1
|
Duan K, Fu H, Fang D, Wang K, Zhang W, Liu H, Sahu SK, Chen X. Genome-Wide Analysis of the MADS-Box Gene Family in Holoparasitic Plants ( Balanophora subcupularis and Balanophora fungosa var. globosa). FRONTIERS IN PLANT SCIENCE 2022; 13:846697. [PMID: 35712591 PMCID: PMC9197559 DOI: 10.3389/fpls.2022.846697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
MADS-box is an important transcription factor family that is involved in the regulation of various stages of plant growth and development, especially flowering regulation and flower development. Being a holoparasitic plant, the body structure of Balanophoraceae has changed dramatically over time, and its vegetative and reproductive organs have been extensively modified, with rudimentary flower organs. Meanwhile, extraordinary gene losses have been identified in holoparasitic plants compared with autotrophs. Our study reveals that the MADS-box gene family contracted sharply in Balanophora subcupularis and Balanophora fungosa var. globosa, and some subfamilies were lost, exhibiting reduced redundancy in both. The genes that functioned in the transition from the vegetative to floral production stages suffered a significant loss, but the ABCE model genes remained intact. We further investigated genes related to flowering regulation in B. subcupularis and B. fungosa var. globosa, vernalization and autonomous ways of regulating flowering time remained comparatively integrated, while genes in photoperiod and circadian clock pathways were almost lost. Convergent gene loss in flowering regulation occurred in Balanophora and another holoparasitic plant Sapria himalayana (Rafflesiaceae). The genome-wide analysis of the MADS-box gene family in Balanophora species provides valuable information for understanding the classification, gene loss pattern, and flowering regulation mechanism of MADS-box gene family in parasitic plants.
Collapse
Affiliation(s)
- Kunyu Duan
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui Fu
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Kaimeng Wang
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Wen Zhang
- China National GeneBank, Beijing Genomics Institute, Shenzhen, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Xiaoli Chen
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| |
Collapse
|
2
|
Wang B, Hu W, Fang Y, Feng X, Fang J, Zou T, Zheng S, Ming R, Zhang J. Comparative Analysis of the MADS-Box Genes Revealed Their Potential Functions for Flower and Fruit Development in Longan ( Dimocarpus longan). FRONTIERS IN PLANT SCIENCE 2022; 12:813798. [PMID: 35154209 PMCID: PMC8829350 DOI: 10.3389/fpls.2021.813798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 06/01/2023]
Abstract
Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mβ, Mγ) and type II (MIKC*, MIKC C ) groups, and MIKC C genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKC C genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKC C genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.
Collapse
Affiliation(s)
- Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenshun Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yaxue Fang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxi Feng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingping Fang
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Tengyue Zou
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoquan Zheng
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
3
|
Dreni L, Ravasio A, Gonzalez-Schain N, Jacchia S, da Silva GJ, Ricagno S, Russo R, Caselli F, Gregis V, Kater MM. Functionally Divergent Splicing Variants of the Rice AGAMOUS Ortholog OsMADS3 Are Evolutionary Conserved in Grasses. FRONTIERS IN PLANT SCIENCE 2020; 11:637. [PMID: 32523596 PMCID: PMC7261849 DOI: 10.3389/fpls.2020.00637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 04/24/2020] [Indexed: 05/31/2023]
Abstract
Within the MADS-box gene family, the AGAMOUS-subfamily genes are particularly important for plant reproduction, because they control stamen and carpel identity. A number of studies in the last three decades have demonstrated that the AGAMOUS (AG) function has been conserved during land plant evolution. However, gene duplication events have led to subfunctionalization and neofunctionalization of AG-like genes in many species. Here we show that alternative splicing in Oryza sativa produces two variants of the AG ortholog OsMADS3 which differ in just one serine residue, S109. Interestingly, this alternative splicing variant is conserved and specific to the grass family. Since in eudicots the S109 residue is absent in AG proteins, stamen and carpel identity determination activity of the two rice isoforms was tested in Arabidopsis thaliana. These experiments revealed that only the eudicot-like OsMADS3 isoform, lacking the serine residue, had ability to specify stamens and carpels in ag mutant flowers, suggesting an important functional role for the serine residue at position 109 in AG proteins of grasses.
Collapse
Affiliation(s)
- Ludovico Dreni
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Andrea Ravasio
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | - Sara Jacchia
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | - Stefano Ricagno
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Rosaria Russo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Francesca Caselli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Veronica Gregis
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Martin M. Kater
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
4
|
Li S, Li Z, Zhang J, Wei D, Wang Z, Tang Q. Flowering signal integrator AGL24 interacts with K domain of AGL18 in Brassica juncea. Biochem Biophys Res Commun 2019; 518:148-153. [DOI: 10.1016/j.bbrc.2019.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 01/16/2023]
|
5
|
Identification and Characterization of the MADS-Box Genes and Their Contribution to Flower Organ in Carnation (Dianthus caryophyllus L.). Genes (Basel) 2018; 9:genes9040193. [PMID: 29617274 PMCID: PMC5924535 DOI: 10.3390/genes9040193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 01/22/2023] Open
Abstract
Dianthus is a large genus containing many species with high ornamental economic value. Extensive breeding strategies permitted an exploration of an improvement in the quality of cultivated carnation, particularly in flowers. However, little is known on the molecular mechanisms of flower development in carnation. Here, we report the identification and description of MADS-box genes in carnation (DcaMADS) with a focus on those involved in flower development and organ identity determination. In this study, 39 MADS-box genes were identified from the carnation genome and transcriptome by the phylogenetic analysis. These genes were categorized into four subgroups (30 MIKCc, two MIKC*, two Mα, and five Mγ). The MADS-box domain, gene structure, and conserved motif compositions of the carnation MADS genes were analysed. Meanwhile, the expression of DcaMADS genes were significantly different in stems, leaves, and flower buds. Further studies were carried out for exploring the expression of DcaMADS genes in individual flower organs, and some crucial DcaMADS genes correlated with their putative function were validated. Finally, a new expression pattern of DcaMADS genes in flower organs of carnation was provided: sepal (three class E genes and two class A genes), petal (two class B genes, two class E genes, and one SHORT VEGETATIVE PHASE (SVP)), stamen (two class B genes, two class E genes, and two class C), styles (two class E genes and two class C), and ovary (two class E genes, two class C, one AGAMOUS-LIKE 6 (AGL6), one SEEDSTICK (STK), one B sister, one SVP, and one Mα). This result proposes a model in floral organ identity of carnation and it may be helpful to further explore the molecular mechanism of flower organ identity in carnation.
Collapse
|
6
|
Wang R, Ming M, Li J, Shi D, Qiao X, Li L, Zhang S, Wu J. Genome-wide identification of the MADS-box transcription factor family in pear ( Pyrus bretschneideri) reveals evolution and functional divergence. PeerJ 2017; 5:e3776. [PMID: 28924499 PMCID: PMC5598432 DOI: 10.7717/peerj.3776] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/17/2017] [Indexed: 11/21/2022] Open
Abstract
MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear.
