of SiCYC had been constrained under purifying selection, whereas the low-expressed helper SiCYC1B appeared to be relaxed under purifying selection after the duplication into SiCYC and SiCYC1B. Heterologous expression of SiCYC in Arabdiopsis showed petal growth retardation which was attributed to limited cell proliferation. While expression shifts of SiCYC and SiCYC1B correlate perfectly to the resulting symmetry phenotype transitions in F1s of WT and DA, there is no certain allelic combination of inherited SiCYC1s associated with specific symmetry phenotypes. This floral transition indicates that although the expression shifts of SiCYC/1B are responsible for the two contrasting actinomorphic reversals in African violet, they are likely to be controlled by upstream trans-acting factors or epigenetic regulations.
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Affiliation(s)
- Hui-Ju Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Wen He
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsi Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Kuan-Ting Hsin
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Jing-Yi Lu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Zhao-Jun Pan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
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24
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Spencer V, Kim M. Re“CYC”ling molecular regulators in the evolution and development of flower symmetry. Semin Cell Dev Biol 2018; 79:16-26. [DOI: 10.1016/j.semcdb.2017.08.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/28/2017] [Indexed: 11/27/2022]
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Sengupta A, Hileman LC. Novel Traits, Flower Symmetry, and Transcriptional Autoregulation: New Hypotheses From Bioinformatic and Experimental Data. FRONTIERS IN PLANT SCIENCE 2018; 9:1561. [PMID: 30416508 PMCID: PMC6212560 DOI: 10.3389/fpls.2018.01561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/05/2018] [Indexed: 05/18/2023]
Abstract
A common feature in developmental networks is the autoregulation of transcription factors which, in turn, positively or negatively regulate additional genes critical for developmental patterning. When a transcription factor regulates its own expression by binding to cis-regulatory sites in its gene, the regulation is direct transcriptional autoregulation (DTA). Indirect transcriptional autoregulation (ITA) involves regulation by proteins expressed downstream of the target transcription factor. We review evidence for a hypothesized role of DTA in the evolution and development of novel flowering plant phenotypes. We additionally provide new bioinformatic and experimental analyses that support a role for transcriptional autoregulation in the evolution of flower symmetry. We find that 5' upstream non-coding regions are significantly enriched for predicted autoregulatory sites in Lamiales CYCLOIDEA genes-an upstream regulator of flower monosymmetry. This suggests a possible correlation between autoregulation of CYCLOIDEA and the origin of monosymmetric flowers near the base of Lamiales, a pattern that may be correlated with independently derived monosymmetry across eudicot lineages. We find additional evidence for transcriptional autoregulation in the flower symmetry program, and report that Antirrhinum DRIF2 may undergo ITA. In light of existing data and new data presented here, we hypothesize how cis-acting autoregulatory sites originate, and find evidence that such sites (and DTA) can arise subsequent to the evolution of a novel phenotype.
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Citerne HL, Reyes E, Le Guilloux M, Delannoy E, Simonnet F, Sauquet H, Weston PH, Nadot S, Damerval C. Characterization of CYCLOIDEA-like genes in Proteaceae, a basal eudicot family with multiple shifts in floral symmetry. ANNALS OF BOTANY 2017; 119:367-378. [PMID: 28025288 PMCID: PMC5314643 DOI: 10.1093/aob/mcw219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/17/2016] [Accepted: 09/14/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The basal eudicot family Proteaceae (approx. 1700 species) shows considerable variation in floral symmetry but has received little attention in studies of evolutionary development at the genetic level. A framework for understanding the shifts in floral symmetry in Proteaceae is provided by reconstructing ancestral states on an upated phylogeny of the family, and homologues of CYCLOIDEA (CYC), a key gene for the control of floral symmetry in both monocots and eudicots, are characterized. METHODS Perianth symmetry transitions were reconstructed on a new species-level tree using parsimony and maximum likelihood. CYC-like genes in 35 species (31 genera) of Proteaceae were sequenced and their phylogeny was reconstructed. Shifts in selection pressure following gene duplication were investigated using nested branch-site models of sequence evolution. Expression patterns of CYC homologues were characterized in three species of Grevillea with different types of floral symmetry. KEY RESULTS Zygomorphy has evolved 10-18 times independently in Proteaceae from actinomorphic ancestors, with at least four reversals to actinomorphy. A single duplication of CYC-like genes occurred prior to the diversification of Proteaceae, with putative loss or divergence of the ProtCYC1 paralogue in more than half of the species sampled. No shifts in selection pressure were detected in the branches subtending the two ProtCYC paralogues. However, the amino acid sequence preceding the TCP domain is strongly divergent in Grevillea ProtCYC1 compared with other species. ProtCYC genes were expressed in developing flowers of both actinomorphic and zygomorphic Grevillea species, with late asymmetric expression in the perianth of the latter. CONCLUSION Proteaceae is a remarkable family in terms of the number of transitions in floral symmetry. Furthermore, although CYC-like genes in Grevillea have unusual sequence characteristics, they display patterns of expression that make them good candidates for playing a role in the establishment of floral symmetry.
