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Fan S, Wang Z, Xiao Y, Liang J, Zhao S, Liu Y, Peng F, Guo J. Genome-Wide Identification of Trehalose-6-phosphate Synthase (TPS) Gene Family Reveals the Potential Role in Carbohydrate Metabolism in Peach. Genes (Basel) 2023; 15:39. [PMID: 38254929 PMCID: PMC10815152 DOI: 10.3390/genes15010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Trehalose-6-phosphate synthase (TPS) is essential for plant growth and development, linking trehalose-6-phosphate (T6P) to carbon metabolism. However, little is known about the TPS gene family in peaches and their potential roles in regulating carbohydrates in peach fruit. In this study, nine TPS genes were identified in the peach genome and named according to the homologous genes in Arabidopsis. Phylogenetic analysis showed that three subfamilies were identified, including TPSI, TPSII-1, and TPSII-2, which were also consistent with gene structure analysis. Considerable cis-elements were enriched in the promoters, including plant hormone-related elements. Tissue-specific analysis showed that these TPS genes were mainly expressed in leaves, stems, and fruit, showing different expression patterns for each gene. In addition, during fruit development, the content of trehalose-6-phosphate (T6P) was positively correlated with the expression of PpTPS7a and negatively with sucrose non-fermenting-1-related kinase 1 (SnRK1) activity. Transient overexpression and silencing of PpTPS7a in peach fruit validated its function in regulating T6P content and SnRK1 activity.
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Affiliation(s)
- Shihao Fan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
| | - Zhe Wang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China; (Z.W.); (Y.X.); (J.L.); (S.Z.); (Y.L.)
| | - Yuansong Xiao
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China; (Z.W.); (Y.X.); (J.L.); (S.Z.); (Y.L.)
| | - Jiahui Liang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China; (Z.W.); (Y.X.); (J.L.); (S.Z.); (Y.L.)
| | - Shilong Zhao
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China; (Z.W.); (Y.X.); (J.L.); (S.Z.); (Y.L.)
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China; (Z.W.); (Y.X.); (J.L.); (S.Z.); (Y.L.)
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
| | - Jian Guo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
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Wang L, Song J, Han X, Yu Y, Wu Q, Qi S, Xu Z. Functional Divergence Analysis of AGL6 Genes in Prunus mume. PLANTS (BASEL, SWITZERLAND) 2022; 12:158. [PMID: 36616287 PMCID: PMC9824310 DOI: 10.3390/plants12010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The AGAMOUS-LIKE6 (AGL6) lineage is an important clade of MADS-box transcription factors that play essential roles in floral organ development. The genome of Prunus mume contains two homoeologous AGL6 genes that are replicated as gene fragments. In this study, two AGL6 homologs, PmAGL6-1 and PmAGL6-2, were cloned from P. mume and then functionally characterized. Sequence alignment and phylogenetic analyses grouped both genes into the AGL6 lineage. The expression patterns and protein-protein interaction patterns showed significant differences between the two genes. However, the ectopic expression of the two genes in Arabidopsis thaliana resulted in similar phenotypes, including the promotion of flowering, alteration of floral organ structure, participation in the formation of the floral meristem and promotion of pod bending. Therefore, gene duplication has led to some functional divergence of PmAGL6-1 and PmAGL6-2 but their functions are similar. We thus speculated that AGL6 genes play a crucial role in flower development in P. mume.
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Beltrame LC, Thompson CE, Freitas LB. Molecular evolution and structural analyses of proteins involved in metabolic pathways of volatile organic compounds in Petunia hybrida (Solanaceae). Genet Mol Biol 2022; 46:e20220114. [PMID: 36534952 PMCID: PMC9762610 DOI: 10.1590/1678-4685-gmb-2022-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
The association between plants and their pollinators is essential for increasing the diversity in angiosperms. Morphological and physiological traits, mainly floral scent, can influence the pollination dynamics and select pollinators for each plant species. In this work, we studied two proteins involved in producing volatile organic compounds in plants, conyferyl alcohol acyltransferase (CFAT) and benzoyl-CoA:benzyl alcohol/phenyl ethanol benzoyl transferase (BPBT) genes. We aimed to understand these proteins with respect to evolutionary and structural aspects and functions in Solanaceae using phylogenetic methods and comparative molecular modeling. We used Bayesian inference to describe the proteins' evolutionary history using Petunia x hybrida as a query to search for homologs in the Solanaceae family. Theoretical 3D models were obtained for both proteins using Panicum virgatum as a template. The phylogenetic tree included several different enzymes with diverse biological roles in Solanaceae, displaying the transferase domain. We identified only one sequence of CFAT in the databases, which belongs to Petunia x hybrida, and found several BPBT sequences from the genera Nicotiana, Solanum, and Capsicum. The 3D structures of CFAT and BPBT have two different domains, and we have identified the amino acid residues essential for the enzymatic activity and interaction with substrates.