Collapse
Affiliation(s)
- Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Meiling Ming
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jiaming Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Shi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
7
|
Niu Q, Li J, Cai D, Qian M, Jia H, Bai S, Hussain S, Liu G, Teng Y, Zheng X. Dormancy-associated MADS-box genes and microRNAs jointly control dormancy transition in pear (Pyrus pyrifolia white pear group) flower bud. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:239-57. [PMID: 26466664 PMCID: PMC4682432 DOI: 10.1093/jxb/erv454] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bud dormancy in perennial plants is indispensable to survival over winter and to regrowth and development in the following year. However, the molecular pathways of endo-dormancy induction, maintenance, and release are still unclear, especially in fruit crops. To identify genes with roles in regulating endo-dormancy, 30 MIKC(C)-type MADS-box genes were identified in the pear genome and characterized. The 30 genes were analysed to determine their phylogenetic relationships with homologous genes, genome locations, gene structure, tissue-specific transcript profiles, and transcriptional patterns during flower bud dormancy in 'Suli' pear (Pyrus pyrifolia white pear group). The roles in regulating bud dormancy varied among the MIKC gene family members. Yeast one-hybrid and transient assays showed that PpCBF enhanced PpDAM1 and PpDAM3 transcriptional activity during the induction of dormancy, probably by binding to the C-repeat/DRE binding site, while DAM proteins inhibited the transcriptional activity of PpFT2 during dormancy release. In the small RNA-seq analysis, 185 conserved, 24 less-conserved, and 32 pear-specific miRNAs with distinct expression patterns during bud dormancy were identified. Joint analyses of miRNAs and MIKC genes together with degradome data showed that miR6390 targeted PpDAM transcripts and degraded them to release PpFT2. Our data show that cross-talk among PpCBF, PpDAM, PpFT2, and miR6390 played important roles in regulating endo-dormancy. A model for the molecular mechanism of dormancy transition is proposed: short-term chilling in autumn activates the accumulation of CBF, which directly promotes DAM expression; DAM subsequently inhibits FT expression to induce endo-dormancy, and miR6390 degrades DAM genes to release endo-dormancy.
Collapse
Affiliation(s)
- Qingfeng Niu
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Jianzhao Li
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Danying Cai
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province 310021, China
| | - Minjie Qian
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Huimin Jia
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Songling Bai
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Sayed Hussain
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Guoqin Liu
- College of Agriculture, Guizhou University, Guiyang, Guizhou Province 550025, China
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058, China The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou, Zhejiang 310058, China Zhejiang Provincial Key Laboratory of Integrative Biology and Utilization of Horticultural Plants, Hangzhou, Zhejiang 310058, China
| | - Xiaoyan Zheng
- Institute of Horticulture and Landscape, College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| |
Collapse
|
8
|
Wang L, Yin X, Cheng C, Wang H, Guo R, Xu X, Zhao J, Zheng Y, Wang X. Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines. Mol Genet Genomics 2014; 290:825-46. [DOI: 10.1007/s00438-014-0961-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]
|
9
|
Tian Y, Dong Q, Ji Z, Chi F, Cong P, Zhou Z. Genome-wide identification and analysis of the MADS-box gene family in apple. Gene 2014; 555:277-90. [PMID: 25447908 DOI: 10.1016/j.gene.2014.11.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 11/01/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
The MADS-box gene family is one of the most widely studied families in plants and has diverse developmental roles in flower pattern formation, gametophyte cell division and fruit differentiation. Although the genome-wide analysis of this family has been performed in some species, little is known regarding MADS-box genes in apple (Malus domestica). In this study, 146 MADS-box genes were identified in the apple genome and were phylogenetically clustered into six subgroups (MIKC(c), MIKC*, Mα, Mβ, Mγ and Mδ) with the MADS-box genes from Arabidopsis and rice. The predicted apple MADS-box genes were distributed across all 17 chromosomes at different densities. Additionally, the MADS-box domain, exon length, gene structure and motif compositions of the apple MADS-box genes were analysed. Moreover, the expression of all of the apple MADS-box genes was analysed in the root, stem, leaf, flower tissues and five stages of fruit development. All of the apple MADS-box genes, with the exception of some genes in each group, were expressed in at least one of the tissues tested, which indicates that the MADS-box genes are involved in various aspects of the physiological and developmental processes of the apple. To the best of our knowledge, this report describes the first genome-wide analysis of the apple MADS-box gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.
Collapse
Affiliation(s)
- Yi Tian
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China
| | - Qinglong Dong
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China
| | - Zhirui Ji
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China
| | - Fumei Chi
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China
| | - Peihua Cong
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
| | - Zongshan Zhou
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 125100, PR China.
| |
Collapse
|
10
|
Serwatowska J, Roque E, Gómez-Mena C, Constantin GD, Wen J, Mysore KS, Lund OS, Johansen E, Beltrán JP, Cañas LA. Two euAGAMOUS genes control C-function in Medicago truncatula. PLoS One 2014; 9:e103770. [PMID: 25105497 PMCID: PMC4126672 DOI: 10.1371/journal.pone.0103770] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 02/07/2023] Open
Abstract
C-function MADS-box transcription factors belong to the AGAMOUS (AG) lineage and specify both stamen and carpel identity and floral meristem determinacy. In core eudicots, the AG lineage is further divided into two branches, the euAG and PLE lineages. Functional analyses across flowering plants strongly support the idea that duplicated AG lineage genes have different degrees of subfunctionalization of the C-function. The legume Medicago truncatula contains three C-lineage genes in its genome: two euAG genes (MtAGa and MtAGb) and one PLENA-like gene (MtSHP). This species is therefore a good experimental system to study the effects of gene duplication within the AG subfamily. We have studied the respective functions of each euAG genes in M. truncatula employing expression analyses and reverse genetic approaches. Our results show that the M. truncatula euAG- and PLENA-like genes are an example of subfunctionalization as a result of a change in expression pattern. MtAGa and MtAGb are the only genes showing a full C-function activity, concomitant with their ancestral expression profile, early in the floral meristem, and in the third and fourth floral whorls during floral development. In contrast, MtSHP expression appears late during floral development suggesting it does not contribute significantly to the C-function. Furthermore, the redundant MtAGa and MtAGb paralogs have been retained which provides the overall dosage required to specify the C-function in M. truncatula.
Collapse
Affiliation(s)
- Joanna Serwatowska
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Gabriela D. Constantin
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Kirankumar S. Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Ole S. Lund
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Elisabeth Johansen
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - José Pío Beltrán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Luis A. Cañas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
- * E-mail:
| |
Collapse
|
11
|
Zhang J, Li Z, Guo C, Liu G, Bao M. Isolation and functional analyses of a putative floral homeotic C-function gene in a basal eudicot London plane tree (Platanus acerifolia). PLoS One 2013; 8:e63389. [PMID: 23691041 PMCID: PMC3655187 DOI: 10.1371/journal.pone.0063389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/02/2013] [Indexed: 11/21/2022] Open
Abstract
The identification of mutants in model plant species has led to the isolation of the floral homeotic function genes that play crucial roles in flower organ specification. However, floral homeotic C-function genes are rarely studied in basal eudicots. Here, we report the isolation and characterization of the AGAMOUS (AG) orthologous gene (PaAG) from a basal eudicot London plane tree (Platanus acerifolia Willd). Phylogenetic analysis showed that PaAG belongs to the C- clade AG group of genes. PaAG was found to be expressed predominantly in the later developmental stages of male and female inflorescences. Ectopic expression of PaAG-1 in tobacco (Nicotiana tabacum) resulted in morphological alterations of the outer two flower whorls, as well as some defects in vegetative growth. Scanning electron micrographs (SEMs) confirmed homeotic sepal-to-carpel transformation in the transgenic plants. Protein interaction assays in yeast cells indicated that PaAG could interact directly with PaAP3 (a B-class MADS-box protein in P. acerifolia), and also PaSEP1 and PaSEP3 (E-class MADS-box proteins in P. acerifolia). This study performed the functional analysis of AG orthologous genes outside core eudicots and monocots. Our findings demonstrate a conserved functional role of AG homolog in London plane tree, which also represent a contribution towards understanding the molecular mechanisms of flower development in this monoecious tree species.