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Affiliation(s)
- Hélène L Citerne
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Elisabeth Reyes
- Laboratoire Ecologie, Systématique et Evolution, UMR 8079 Université Paris-Sud, CNRS, AgroParisTech, 91405 Orsay, France
| | - Martine Le Guilloux
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Franck Simonnet
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Hervé Sauquet
- Laboratoire Ecologie, Systématique et Evolution, UMR 8079 Université Paris-Sud, CNRS, AgroParisTech, 91405 Orsay, France
| | - Peter H Weston
- National Herbarium of New South Wales, The Royal Botanic Garden Sydney, Australia
| | - Sophie Nadot
- Laboratoire Ecologie, Systématique et Evolution, UMR 8079 Université Paris-Sud, CNRS, AgroParisTech, 91405 Orsay, France
| | - Catherine Damerval
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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Madrigal Y, Alzate JF, Pabón-Mora N. Evolution and Expression Patterns of TCP Genes in Asparagales. FRONTIERS IN PLANT SCIENCE 2017; 8:9. [PMID: 28144250 PMCID: PMC5239819 DOI: 10.3389/fpls.2017.00009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/03/2017] [Indexed: 05/09/2023]
Abstract
CYCLOIDEA-like genes are involved in the symmetry gene network, limiting cell proliferation in the dorsal regions of bilateral flowers in core eudicots. CYC-like and closely related TCP genes (acronym for TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR) have been poorly studied in Asparagales, the largest order of monocots that includes both bilateral flowers in Orchidaceae (ca. 25.000 spp) and radially symmetrical flowers in Hypoxidaceae (ca. 200 spp). With the aim of assessing TCP gene evolution in the Asparagales, we isolated TCP-like genes from publicly available databases and our own transcriptomes of Cattleya trianae (Orchidaceae) and Hypoxis decumbens (Hypoxidaceae). Our matrix contains 452 sequences representing the three major clades of TCP genes. Besides the previously identified CYC specific core eudicot duplications, our ML phylogenetic analyses recovered an early CIN-like duplication predating all angiosperms, two CIN-like Asparagales-specific duplications and a duplication prior to the diversification of Orchidoideae and Epidendroideae. In addition, we provide evidence of at least three duplications of PCF-like genes in Asparagales. While CIN-like and PCF-like genes have multiplied in Asparagales, likely enhancing the genetic network for cell proliferation, CYC-like genes remain as single, shorter copies with low expression. Homogeneous expression of CYC-like genes in the labellum as well as the lateral petals suggests little contribution to the bilateral perianth in C. trianae. CIN-like and PCF-like gene expression suggests conserved roles in cell proliferation in leaves, sepals and petals, carpels, ovules and fruits in Asparagales by comparison with previously reported functions in core eudicots and monocots. This is the first large scale analysis of TCP-like genes in Asparagales that will serve as a platform for in-depth functional studies in emerging model monocots.