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Affiliation(s)
- Lucas C. Beltrame
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Claudia E. Thompson
- Universidade Federal de Ciências da Saúde de Porto Alegre, Departamento de Farmacociências, Porto Alegre, RS, Brazil
| | - Loreta B. Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
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Li X, Kuang Y, Ye Y, Chen Z, Zhang M. Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae). Gene X 2022; 839:146732. [PMID: 35840006 DOI: 10.1016/j.gene.2022.146732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.
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Affiliation(s)
- Xiumei Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yanfeng Kuang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yushi Ye
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Zhongjian Chen
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Mingyong Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Liu H, Yang L, Tu Z, Zhu S, Zhang C, Li H. Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. Sci Rep 2021; 11:6585. [PMID: 33753780 PMCID: PMC7985208 DOI: 10.1038/s41598-021-85927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/09/2021] [Indexed: 11/09/2022] Open
Abstract
The organogenesis and development of reproductive organs, i.e., stamen and gynoecium, are important floral characteristics that are closely related to pollinators and reproductive fitness. As a genus from Magnoliaceae, Liriodendron has only two relict species: L. chinense and L. tulipifera. Despite the similar flower shapes of these species, their natural seed-setting rates differ significantly, implying interspecies difference in floral organogenesis and development. MADS-box genes, which participate in floral organogenesis and development, remain unexplored in Liriodendron. Here, to explore the interspecies difference in floral organogenesis and development and identify MADS-box genes in Liriodendron, we examined the stamen and gynoecium primordia of the two Liriodendron species by scanning electron microscopy combined with paraffin sectioning, and then collected two types of primordia for RNA-seq. A total of 12 libraries were constructed and 42,268 genes were identified, including 35,269 reference genes and 6,999 new genes. Monoterpenoid biosynthesis was enriched in L. tulipifera. Genome-wide analysis of 32 MADS-box genes was conducted, including phylogenetic trees, exon/intron structures, and conserved motif distributions. Twenty-six genes were anchored on 17 scaffolds, and six new genes had no location information. The expression profiles of MIKC-type genes via RT-qPCR acrossing six stamen and gynoecium developmental stages indicates that the PI-like, AG/STK-like, SEP-like, and SVP-like genes may contribute to the species-specific differentiation of the organogenesis and development of reproductive organs in Liriodendron. Our findings laid the groundwork for the future exploration of the mechanism underlying on the interspecific differences in reproductive organ development and fitness in Liriodendron.
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Affiliation(s)
- Huanhuan Liu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lichun Yang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhonghua Tu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shenghua Zhu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Chengge Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Huogen Li
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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Liu M, Sun W, Ma Z, Yu G, Li J, Wang Y, Wang X. Comprehensive multiomics analysis reveals key roles of NACs in plant growth and development and its environmental adaption mechanism by regulating metabolite pathways. Genomics 2020; 112:4897-4911. [PMID: 32916257 DOI: 10.1016/j.ygeno.2020.08.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/17/2023]
Abstract
Abnormal environmental conditions induce polyploidization and exacerbate vulnerability to agricultural production. Polyploidization is a pivotal event for plant adaption to stress and the expansion of transcription factors. NACs play key roles in plant stress resistance and growth and development, but the adaptive mechanism of NACs during plant polyploidization remain to be explored. Here, we identified and analyzed NACs from 15 species and found that the expansion of NACs was contributed by polyploidization. The regulatory networks were systematically analyzed based on polyomics. NACs might influence plant phenotypes and were correlated with amino acids acting as nitrogen source, indicating that NACs play a vital role in plant development. More importantly, in quinoa and Arabidopsis thaliana, NACs enabled plants to resist stress by regulating flavonoid pathways, and the universality was further confirmed by the Arabidopsis population. Our study provides a cornerstone for future research into improvement of important agronomic traits by transcription factors in a changing global environment.
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Affiliation(s)
- Moyang Liu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Wenjun Sun
- Sichuan Agricultural University, College of Life Science, Ya'an, China.
| | - Zhaotang Ma
- Sichuan Agricultural University, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Chengdu, China.
| | - Guolong Yu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Jiahao Li
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Yudong Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Xu Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
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Li X, Fan T, Zou P, Zhang W, Wu X, Zhang Y, Liao J. Can the anatomy of abnormal flowers elucidate relationships of the androecial members in the ginger (Zingiberaceae)? EvoDevo 2020; 11:12. [PMID: 32537122 PMCID: PMC7285767 DOI: 10.1186/s13227-020-00157-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/29/2020] [Indexed: 11/10/2022] Open
Abstract
Background Interpretation of the floral structure of Zingiberaceae has long concentrated on the relationships of the androecial members. It suggested that labellum is composed of two structures rather than three or five, and glands are interpreted either as gynoecial part or as androecial members. Methods Serial sections were used to observe the vasculature of normal and two-staminate flowers in Alpinia intermedia ‘shengzhen’. Floral diagrams were drawn to interpret the morphological category of the floral organs and the relationships of the androecial members. Androecial vascular bundles were associated with carpellary dorsal bundles (CDBs) and parietal bundles (PBs) in a Zingiberales phylogeny setting using ancestral state reconstruction. Results Anatomical observations demonstrate that the fertile stamen(s) incorporate parietal bundles both in normal and two-staminate flowers. The three appendages represent the three members of the outer whorl of the androecium, while the labellum represents the inner whorl of the androecium in the two-staminate flower. Reconstruction of the origin of the vascular system in the androecium suggests that the outer whorl of androecium receives its vascular supply from the CDBs, and the inner whorl of androecium receives from the PBs in both the basal banana group and the more derived ginger clade. Conclusions The present study adds to a growing body of literature suggesting that the anatomy of abnormal flowers may not provide enough evidence for elucidating the relationships of the androecial members, and help us to better understand how the vascular system is constructed during the androecial petaloidy evolution.