Collapse
Affiliation(s)
- Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Zhineng Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Cong Guo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Guofeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| |
Collapse
|
12
|
Developmental genetics of the perianthless flowers and bracts of a paleoherb species, Saururus chinensis. PLoS One 2013; 8:e53019. [PMID: 23382831 PMCID: PMC3559744 DOI: 10.1371/journal.pone.0053019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 11/22/2012] [Indexed: 11/19/2022] Open
Abstract
Saururus chinensis is a core member of Saururaceae, a perianthless (lacking petals or sepals) family. Due to its basal phylogenetic position and unusual floral composition, study of this plant family is important for understanding the origin and evolution of perianthless flowers and petaloid bracts among angiosperm species. To isolate genes involved in S. chinensis flower development, subtracted floral cDNA libraries were constructed by using suppression subtractive hybridization (SSH) on transcripts isolated from developing inflorescences and seedling leaves. The subtracted cDNA libraries contained a total of 1,141 ESTs and were used to create cDNA microarrays to analyze transcript profiles of developing inflorescence tissues. Subsequently, qRT-PCR analyses of eight MADS-box transcription factors and in situ hybridizations of two B-class MADS-box transcription factors were performed to verify and extend the cDNA microarray results. Finally, putative phylogenetic relationships within the B-class MADS-box gene family were determined using the discovered S. chinensis B-class genes to compare K-domain sequences with B genes from other basal angiosperms. Two hundred seventy-seven of the 1,141 genes were found to be expressed differentially between S. chinensis inflorescence tissues and seedling leaves, 176 of which were grouped into at least one functional category, including transcription (14.75%), energy (12.59%), metabolism (9.12%), protein-related function (8.99%), and cellular transport (5.76%). qRT-PCR and in situ hybridization of selected MADS-box genes supported our microarray data. Phylogenetic analysis indicated that a total of six B-class MADS-box genes were isolated from S. chinensis. The differential regulation of S. chinensis B-class MADS-box transcription factors likely plays a role during the development of subtending bracts and perianthless flowers. This study contributes to our understanding of inflorescence development in Saururus, and represents an initial step toward understanding the formation of petaloid bracts in this species.
Collapse
|
13
|
Kakinuma M, Inoue M, Morita T, Tominaga H, Maegawa M, Coury DA, Amano H. Isolation and characterization of a SEPALLATA-like gene, ZjMADS1, from marine angiosperm Zostera japonica. MARINE ENVIRONMENTAL RESEARCH 2012; 76:128-137. [PMID: 22014762 DOI: 10.1016/j.marenvres.2011.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/31/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
In flowering plants, floral homeotic MADS-box genes, which constitute a large multigene family, play important roles in the specification of floral organs as defined by the ABCDE model. In this study, a MADS-box gene, ZjMADS1, was isolated and characterized from the marine angiosperm Zostera japonica. The predicted length of the ZjMADS1 protein was 246 amino acids (AA), and the AA sequence was most similar to those of the SEPALLATA (SEP) subfamily, corresponding to E-function genes. Southern blot analysis suggested the presence of two SEP3-like genes in the Z. japonica genome. ZjMADS1 mRNA levels were extremely high in the spadices, regardless of the developmental stage, compared to other organs from the reproductive and vegetative shoots. These results suggest that the ZjMADS1 gene may be involved in spadix development in Z. japonica and act as an E-function gene in floral organ development in marine angiosperms.
Collapse
Affiliation(s)
- Makoto Kakinuma
- Laboratory of Marine Biochemistry, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | | | | | | | | | | | | |
Collapse
|
14
|
Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. ANNALS OF BOTANY 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
Collapse
Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, de los Ángeles Miccono M, Ramos R, Le Cunff L, Boursiquot JM, Hinrichsen P, Adam-Blondon AF. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC PLANT BIOLOGY 2011; 11:57. [PMID: 21447172 PMCID: PMC3076230 DOI: 10.1186/1471-2229-11-57] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 03/29/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. RESULTS Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. CONCLUSION We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.
Collapse
Affiliation(s)
- Nilo Mejía
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Braulio Soto
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Marcos Guerrero
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Ximena Casanueva
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Cléa Houel
- UMR INRA CNRS University of Evry on Plant Genomics, 2 rue Gaston Crémieux, BP 5708, 91057, Evry, France
| | | | - Rodrigo Ramos
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Loïc Le Cunff
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Michel Boursiquot
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Patricio Hinrichsen
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | | |
Collapse
|
16
|
Zhang J, Guo C, Liu G, Li Z, Li X, Bao M. Genetic alteration with variable intron/exon organization amongst five PI-homoeologous genes in Platanus acerifolia. Gene 2011; 473:82-91. [DOI: 10.1016/j.gene.2010.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 11/04/2010] [Accepted: 11/12/2010] [Indexed: 11/27/2022]
|
17
|
Lin EP, Peng HZ, Jin QY, Deng MJ, Li T, Xiao XC, Hua XQ, Wang KH, Bian HW, Han N, Zhu MY. Identification and characterization of two bamboo (Phyllostachys praecox) AP1/SQUA-like MADS-box genes during floral transition. PLANTA 2009; 231:109-20. [PMID: 19855996 DOI: 10.1007/s00425-009-1033-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Accepted: 09/24/2009] [Indexed: 05/20/2023]
Abstract
Bamboo (Bambusoideae) is by far the largest member of the grass family Poaceae, which is vital to the economy of many countries in the tropics and subtropics. However, the mechanism of flowering of bamboo (Phyllostachys praecox) is still unknown. In this study, we isolated two novel genes from P. praecox and evaluated their functional characteristics. The sequence and phylogenetic analysis indicated that these two genes, named PpMADS1 and PpMADS2, belong to FUL3 and FUL1 clade of Poaceae AP1/SQUA-like genes, respectively. The PpMADS2 possesses a truncated C terminus lacking the highly conserved paleoAP1 motif. It was further confirmed that the truncated C-terminal region was produced by natural sequence deletion in exons, but not by alternative splicing. Ectopic expression of PpMADS1 and PpMADS2 significantly promoted early flowering through upregulation of AP1 in Arabidopsis. Yeast two-hybrid experiments demonstrated that AP1 protein can interact with PpMADS1 but not PpMADS2, suggesting that these two genes may act differently in signaling early flowering of bamboo plants. RT-qPCR and in situ hybridization analysis revealed distinct expression patterns of these two genes in vegetative and reproductive tissues of bamboo. Taken together, our results suggest that both PpMADS1 and PpMADS2 are involved in floral transition, and PpMADS2 might play more important roles than PpMADS1 in floral development of Phyllostachys praecox.