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Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Facultad de Medicina, Universidad de AntioquiaMedellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
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28
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Sun Y, Wang G, Li Y, Jiang L, Yang Y, Guan S. De novo transcriptome sequencing and comparative analysis to discover genes related to floral development in Cymbidium faberi Rolfe. SPRINGERPLUS 2016; 5:1458. [PMID: 27833829 PMCID: PMC5082062 DOI: 10.1186/s40064-016-3089-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 08/17/2016] [Indexed: 12/15/2022]
Abstract
Cymbidium faberi is a traditional orchid flower in China that is highly appreciated for its fragrant aroma from its zygomorphic flowers. One bottleneck of the commercial production of C. faberi is the long vegetative growth phase of the orchid and the difficulty of the regulation of its flowering time. Moreover, its flower size, shape and color are often targeting traits for orchid breeders. Understanding the molecular mechanisms of floral development in C. faberi will ultimately benefit the genetic improvement of this orchid plant. The goal of this study is to identify potential genes and regulatory networks related to the floral development in C. faberi by using transcriptome sequencing, de novo assembly and computational analyses. The vegetative and flower buds of C. faberi were sampled for such comparisons. The RNA-seq yielded about 189,300 contigs that were assembled into 172,959 unigenes. Furthermore, a total of 13,484 differentially expressed unigenes (DEGs) were identified between the vegetative and flower buds. There were 7683 down-regulated and 5801 up-regulated DEGs in the flower buds compared to those in the vegetative buds, among which 3430 and 6556 DEGs were specifically enriched in the flower or vegetative buds, respectively. A total of 173 DEGs orthologous to known genes associated with the floral organ development, floral symmetry and flowering time were identified, including 12 TCP transcription factors, 34 MADS-box genes and 28 flowering time related genes. Furthermore, expression levels of ten genes potentially involved in floral development and flowering time were verified by quantitative real-time PCR. The identified DEGs will facilitate the functional genetic studies for further understanding the flower development of C. faberi.
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Affiliation(s)
- Yuying Sun
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Guangdong Wang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuxia Li
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Li Jiang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuxia Yang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shuangxue Guan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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29
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De Paolo S, Gaudio L, Aceto S. Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica. Sci Rep 2015; 5:16265. [PMID: 26531864 PMCID: PMC4632031 DOI: 10.1038/srep16265] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/13/2015] [Indexed: 11/09/2022] Open
Abstract
TCP proteins are plant-specific transcription factors involved in many different processes. Because of their involvement in a large number of developmental pathways, their roles have been investigated in various plant species. However, there are almost no studies of this transcription factor family in orchids. Based on the available transcriptome of the inflorescence of the orchid Orchis italica, in the present study we identified 12 transcripts encoding TCP proteins. The phylogenetic analysis showed that they belong to different TCP classes (I and II) and groups (PCF, CIN and CYC/TB1), and that they display a number of conserved motifs when compared with the TCPs of Arabidopsis and Oryza. The presence of a specific cleavage site for the microRNA miRNA319, an important post-transcriptional regulator of several TCP genes in other species, was demonstrated for one transcript of O. italica, and the analysis of the expression pattern of the TCP transcripts in different inflorescence organs and in leaf tissue suggests that some TCP transcripts of O. italica exert their role only in specific tissues, while others may play multiple roles in different tissues. In addition, the evolutionary analysis showed a general purifying selection acting on the coding region of these transcripts.
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Affiliation(s)
- Sofia De Paolo
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Luciano Gaudio
- Department of Biology, University of Naples Federico II, Napoli, Italy
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, Napoli, Italy
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30
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Bartlett ME, Williams SK, Taylor Z, DeBlasio S, Goldshmidt A, Hall DH, Schmidt RJ, Jackson DP, Whipple CJ. The Maize PI/GLO Ortholog Zmm16/sterile tassel silky ear1 Interacts with the Zygomorphy and Sex Determination Pathways in Flower Development. THE PLANT CELL 2015; 27:3081-98. [PMID: 26518212 PMCID: PMC4682306 DOI: 10.1105/tpc.15.00679] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/03/2015] [Indexed: 05/07/2023]
Abstract
In monocots and eudicots, B class function specifies second and third whorl floral organ identity as described in the classic ABCE model. Grass B class APETALA3/DEFICIENS orthologs have been functionally characterized; here, we describe the positional cloning and characterization of a maize (Zea mays) PISTILLATA/GLOBOSA ortholog Zea mays mads16 (Zmm16)/sterile tassel silky ear1 (sts1). We show that, similar to many eudicots, all the maize B class proteins bind DNA as obligate heterodimers and positively regulate their own expression. However, sts1 mutants have novel phenotypes that provide insight into two derived aspects of maize flower development: carpel abortion and floral asymmetry. Specifically, we show that carpel abortion acts downstream of organ identity and requires the growth-promoting factor grassy tillers1 and that the maize B class genes are expressed asymmetrically, likely in response to zygomorphy of grass floral primordia. Further investigation reveals that floral phyllotactic patterning is also zygomorphic, suggesting significant mechanistic differences with the well-characterized models of floral polarity. These unexpected results show that despite extensive study of B class gene functions in diverse flowering plants, novel insights can be gained from careful investigation of homeotic mutants outside the core eudicot model species.