Collapse
Affiliation(s)
- Er-Pei Lin
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Mondragón-Palomino M, Hiese L, Härter A, Koch MA, Theissen G. Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses. BMC Evol Biol 2009; 9:81. [PMID: 19383167 PMCID: PMC2680841 DOI: 10.1186/1471-2148-9-81] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 04/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising DEF-like and GLO-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged. RESULTS The DEF-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid GLO-like genes form a single clade of ancient orthologues and recent paralogues. DEF-like genes from orchid clade 2 (OMADS3-like genes) are under less stringent purifying selection than the other orchid DEF-like and GLO-like genes. In comparison with orchids, purifying selection was less stringent in DEF-like and GLO-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret. CONCLUSION In DEF-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.
Collapse
|
19
|
Cai S, Lashbrook CC. Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2. PLANT PHYSIOLOGY 2008; 146:1305-21. [PMID: 18192438 PMCID: PMC2259061 DOI: 10.1104/pp.107.110908] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 01/08/2008] [Indexed: 05/18/2023]
Abstract
Organ detachment requires cell separation within abscission zones (AZs). Physiological studies have established that ethylene and auxin contribute to cell separation control. Genetic analyses of abscission mutants have defined ethylene-independent detachment regulators. Functional genomic strategies leading to global understandings of abscission have awaited methods for isolating AZ cells of low abundance and very small size. Here, we couple laser capture microdissection of Arabidopsis thaliana stamen AZs and GeneChip profiling to reveal the AZ transcriptome responding to a developmental shedding cue. Analyses focus on 551 AZ genes (AZ(551)) regulated at the highest statistical significance (P < or = 0.0001) over five floral stages linking prepollination to stamen shed. AZ(551) includes mediators of ethylene and auxin signaling as well as receptor-like kinases and extracellular ligands thought to act independent of ethylene. We hypothesized that novel abscission regulators might reside in disproportionately represented Gene Ontology Consortium functional categories for cell wall modifying proteins, extracellular regulators, and nuclear-residing transcription factors. Promoter-beta-glucuronidase expression of one transcription factor candidate, ZINC FINGER PROTEIN2 (AtZFP2), was elevated in stamen, petal, and sepal AZs. Flower parts of transgenic lines overexpressing AtZFP2 exhibited asynchronous and delayed abscission. Abscission defects were accompanied by altered floral morphology limiting pollination and fertility. Hand-pollination restored transgenic fruit development but not the rapid abscission seen in wild-type plants, demonstrating that pollination does not assure normal rates of detachment. In wild-type stamen AZs, AtZFP2 is significantly up-regulated postanthesis. Phenotype data from transgene overexpression studies suggest that AtZFP2 participates in processes that directly or indirectly influence organ shed.
Collapse
Affiliation(s)
- Suqin Cai
- Department of Horticulture, Iowa State University, Ames, IA 50011-1100, USA
| | | |
Collapse
|
20
|
Su K, Zhao S, Shan H, Kong H, Lu W, Theissen G, Chen Z, Meng Z. The MIK region rather than the C-terminal domain of AP3-like class B floral homeotic proteins determines functional specificity in the development and evolution of petals. THE NEW PHYTOLOGIST 2008; 178:544-558. [PMID: 18298432 DOI: 10.1111/j.1469-8137.2008.02382.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In core eudicots, euAP3-type MADS-box genes encode a PISTILLATA (PI)-derived motif, as well as a C-terminal euAP3 motif that originated from a paleoAP3 motif of an ancestral APETALA3 (AP3)-like protein through a translational frameshift mutation. To determine the functional and evolutionary relevance of these motifs, a series of point mutation and domain-swap constructs were generated, involving CsAP3, a paleoAP3-type gene from the basal angiosperm Chloranthus spicatus encoding a truncated paleoAP3 motif, and AtAP3, a euAP3-type gene from the core eudicot Arabidopsis thaliana. The chimeric constructs were expressed in A. thaliana under the control of the AP3 promoter or the CaMV 35S promoter in an ap3 mutant or wild-type background, respectively. Significant recovery of AP3 function was obtained in both complementation and ectopic expression experiments whenever the region upstream of the C-terminal motifs (MIK region) from A. thaliana was taken, even when the PI-derived motif and the truncated paleoAP3 motif of CsAP3 substituted for the corresponding sequences from AtAP3. However, no or very weak complementation or gain-of-function was seen when the MIK region was from CsAP3. Our data suggest that changes in the MIK region rather than mutations in the C-terminal domain were of crucial importance for the evolution of the functional specificity of euAP3-type proteins in stamen and petal development.
Collapse
Affiliation(s)
- Kunmei Su
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Tan FC, Swain SM. Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). PHYSIOLOGIA PLANTARUM 2007; 131:481-95. [PMID: 18251886 DOI: 10.1111/j.1399-3054.2007.00971.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flowering and flower formation are defining features of angiosperms and the control of these developmental processes involves a common repertoire of genes which are shared among different species of flowering plants. These genes were first identified using various homeotic and flowering time mutants of Arabidopsis and snapdragon, and homologous genes have subsequently been isolated from a wide range of different plant species based on the conservation of protein sequence and function. Using degenerate reverse-transcriptase polymerase chain reaction, we have isolated one APETALA3-like (CitMADS8) and two SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1)-like (CsSL1 and CsSL2) homologues from sweet orange (Citrus sinensis L.). Although the translated amino acid sequence of CitMADS8 shares many similarities with other higher plant APETALA3 proteins, CitMADS8 fails to complement the floral organ identity defects of the Arabidopsis ap3-3 mutant. By contrast, the two citrus SOC1-like genes, particularly CsSL1, are able to shorten the time taken to flower in the Arabidopsis wild-type ecotypes Columbia and C24, and functionally complement the late flowering phenotype of the soc1 mutant, essentially performing the endogenous function of Arabidopsis SOC1. Once flowering has commenced, interactions between specific flowering genes and a gene required for meristem maintenance, WUSCHEL, ensure that the Arabidopsis flower is a determinate structure with four whorls. We have isolated a citrus WUSCHEL homologue (CsWUS) that is capable of restoring most of the meristem function to the shoots and flowers of the Arabidopsis wus-1 mutant, implying that CsWUS is the functional equivalent of Arabidopsis WUSCHEL.
Collapse
Affiliation(s)
- Fui-Ching Tan
- CSIRO Plant Industry, Private Mail Bag, Merbein, Victoria 3505, Australia
| | | |
Collapse
|
22
|
Shan H, Zhang N, Liu C, Xu G, Zhang J, Chen Z, Kong H. Patterns of gene duplication and functional diversification during the evolution of the AP1/SQUA subfamily of plant MADS-box genes. Mol Phylogenet Evol 2007; 44:26-41. [PMID: 17434760 DOI: 10.1016/j.ympev.2007.02.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 02/07/2007] [Accepted: 02/19/2007] [Indexed: 01/30/2023]
Abstract
Members of the AP1/SQUA subfamily of plant MADS-box genes play broad roles in the regulation of reproductive meristems, the specification of sepal and petal identities, and the development of leaves and fruits. It has been shown that AP1/SQUA-like genes are angiosperm-specific, and have experienced several major duplication events. However, the evolutionary history of this subfamily is still uncertain. Here, we report the isolation of 14 new AP1/SQUA-like genes from seven early-diverging eudicots and the identification of 11 previously uncharacterized ESTs and genomic sequences from public databases. Sequence comparisons of these and other published sequences reveal a conserved C-terminal region, the FUL motif, in addition to the known euAP1/paleoAP1 motif, in AP1/SQUA-like proteins. Phylogenetic analyses further suggest that there are three major lineages (euAP1, euFUL, and AGL79) in core eudicots, likely resulting from two close duplication events that predated the divergence of core eudicots. Among the three lineages, euFUL is structurally very similar to FUL-like genes from early-diverging eudicots and basal angiosperms, whereas euAP1 might have originally been generated through a 1-bp deletion in the exon 8 of an ancestral euFUL- or FUL-like gene. Because euFUL- and FUL-like genes usually have broad expression patterns, we speculate that AP1/SQUA-like genes initially had broad functions. Based on these observations, the evolutionary fates of duplicate genes and the contributions of the frameshift mutation and alternative splicing to functional diversity are discussed.
Collapse
Affiliation(s)
- Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Xiangshan, Beijing, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
23
|
Adamczyk BJ, Lehti-Shiu MD, Fernandez DE. The MADS domain factors AGL15 and AGL18 act redundantly as repressors of the floral transition in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:1007-19. [PMID: 17521410 DOI: 10.1111/j.1365-313x.2007.03105.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The developmental roles of AGL15 and AGL18, members of the AGL15-like clade of MADS domain regulatory factors, have not been defined previously. Analysis of transgenic Arabidopsis plants showed that overexpression of AGL18 produces the same phenotypic changes as overexpression of AGL15, and the two genes have partially overlapping expression patterns. Functional redundancy was confirmed through analysis of loss-of-function mutants. agl15 agl18 double mutants, but not single mutants, flower early under non-inductive conditions, indicating that AGL15 and AGL18 act in a redundant fashion as repressors of the floral transition. Further genetic analyses and expression studies were used to examine the relationship between AGL15 and AGL18 activity and other regulators of the floral transition. AGL15 and AGL18 act upstream of the floral integrator FT, and a combination of agl15 and agl18 mutations partially suppresses defects in the photoperiod pathway. agl15 agl18 mutations show an additive relationship with mutations in genes encoding other MADS domain floral repressors, and further acceleration of flowering is seen in triple and quadruple mutants under both inductive and non-inductive conditions. Thus, flowering time is determined by the additive effect of multiple MADS domain floral repressors, with important contributions from AGL15 and AGL18.
Collapse
Affiliation(s)
- Benjamin J Adamczyk
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706-1381, USA
| | | | | |
Collapse
|
24
|
Hernández-Hernández T, Martínez-Castilla LP, Alvarez-Buylla ER. Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events. Mol Biol Evol 2006; 24:465-81. [PMID: 17135333 DOI: 10.1093/molbev/msl182] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
B-class MADS-box genes have been shown to be the key regulators of petal and stamen specification in several eudicot model species such as Arabidopsis thaliana, Antirrhinum majus, and Petunia hybrida. Orthologs of these genes have been found across angiosperms and gymnosperms, and it is thought that the basic regulatory function of B proteins is conserved in seed plant lineages. The evolution of B genes is characterized by numerous duplications that might represent key elements fostering the functional diversification of duplicates with a deep impact on their role in the evolution of the floral developmental program. To evaluate this, we performed a rigorous statistical analysis with B gene sequences. Using maximum likelihood and Bayesian methods, we estimated molecular substitution rates and determined the selective regimes operating at each residue of B proteins. We implemented tests that rely on phylogenetic hypotheses and codon substitution models to detect significant differences in substitution rates (DSRs) and sites under positive adaptive selection (PS) in specific lineages before and after duplication events. With these methods, we identified several protein residues fixed by PS shortly after the origin of PISTILLATA-like and APETALA3-like lineages in angiosperms and shortly after the origin of the euAP3-like lineage in core eudicots, the 2 main B gene duplications. The residues inferred to have been fixed by positive selection lie mostly within the K domain of the protein, which is key to promote heterodimerization. Additionally, we used a likelihood method that accommodates DSRs among lineages to estimate duplication dates for AP3-PI and euAP3-TM6, calibrating with data from the fossil record. The dates obtained are consistent with angiosperm origins and diversification of core eudicots. Our results strongly suggest that novel multimer formation with other MADS proteins could have been crucial for the functional divergence of B MADS-box genes. We thus propose a mechanism of functional diversification and persistence of gene duplicates by the appearance of novel multimerization capabilities after duplications. Multimer formation in different combinations of regulatory proteins can be a mechanistic basis for the origin of novel regulatory functions and a gene regulatory mechanism for the appearance of morphological innovations.
Collapse
Affiliation(s)
- Tania Hernández-Hernández
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México D.F., México
| | | | | |
Collapse
|
25
|
Duan K, Li L, Hu P, Xu SP, Xu ZH, Xue HW. A brassinolide-suppressed rice MADS-box transcription factor, OsMDP1, has a negative regulatory role in BR signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:519-31. [PMID: 16827922 DOI: 10.1111/j.1365-313x.2006.02804.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The MADS-box transcription factor-encoding genes are expressed mainly during plant reproductive development, where they play important roles in controlling floral organ initiation and identity. Few previous reports have investigated the functions of MADS-box transcription factors expressed in vegetative tissues. Here we describe the functional characterization of a rice AG-like MADS-box protein, OsMDP1 (Oryza sativa MADS-domain-containing protein 1). A partial cDNA encoding a MADS-box domain was identified via high-throughput screening of rice brassinolide-regulated genes, and the full-length cDNA was subsequently isolated via screening of a cDNA library constructed from rice materials at tillering stage. Expression pattern analyses indicated that OsMDP1 is transcribed mainly in vegetative tissues, including the mature leaf, coleoptile, root-elongation zone, culm internode, and especially the joint region between the leaf blade and sheath. Further studies revealed that transcription of OsMDP1 is stimulated by darkness and suppressed by brassinolide treatment. OsMDP1 deficiency resulted in shortened primary roots, elongated coleoptiles and enhanced lamina joint inclinations. Moreover, transgenic plants showed hypersensitivities to exogenous brassinolide in terms of lamina joint inclination and coleoptile elongation. OsMDP1 deficiency resulted in enhanced expression of OsXTR1, which encodes xyloglucan endotransglycosylase, the cell-wall loosening enzyme necessary for cell elongation, and modulated expressions of multiple genes involved in cell signalling and gene transcription, indicating the key negative regulatory role of OsMDP1 in BR signalling.
Collapse
Affiliation(s)
- Ke Duan
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun Road, 100093 Beijing, China
| | | | | | | | | | | |
Collapse
|
26
|
Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H. Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evol Dev 2006; 8:30-45. [PMID: 16409381 DOI: 10.1111/j.1525-142x.2006.05073.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The MADS-box gene AGAMOUS (AG) plays a key role in determining floral meristem and organ identities. We identified three AG homologs, EScaAG1, EScaAG2, and EScaAGL11 from the basal eudicot Eschscholzia californica (California poppy). Phylogenetic analyses indicate that EScaAG1 and EScaAG2 are recent paralogs within the AG clade, independent of the duplication in ancestral core eudicots that gave rise to the euAG and PLENA (PLE) orthologs. EScaAGL11 is basal to core eudicot AGL11 orthologs in a clade representing an older duplication event after the divergence of the angiosperm and gymnosperm lineages. Detailed in situ hybridization experiments show that expression of EScaAG1 and EScaAG2 is similar to AG; however, both genes appear to be expressed earlier in floral development than described in the core eudicots. A thorough examination of available expression and functional data in a phylogenetic context for members of the AG and AGL11 clades reveals that gene expression has been quite variable throughout the evolutionary history of the AG subfamily and that ovule-specific expression might have evolved more than twice. Although sub- and neofunctionalization are inferred to have occurred following gene duplication, functional divergence among orthologs is evident, as is convergence, among paralogs sampled from different species. We propose that retention of multiple AG homologs in several paralogous lineages can be explained by the conservation of ancestral protein activity combined with evolutionarily labile regulation of expression in the AG and AGL11 clades such that the collective functions of the AG subfamily in stamen and carpel development are maintained following gene duplication.