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Affiliation(s)
| | | | - Zac Taylor
- Department of Biology, Brigham Young University, Provo, Utah 84602
| | - Stacy DeBlasio
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Darren H Hall
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116
| | - Robert J Schmidt
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116
| | - David P Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
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31
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Hileman LC. Trends in flower symmetry evolution revealed through phylogenetic and developmental genetic advances. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0348. [PMID: 24958922 DOI: 10.1098/rstb.2013.0348] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A striking aspect of flowering plant (angiosperm) diversity is variation in flower symmetry. From an ancestral form of radial symmetry (polysymmetry, actinomorphy), multiple evolutionary transitions have contributed to instances of non-radial forms, including bilateral symmetry (monosymmetry, zygomorphy) and asymmetry. Advances in flowering plant molecular phylogenetic research and studies of character evolution as well as detailed flower developmental genetic studies in a few model species (e.g. Antirrhinum majus, snapdragon) have provided a foundation for deep insights into flower symmetry evolution. From phylogenetic studies, we have a better understanding of where during flowering plant diversification transitions from radial to bilateral flower symmetry (and back to radial symmetry) have occurred. From developmental studies, we know that a genetic programme largely dependent on the functional action of the CYCLOIDEA gene is necessary for differentiation along the snapdragon dorsoventral flower axis. Bringing these two lines of inquiry together has provided surprising insights into both the parallel recruitment of a CYC-dependent developmental programme during independent transitions to bilateral flower symmetry, and the modifications to this programme in transitions back to radial flower symmetry, during flowering plant evolution.
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Affiliation(s)
- Lena C Hileman
- Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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32
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Horn S, Pabón-Mora N, Theuß VS, Busch A, Zachgo S. Analysis of the CYC/TB1 class of TCP transcription factors in basal angiosperms and magnoliids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:559-71. [PMID: 25557238 DOI: 10.1111/tpj.12750] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 05/08/2023]
Abstract
Flower monosymmetry contributes to specialized interactions between plants and their insect pollinators. In the magnoliids, flower monosymmetry is exhibited only in the Aristolochiaceae (Piperales). Aristolochia flowers develop a calyx-derived monosymmetric perianth that enhances pollination success by a flytrap mechanism. Aristolochia arborea forms additionally a special perianth outgrowth that mimics a mushroom to attract flies, the mushroom mimicry structure (MMS). In core eudicots, members of the CYC2 clade of TCP transcription factors are key regulators of corolla monosymmetry establishment. The CYC2 clade arose via core eudicot-specific duplications from ancestral CYC/TB1 genes. CYC/TB1 genes are also thought to affect monosymmetry formation in early diverging eudicot and monocot species. Here, we demonstrate that CYC/TB1 genes, named CYC-like genes (CYCL) are present in basal angiosperms and magnoliids. Expression analyses in A. arborea indicate that CYCL genes participate in perianth and MMS differentiation processes and do not support a CYCL gene function in initial flower monosymmetry formation. Heterologous CYCL and CYC2 gene overexpression studies in Arabidopsis show that Aristolochia CYCL proteins only perform a CYC2-like function when the CYCL TCP domain is replaced by a CYC2 domain. Comparative TCP domain analyses revealed that an LxxLL motif, known to mediate protein-protein interactions, evolved in the second helix of the TCP domain in the CYC2 lineage and contributes to CYC2-related functions. Our data imply that divergent evolution of the CYC/TB1 lineages caused significant changes in their coding regions, which together with cis-regulatory changes established the key CYC2 function in regulating eudicot flower monosymmetry.