Collapse
Affiliation(s)
- Laura M Zahn
- Department of Biology, The Huck Institutes of the Life Sciences, and the Institute for Molecular Genetics and Evolution, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Kramer EM, Su HJ, Wu CC, Hu JM. A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage. BMC Evol Biol 2006; 6:30. [PMID: 16563166 PMCID: PMC1513400 DOI: 10.1186/1471-2148-6-30] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 03/24/2006] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ancestral paleoAP3 lineage was duplicated at some point within the basal eudicots to give rise to the paralogous TM6 and euAP3 lineages. This event was followed in euAP3 orthologs by the replacement of the C-terminal paleoAP3 motif with the derived euAP3 motif. It has been suggested that the new motif was created by an eight-nucleotide insertion that produced a translational frameshift. RESULTS The addition of 25 eudicot AP3 homologs to the existing dataset has allowed us to clarify the process by which the euAP3 motif evolved. Phylogenetic analysis indicates that the euAP3/TM6 duplication maps very close to the base of the core eudicots, associated with the families Trochodendraceae and Buxaceae. We demonstrate that although the transformation of paleoAP3 into euAP3 was due to a frameshift mutation, this was the result of a single nucleotide deletion. The use of ancestral character state reconstructions has allowed us to demonstrate that the frameshift was accompanied by few other nucleotide changes. We further confirm that the sequence is evolving as coding region. CONCLUSION This study demonstrates that the simplest of genetic changes can result in the remodeling of protein sequence to produce a kind of molecular 'hopeful monster.' Moreover, such a novel protein motif can become conserved almost immediately on the basis of what appears to be a rapidly generated new function. Given that the existing data on the function of such C-terminal motifs are somewhat disparate and contradictory, we have sought to synthesize previous findings within the context of the current analysis and thereby highlight specific hypotheses that require further investigation before the significance of the euAP3 frameshift event can be fully understood.
Collapse
Affiliation(s)
- Elena M Kramer
- Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138, USA
| | - Huei-Jiun Su
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Chiang Wu
- Dept. of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138, USA
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
28
|
Adam H, Jouannic S, Morcillo F, Richaud F, Duval Y, Tregear JW. MADS box genes in oil palm (Elaeis guineensis): patterns in the evolution of the SQUAMOSA, DEFICIENS, GLOBOSA, AGAMOUS, and SEPALLATA subfamilies. J Mol Evol 2005; 62:15-31. [PMID: 16320117 DOI: 10.1007/s00239-005-0333-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Accepted: 08/01/2005] [Indexed: 11/24/2022]
Abstract
MADS box genes code for a large family of transcription factors which regulate development in higher plants, notably flower formation. We describe here a study of members of the MADS box gene family in oil palm (Elaeis guineensis Jacq.), a representative of the family Arecaceae and order Arecales, a key group of monocotyledons which has been unreported in previous phylogenetic reconstructions of the different recognized clades of MADS box genes. In this study, 13 oil palm MADS box genes were identified and characterized. They were found to belong to five different subfamilies, namely, the previously defined SQUAMOSA, AGAMOUS, AGAMOUS-like2, DEFICIENS, and GLOBOSA groups. Genes belonging to each of these groups play a critical role in the determination of flower structure as defined by the ABCDE model. The in planta expression profiles of the oil palm MADS box genes were studied by RT-PCR and phylogenetic sequence diversity within individual subfamilies was investigated by comparing their deduced protein sequences with those of other angiosperms. Most of the oil palm sequences studied were observed to group with distinct supported clades within their subfamily. Some unexpected groupings were observed between monocot sequences (including oil palm ones) of non-Poaceae origin, probably illustrating the importance of obtaining adequate taxon representation in monocot molecular phylogenies.
Collapse
Affiliation(s)
- Hélène Adam
- CIRAD/IRD Palm Developmental Biology Laboratory, UMR 1098, Centre IRD Montpellier, BP 64501, 911 avenue Agropolis, 34394 Montpellier Cedex 5, France
| | | | | | | | | | | |
Collapse
|
29
|
Skipper M, Johansen LB, Pedersen KB, Frederiksen S, Johansen BB. Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.). Gene 2005; 366:266-74. [PMID: 16236468 DOI: 10.1016/j.gene.2005.08.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 08/23/2005] [Accepted: 08/25/2005] [Indexed: 10/25/2022]
Abstract
Studies have shown that several plant species possess AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium thyrsiflorum, named DthyrAG1 and DthyrAG2, respectively, and analyzed their expression patterns. Quantification by real-time RT-PCR analysis shows that both are transcribed in the mature flowers and during ovule development. Localization of the transcripts by in situ hybridization analysis in flowers reveals that both genes are transcribed in the rostellum, stigma, and stylar canal. Expression analysis during ovule development shows that DthyrAG1 is expressed only in the initial periods of placenta- and ovule development, whereas the DthyrAG2 is transcribed throughout ovule development. These results suggest that both C- and D lineage orthologs are involved in various aspects of flower development and that DthyrAG2 have a more prominent role than DthyrAG1 in late ovule development in D. thyrsiflorum.
Collapse
Affiliation(s)
- Martin Skipper
- Institute of Biology, University of Copenhagen, Gothersgade 140, DK-1123 Copenhagen K, Denmark.
| | | | | | | | | |
Collapse
|
30
|
Li GS, Meng Z, Kong HZ, Chen ZD, Theissen G, Lu AM. Characterization of candidate class A, B and E floral homeotic genes from the perianthless basal angiosperm Chloranthus spicatus (Chloranthaceae). Dev Genes Evol 2005; 215:437-49. [PMID: 16028057 DOI: 10.1007/s00427-005-0002-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Accepted: 04/29/2005] [Indexed: 10/25/2022]
Abstract
The classic ABC model explains the activities of each class of floral homeotic genes in specifying the identity of floral organs. Thus, changes in these genes may underlay the origin of floral diversity during evolution. In this study, three MADS-box genes were isolated from the perianthless basal angiosperm Chloranthus spicatus. Sequence and phylogenetic analyses revealed that they are AP1-like, AP3-like and SEP3-like genes, and hence these genes were termed CsAP1, CsAP3 and CsSEP3, respectively. Due to these assignments, they represent candidate class A, class B and class E genes, respectively. Expression patterns suggest that the CsAP1, CsAP3 and CsSEP3 genes function during flower development of C. spicatus. CsAP1 is expressed broadly in the flower, which may reflect the ancestral function of SQUA-like genes in the specification of inflorescence and floral meristems rather than in patterning of the flower. CsAP3 is exclusively expressed in male floral organs, providing the evidence that AP3-like genes have ancestral function in differentiation between male and female reproductive organs. CsSEP3 expression is not detectable in spike meristems, but its mRNA accumulates throughout the flower, supporting the view that SEP-like genes have conserved expression pattern and function throughout angiosperm. Studies of synonymous vs nonsynonymous nucleotide substitutions indicate that these genes have not evolved under changes in evolutionary forces. All the data above suggest that the genes may have maintained at least some ancestral functions despite the lack of perianth in the flowers of C. spicatus.
Collapse
Affiliation(s)
- Gui-Sheng Li
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, People's Republic of China
| | | | | | | | | | | |
Collapse
|
31
|
Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, Depamphilis CW, Ma H. The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics 2005; 169:2209-23. [PMID: 15687268 PMCID: PMC1449606 DOI: 10.1534/genetics.104.037770] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the "floral state" by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and seem to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest that SEP genes may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence. The first duplication occurred prior to the origin of the extant angiosperms, resulting in the AGL2/3/4 and AGL9 clades. Subsequent duplications occurred within these clades in the eudicots and monocots. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower.
Collapse
Affiliation(s)
- Laura M Zahn
- Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, 16802, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Kim S, Yoo MJ, Albert VA, Farris JS, Soltis PS, Soltis DE. Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. AMERICAN JOURNAL OF BOTANY 2004; 91:2102-2118. [PMID: 21652358 DOI: 10.3732/ajb.91.12.2102] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
B-function MADS-box genes play crucial roles in floral development in model angiosperms. We reconstructed the structural and functional implications of B-function gene phylogeny in the earliest extant flowering plants based on analyses that include 25 new AP3 and PI sequences representing critical lineages of the basalmost angiosperms: Amborella, Nuphar (Nymphaeaceae), and Illicium (Austrobaileyales). The ancestral size of exon 5 in PI-homologues is 42 bp, typical of exon 5 in other plant MADS-box genes. This 42-bp length is found in PI-homologues from Amborella and Nymphaeaceae, successive sisters to all other angiosperms. Following these basalmost branches, a deletion occurred in exon 5, yielding a length of 30 bp, a condition that unites all other angiosperms. Several shared amino acid strings, including a prominent "DEAER" motif, are present in the AP3- and PI-homologues of Amborella. These may be ancestral motifs that were present before the duplication that yielded the AP3 and PI lineages and subsequently were modified after the divergence of Amborella. Other structural features were identified, including a motif that unites the previously described TM6 clade and a deletion in AP3-homologues that unites all Magnoliales. Phylogenetic analyses of AP3- and PI-homologues yielded gene trees that generally track organismal phylogeny as inferred by multigene data sets. With both AP3 and PI amino acid sequences, Amborella and Nymphaeaceae are sister to all other angiosperms. Using nonparametric rate smoothing (NPRS), we estimated that the duplication that produced the AP3 and PI lineages occurred approximately 260 mya (231-290). This places the duplication after the split between extant gymnosperms and angiosperms, but well before the oldest angiosperm fossils. A striking similarity in the multimer-signalling C domains of the Amborella proteins suggests the potential for the formation of unique transcription-factor complexes. The earliest angiosperms may have been biochemically flexible in their B function and "tinkered" with floral organ identity.
Collapse
Affiliation(s)
- Sangtae Kim
- Department of Botany, University of Florida, Gainesville, Florida 32611 USA
| | | | | | | | | | | |
Collapse
|
33
|
Kramer EM, Jaramillo MA, Di Stilio VS. Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics 2004; 166:1011-23. [PMID: 15020484 PMCID: PMC1470751 DOI: 10.1534/genetics.166.2.1011] [Citation(s) in RCA: 332] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG-like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity.
Collapse
Affiliation(s)
- Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | | | | |
Collapse
|
34
|
Bielenberg DG, Wang Y, Fan S, Reighard GL, Scorza R, Abbott AG. A Deletion Affecting Several Gene Candidates is Present in the Evergrowing Peach Mutant. J Hered 2004; 95:436-44. [PMID: 15388771 DOI: 10.1093/jhered/esh057] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evergrowing (EVG) peach is one of only two described mutants affecting winter dormancy in woody perennial species. EVG peach does not set terminal buds, cease new leaf growth, nor enter into a dormant resting phase in response to winter conditions. The EVG mutation segregates in F2 progeny as a single recessive nuclear gene. A local molecular genetic linkage map around EVG was previously developed using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, and a bacterial artificial chromosome (BAC) contig that contains the EVG mutation was assembled. A MADS box coding open reading frame (ORF) was found in a BAC of this contig and used as a probe. The probe detected a polymorphism between the wild-type and mutant genomes, and the polymorphism is indicative of a deletion in EVG peach. The EVG gene region contained six potential MADS-box transcription factor sequences, and the deletion in EVG affected at least four of these. The deletion was bracketed using RFLP analysis, which showed that it is contained within a segment of the genome no greater than 180 kb.
Collapse
Affiliation(s)
- D G Bielenberg
- Department of Horticulture, Clemson University, Clemson, SC 29634, USA.
| | | | | | | | | | | |
Collapse
|
35
|
Borrone JW, Kuhn DN, Schnell RJ. Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:495-507. [PMID: 15148571 DOI: 10.1007/s00122-004-1662-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2002] [Accepted: 03/08/2004] [Indexed: 05/08/2023]
Abstract
There is currently an international effort in improving disease resistance and crop yield in Theobroma cacao L., an economically important crop of the tropics, using marker-assisted selection for breeding. We are developing molecular genetic markers focusing upon gene families involved with disease resistance. One such family is the WRKY proteins, which are plant-specific transcriptional factors associated with regulating defense responses to both abiotic and biotic stresses. Degenerate PCR primers were designed to the highly conserved DNA-binding domain and other conserved motifs of group I and group II, subgroups a-c, WRKY genes. Sixteen individual WRKY fragments were isolated from a mixture of T. cacao DNA using one pair of primers. Of the 16 WRKY loci investigated, seven contained single nucleotide polymorphisms within the intron as detected by sequence comparison of the PCR products. Four of these were successfully converted into molecular markers and mapped in an F2 population by capillary electrophoresis-single strand conformation polymorphism analysis. This is the first report of a pair of degenerate primers amplifying WRKY loci directly from genomic DNA and demonstrates a simple method for developing useful genetic markers from members of a large gene family.
Collapse
Affiliation(s)
- James W Borrone
- Department of Biological Sciences, Florida International University, Miami 33199, FL, USA
| | | | | |
Collapse
|
36
|
Tsai WC, Kuoh CS, Chuang MH, Chen WH, Chen HH. Four DEF-like MADS box genes displayed distinct floral morphogenetic roles in Phalaenopsis orchid. PLANT & CELL PHYSIOLOGY 2004; 45:831-44. [PMID: 15295066 DOI: 10.1093/pcp/pch095] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The complex flower organization of orchids offers an opportunity to discover new variant genes and different levels of complexity in the morphogenesis of flowers. In this study, four B-class Phalaenopsis DEF-like MADS-box genes were identified and characterized, including PeMADS2, PeMADS3, PeMADS4 and PeMADS5. Differential expression profiles of these genes were detected in the floral organs of P. equestris, suggesting distinctive roles in the floral morphogenesis of orchids. Furthermore, expressions of these genes were varied to different extents in the peloric mutants with lip-like petals. Expression of PeMADS4 was in lips and columns of wild type, and it extended to the lip-like petals in the peloric mutant. Expression of PeMADS5 was mainly in petals and to a lesser extent in columns in the wild type, whereas it was completely eliminated in the peloric mutant. Disruption of the PeMADS5 promoter region of the peloric mutant was detected at nucleotide +312 relative to the upstream of translational start codon, suggesting that a DNA rearrangement has occurred in the peloric mutant. Genomic structure analysis of the PeMADS5 showed that the exon length was conserved in exons 1-6, similar to DEF-like genes of other plants. Collectively, this is the first report that four DEF-like MADS genes were identified in a single monocotyledonous species and that they may play distinctive morphogenetic roles in the floral development of an orchid.