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Affiliation(s)
- Stefanie Horn
- Botany Department, Osnabrück University, 49076, Osnabrück, Germany
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Zhong J, Kellogg EA. Duplication and expression of CYC2-like genes in the origin and maintenance of corolla zygomorphy in Lamiales. THE NEW PHYTOLOGIST 2015; 205:852-868. [PMID: 25329857 DOI: 10.1111/nph.13104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/29/2014] [Indexed: 05/28/2023]
Abstract
Duplication, retention, and expression of CYCLOIDEA2 (CYC2)-like genes are thought to affect evolution of corolla symmetry. However, exactly what and how changes in CYC2-like genes correlate with the origin of corolla zygomorphy are poorly understood. We inferred and calibrated a densely sampled phylogeny of CYC2-like genes across the Lamiales and examined their expression in early diverging (EDL) and higher core clades (HCL). CYC2-like genes duplicated extensively in Lamiales, at least six times in core Lamiales (CL) around the Cretaceous-Paleogene (K-Pg) boundary, and seven more in EDL relatively more recently. Nested duplications and losses of CYC2-like paralogs are pervasive but may not correlate with transitions in corolla symmetry. We found evidence for dN/dS (ω) variation following gene duplications. CYC2-like paralogs in HCL show differential expression with higher expression in adaxial petals. Asymmetric expression but not recurrent duplication of CYC2-like genes correlates with the origin of corolla zygomorphy. Changes in both cis-regulatory and coding domains of CYC2-like genes are probably crucial for the evolution of corolla zygomorphy. Multiple selection regimes appear likely to play important roles in gene retention. The parallel duplications of CYC2-like genes are after the initial diversification of bumble bees and Euglossine bees.
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Affiliation(s)
- Jinshun Zhong
- Department of Biology, The University of Missouri-St Louis, One University Blvd, St Louis, MO, 63121, USA; Department of Plant Biology, The University of Vermont, Carrigan Drive, Burlington, VT 05405, USA
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Zhao J, Favero DS, Qiu J, Roalson EH, Neff MM. Insights into the evolution and diversification of the AT-hook Motif Nuclear Localized gene family in land plants. BMC PLANT BIOLOGY 2014; 14:266. [PMID: 25311531 PMCID: PMC4209074 DOI: 10.1186/s12870-014-0266-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/25/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Members of the ancient land-plant-specific transcription factor AT-Hook Motif Nuclear Localized (AHL) gene family regulate various biological processes. However, the relationships among the AHL genes, as well as their evolutionary history, still remain unexplored. RESULTS We analyzed over 500 AHL genes from 19 land plant species, ranging from the early diverging Physcomitrella patens and Selaginella to a variety of monocot and dicot flowering plants. We classified the AHL proteins into three types (Type-I/-II/-III) based on the number and composition of their functional domains, the AT-hook motif(s) and PPC domain. We further inferred their phylogenies via Bayesian inference analysis and predicted gene gain/loss events throughout their diversification. Our analyses suggested that the AHL gene family emerged in embryophytes and further evolved into two distinct clades, with Type-I AHLs forming one clade (Clade-A), and the other two types together diversifying in another (Clade-B). The two AHL clades likely diverged before the separation of Physcomitrella patens from the vascular plant lineage. In angiosperms, Clade-A AHLs expanded into 5 subfamilies; while, the ones in Clade-B expanded into 4 subfamilies. Examination of their expression patterns suggests that the AHLs within each clade share similar expression patterns with each other; however, AHLs in one monophyletic clade exhibit distinct expression patterns from the ones in the other clade. Over-expression of a Glycine max AHL PPC domain in Arabidopsis thaliana recapitulates the phenotype observed when over-expressing its Arabidopsis thaliana counterpart. This result suggests that the AHL genes from different land plant species may share conserved functions in regulating plant growth and development. Our study further suggests that such functional conservation may be due to conserved physical interactions among the PPC domains of AHL proteins. CONCLUSIONS Our analyses reveal a possible evolutionary scenario for the AHL gene family in land plants, which will facilitate the design of new studies probing their biological functions. Manipulating the AHL genes has been suggested to have tremendous effects in agriculture through increased seedling establishment, enhanced plant biomass and improved plant immunity. The information gleaned from this study, in turn, has the potential to be utilized to further improve crop production.
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Affiliation(s)
- Jianfei Zhao
- />Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164 USA
- />Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
- />Present Address: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - David S Favero
- />Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164 USA
- />Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
| | - Jiwen Qiu
- />Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
| | - Eric H Roalson
- />Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164 USA
- />School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Michael M Neff
- />Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164 USA
- />Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
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Jabbour F, Cossard G, Le Guilloux M, Sannier J, Nadot S, Damerval C. Specific duplication and dorsoventrally asymmetric expression patterns of Cycloidea-like genes in zygomorphic species of Ranunculaceae. PLoS One 2014; 9:e95727. [PMID: 24752428 PMCID: PMC3994137 DOI: 10.1371/journal.pone.0095727] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/28/2014] [Indexed: 11/23/2022] Open
Abstract
Floral bilateral symmetry (zygomorphy) has evolved several times independently in angiosperms from radially symmetrical (actinomorphic) ancestral states. Homologs of the Antirrhinum majus Cycloidea gene (Cyc) have been shown to control floral symmetry in diverse groups in core eudicots. In the basal eudicot family Ranunculaceae, there is a single evolutionary transition from actinomorphy to zygomorphy in the stem lineage of the tribe Delphinieae. We characterized Cyc homologs in 18 genera of Ranunculaceae, including the four genera of Delphinieae, in a sampling that represents the floral morphological diversity of this tribe, and reconstructed the evolutionary history of this gene family in Ranunculaceae. Within each of the two RanaCyL (Ranunculaceae Cycloidea-like) lineages previously identified, an additional duplication possibly predating the emergence of the Delphinieae was found, resulting in up to four gene copies in zygomorphic species. Expression analyses indicate that the RanaCyL paralogs are expressed early in floral buds and that the duration of their expression varies between species and paralog class. At most one RanaCyL paralog was expressed during the late stages of floral development in the actinomorphic species studied whereas all paralogs from the zygomorphic species were expressed, composing a species-specific identity code for perianth organs. The contrasted asymmetric patterns of expression observed in the two zygomorphic species is discussed in relation to their distinct perianth architecture.
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Affiliation(s)
- Florian Jabbour
- Université Paris-Sud, UMR 0320/UMR 8120, Génétique Végétale, Gif-sur-Yvette, France
- Université Paris-Sud, Laboratoire Ecologie, Systématique, Evolution, CNRS UMR 8079, AgroParisTech, Orsay, France
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, UMR 7205 ISYEB MNHN-CNRS-UPMC-EPHE, Paris, France
| | - Guillaume Cossard
- Université Paris-Sud, Laboratoire Ecologie, Systématique, Evolution, CNRS UMR 8079, AgroParisTech, Orsay, France
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | | | - Julie Sannier
- Université Paris-Sud, Laboratoire Ecologie, Systématique, Evolution, CNRS UMR 8079, AgroParisTech, Orsay, France
| | - Sophie Nadot
- Université Paris-Sud, Laboratoire Ecologie, Systématique, Evolution, CNRS UMR 8079, AgroParisTech, Orsay, France
| | - Catherine Damerval
- CNRS, UMR 0320/UMR 8120, Génétique Végétale, Gif-sur-Yvette, France
- * E-mail:
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Combining phylogenetic and syntenic analyses for understanding the evolution of TCP ECE genes in eudicots. PLoS One 2013; 8:e74803. [PMID: 24019982 PMCID: PMC3760840 DOI: 10.1371/journal.pone.0074803] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/05/2013] [Indexed: 11/24/2022] Open
Abstract
TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core eudicots, but the evolutionary history of this gene family is unknown in basal eudicots. Reconstructing the phylogeny of ECE genes in basal eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal eudicots and Gunnera which belongs to the sister clade to all other core eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse eudicot lineages may be due to genome-wide duplications. The three major core-eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanumlycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal eudicots Aquilegiacoerulea and Nelumbonucifera suggests that the two TCP ECE paralogs in these species are also derived from large-scale duplications. TCP ECE loci from basal eudicots share many features with the three main core eudicot loci, and allow us to infer the makeup of the ancestral eudicot locus.