Collapse
Affiliation(s)
- Wen-Chieh Tsai
- Department of Biology, National Cheng Kung University, Tainan 701, Taiwan
| | | | | | | | | |
Collapse
|
37
|
Kramer EM, Jaramillo MA, Di Stilio VS. Patterns of Gene Duplication and Functional Evolution During the Diversification of the AGAMOUS Subfamily of MADS Box Genes in Angiosperms. Genetics 2004. [DOI: 10.1093/genetics/166.2.1011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG -like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity.
Collapse
Affiliation(s)
- Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - M Alejandra Jaramillo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | | |
Collapse
|
38
|
Ferrario S, Immink RGH, Angenent GC. Conservation and diversity in flower land. CURRENT OPINION IN PLANT BIOLOGY 2004; 7:84-91. [PMID: 14732446 DOI: 10.1016/j.pbi.2003.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
During the past decade, enormous progress has been made in understanding the molecular regulation of flower development. In particular, homeotic genes that determine the identity of the floral organs have been characterised from different flowering plants, revealing considerable conservation among angiosperm species. On the other hand, evolutionary diversification has led to enormous variation in flower morphology. Increasing numbers of reports have described differences in the regulation, redundancy and function of homeotic genes from various species. These fundamentals of floral organ specification are therefore an ideal subject for comparative analyses of flower development, which will lead to a better understanding of plant evolution, plant development and the complexity of molecular mechanisms that control flower development and morphology.
Collapse
Affiliation(s)
- Silvia Ferrario
- Business Unit Bioscience, Plant Research International, Wageningen, The Netherlands
| | | | | |
Collapse
|
39
|
Stellari GM, Jaramillo MA, Kramer EM. Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol Biol Evol 2003; 21:506-19. [PMID: 14694075 DOI: 10.1093/molbev/msh044] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The B class genes, including homologs of the Arabidopsis loci APETALA3 (AP3) and PISTILLATA (PI ), appear to play a conserved role in the determination of petal and stamen identity across core eudicot angiosperms. Understanding how and when these functions evolved is a critical component of elucidating the evolution of flowers, particularly the appearance of petaloid perianth organs. Before comparisons of gene expression patterns or functions can be made, however, it is necessary to establish the orthology of AP3 and PI homologs from basal angiosperms. Here, we report the identification and analysis of 29 new representatives of the B gene lineage from basal ANITA and magnoliid dicot angiosperms. These studies indicate that gene duplications have occurred at every phylogenetic level, both before and after the duplication that produced the separate AP3 and PI lineages. Comparison of genomic structure among PI homologs indicates that a 12-nucleotide deletion that had been considered synapomorphic for the whole PI lineage actually arose within the ANITA grade, after the split of the Nymphaeales but before the separation of the Austrobaileyales. Evidence for alternative splicing of the Nymphaea AP3 homolog is also presented. The implications of these findings for angiosperm systematics, the conservation of AP3 and PI gene function, and the evolution of the ABC program are discussed.
Collapse
Affiliation(s)
- Giulia M Stellari
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | | | | |
Collapse
|
40
|
|
41
|
Martinez-Castilla LP, Alvarez-Buylla ER. Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny. Proc Natl Acad Sci U S A 2003; 100:13407-12. [PMID: 14597714 PMCID: PMC263827 DOI: 10.1073/pnas.1835864100] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2003] [Indexed: 11/18/2022] Open
Abstract
Gene duplication is a substrate of evolution. However, the relative importance of positive selection versus relaxation of constraints in the functional divergence of gene copies is still under debate. Plant MADS-box genes encode transcriptional regulators key in various aspects of development and have undergone extensive duplications to form a large family. We recovered 104 MADS sequences from the Arabidopsis genome. Bayesian phylogenetic trees recover type II lineage as a monophyletic group and resolve a branching sequence of monophyletic groups within this lineage. The type I lineage is comprised of several divergent groups. However, contrasting gene structure and patterns of chromosomal distribution between type I and II sequences suggest that they had different evolutionary histories and support the placement of the root of the gene family between these two groups. Site-specific and site-branch analyses of positive Darwinian selection (PDS) suggest that different selection regimes could have affected the evolution of these lineages. We found evidence for PDS along the branch leading to flowering time genes that have a direct impact on plant fitness. Sites with high probabilities of having been under PDS were found in the MADS and K domains, suggesting that these played important roles in the acquisition of novel functions during MADS-box diversification. Detected sites are targets for further experimental analyses. We argue that adaptive changes in MADS-domain protein sequences have been important for their functional divergence, suggesting that changes within coding regions of transcriptional regulators have influenced phenotypic evolution of plants.
Collapse
Affiliation(s)
- León Patricio Martinez-Castilla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, National Autonomous University of Mexico, Ap Postal 70-275, Mexico D.F., 04510, Mexico
| | | |
Collapse
|
42
|
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J. Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A 2003; 100:6263-8. [PMID: 12730378 PMCID: PMC156360 DOI: 10.1073/pnas.0937399100] [Citation(s) in RCA: 764] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Winter wheats require several weeks at low temperature to flower. This process, vernalization, is controlled mainly by the VRN1 gene. Using 6,190 gametes, we found VRN1 to be completely linked to MADS-box genes AP1 and AGLG1 in a 0.03-centimorgan interval flanked by genes Cysteine and Cytochrome B5. No additional genes were found between the last two genes in the 324-kb Triticum monococcum sequence or in the colinear regions in rice and sorghum. Wheat AP1 and AGLG1 genes were similar to Arabidopsis meristem identity genes AP1 and AGL2, respectively. AP1 transcription was regulated by vernalization in both apices and leaves, and the progressive increase of AP1 transcription was consistent with the progressive effect of vernalization on flowering time. Vernalization was required for AP1 transcription in apices and leaves in winter wheat but not in spring wheat. AGLG1 transcripts were detected during spike differentiation but not in vernalized apices or leaves, suggesting that AP1 acts upstream of AGLG1. No differences were detected between genotypes with different VRN1 alleles in the AP1 and AGLG1 coding regions, but three independent deletions were found in the promoter region of AP1. These results suggest that AP1 is a better candidate for VRN1 than AGLG1. The epistatic interactions between vernalization genes VRN1 and VRN2 suggested a model in which VRN2 would repress directly or indirectly the expression of AP1. A mutation in the promoter region of AP1 would result in the lack of recognition of the repressor and in a dominant spring growth habit.
Collapse
Affiliation(s)
- L Yan
- Department of Agronomy and Range Science, University of California, Davis 95616, USA
| | | | | | | | | | | |
Collapse
|