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Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, Bian C, Chen J, Fan G, Kaufmann K, Hall JC, Becker A, Bräutigam A, Weber AP, Shi C, Zheng Z, Li W, Lv M, Tao Y, Wang J, Zou H, Quan Z, Hibberd JM, Zhang G, Zhu XG, Xu X, Schranz ME. The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. THE PLANT CELL 2013; 25:2813-30. [PMID: 23983221 PMCID: PMC3784582 DOI: 10.1105/tpc.113.113480] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/06/2013] [Accepted: 08/06/2013] [Indexed: 05/18/2023]
Abstract
The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for minichromosome maintenance1, AGAMOUS, DEFICIENS and serum response factor) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical serine receptor kinase receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.
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Affiliation(s)
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Peng Zeng
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Xiao Zhong
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Jiajia Xu
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Xin Liu
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Johannes Hofberger
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Suzanne de Bruijn
- Molecular Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Amey S. Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University, 35392 Giessen, Germany
| | - Canan Kuelahoglu
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | - Chao Bian
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Jing Chen
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Guangyi Fan
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Kerstin Kaufmann
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Jocelyn C. Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University, 35392 Giessen, Germany
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | - Andreas P.M. Weber
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | | | - Zhijun Zheng
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Wujiao Li
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Mingju Lv
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Yimin Tao
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Junyi Wang
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Hongfeng Zou
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Key Laboratory of Genomics, Ministry of Agriculture, Beijing Genomics Institute, 518083 Shenzhen, China
| | - Zhiwu Quan
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Key Laboratory of Genomics, Ministry of Agriculture, Beijing Genomics Institute, 518083 Shenzhen, China
| | - Julian M. Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Gengyun Zhang
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xin-Guang Zhu
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Xun Xu
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Address correspondence to
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Damerval C, Citerne H, Le Guilloux M, Domenichini S, Dutheil J, Ronse de Craene L, Nadot S. Asymmetric morphogenetic cues along the transverse plane: shift from disymmetry to zygomorphy in the flower of Fumarioideae. AMERICAN JOURNAL OF BOTANY 2013; 100:391-402. [PMID: 23378492 DOI: 10.3732/ajb.1200376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Zygomorphy has evolved multiple times in angiosperms. Near-actinomorphy is the ancestral state in the early diverging eudicot family Papaveraceae. Zygomorphy evolved once in the subfamily Fumarioideae from a disymmetric state. Unusual within angiosperms, zygomorphy takes place along the transverse plane of the flower. METHODS We investigated floral development to understand the developmental bases of the evolution of floral symmetry in Papaveraceae. We then assessed the expression of candidate genes for the key developmental events responsible for the shift from disymmetry to transverse zygomorphy, namely CrabsClaw for nectary formation (PapCRC), ShootMeristemless (PapSTL) for spur formation, and Cycloidea (PapCYL) for growth control. KEY RESULTS We found that an early disymmetric groundplan is common to all species studied, and that actinomorphy was acquired after sepal initiation in Papaveroideae. The shift from disymmetry to zygomorphy in Fumarioideae was associated with early asymmetric growth of stamen filaments, followed by asymmetric development of nectary outgrowth and spur along the transverse plane. Patterns of PapSTL expression could not be clearly related to spur formation. PapCRC and PapCYL genes were expressed in the nectary outgrowths, with a pattern of expression correlated with asymmetric nectary development in the zygomorphic species. Additionally, PapCYL genes were found asymmetrically expressed along the transverse plane in the basal region of outer petals in the zygomorphic species. CONCLUSION Genes of PapCRC and PapCYL families could be direct or indirect targets of the initial transversally asymmetric cue responsible for the shift from disymmetry to zygomorphy in Fumarioideae.
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Affiliation(s)
- Catherine Damerval
- UMR de Génétique Végétale, CNRS/Université Paris-Sud/INRA, Ferme du Moulon 91190 Gif-sur-Yvette, France.
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