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Affiliation(s)
- Xiumei Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agricultural Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Tian Fan
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Pu Zou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Wenhu Zhang
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agricultural Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiuju Wu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agricultural Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yixin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
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Ma J, Deng S, Jia Z, Sang Z, Zhu Z, Zhou C, Ma L, Chen F. Conservation and divergence of ancestral AGAMOUS/SEEDSTICK subfamily genes from the basal angiosperm Magnolia wufengensis. TREE PHYSIOLOGY 2020; 40:90-107. [PMID: 31553477 DOI: 10.1093/treephys/tpz091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
AGAMOUS/SEEDSTICK (AG/STK) subfamily genes play crucial roles in the reproductive development of plants. However, most of our current knowledge of AG/STK subfamily genes is restricted to core eudicots and grasses, and the knowledge of ancestral exon-intron structures, expression patterns, protein-protein interaction patterns and functions of AG/STK subfamily genes remains unclear. To determine these, we isolated AG/STK subfamily genes (MawuAG1, MawuAG2 and MawuSTK) from a woody basal angiosperm Magnolia wufengensis (Magnoliaceae). MawuSTK arose from the gene duplication event occurring before the diversification of extant angiosperms, and MawuAG1 and MawuAG2 may result from a gene duplication event occurring before the divergence of Magnoliaceae and Lauraceae. Gene duplication led to apparent diversification in their expression and interaction patterns. It revealed that expression in both stamens and carpels likely represents the ancestral expression profiles of AG lineage genes, and expression of STK-like genes in stamens may have been lost soon after the appearance of the STK lineage. Moreover, AG/STK subfamily proteins may have immediately established interactions with the SEPALLATA (SEP) subfamily proteins following the emergence of the SEP subfamily; however, their interactions with the APETALA1/FRUITFULL subfamily proteins or themselves differ from those found in monocots and basal and core eudicots. MawuAG1 plays highly conserved roles in the determinacy of stamen, carpel and ovule identity, while gene duplication contributed to the functional diversification of MawuAG2 and MawuSTK. In addition, we investigated the evolutionary history of exon-intron structural changes of the AG/STK subfamily, and a novel splice-acceptor mode (GUU-AU) and the convergent evolution of N-terminal extension in the euAG and PLE subclades were revealed for the first time. These results further advance our understanding of ancestral AG/STK subfamily genes in terms of phylogeny, exon-intron structures, expression and interaction patterns, and functions, and provide strong evidence for the significance of gene duplication in the expansion and evolution of the AG/STK subfamily.
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Affiliation(s)
- Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Shixin Deng
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Zhongkui Jia
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Ziyang Sang
- Forestry Bureau of Wufeng County, Yichang, 443002, Hubei Province, PR China
| | - Zhonglong Zhu
- Wufeng Bo Ling Magnolia Wufengensis Technology Development Co., Ltd, Yichang, 443002, Hubei Province, PR China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang 443002, PR China
| | - Lvyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang 443002, PR China
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Ma J, Deng S, Chen L, Jia Z, Sang Z, Zhu Z, Ma L, Chen F. Gene duplication led to divergence of expression patterns, protein-protein interaction patterns and floral development functions of AGL6-like genes in the basal angiosperm Magnolia wufengensis (Magnoliaceae). TREE PHYSIOLOGY 2019; 39:861-876. [PMID: 31034013 DOI: 10.1093/treephys/tpz010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/07/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
The MADS-box family genes play critical roles in the regulation of growth and development of flowering plants. AGAMOUS-LIKE 6 (AGL6)-like genes are one of the most enigmatic subfamilies of the MADS-box family because of highly variable expression patterns and ambiguous functions, which have long puzzled researchers. A lot of AGL6 homologs have been identified from gymnosperms and angiosperms. However, only a few have been characterized, especially for basal angiosperm taxa. Magnolia wufengensis is a woody basal angiosperm from the family Magnoliaceae. In the current study, the phylogenesis, expression and protein-protein interaction (PPI) patterns, and functions of two AGL6 homologs from M. wufengensis, MawuAGL6-1 and MawuAGL6-2, were analyzed. Phylogenetic analysis indicated that the two AGL6 duplicates may have arisen by gene duplication before the divergence of Magnoliaceae and Lauraceae, with the diversification of their expression and PPI patterns after gene duplication. Functional analysis revealed that, in addition to common functions in accelerating flowering, MawuAGL6-1 might be responsible for flower meristem determinacy, while MawuAGL6-2 is preferentially recruited to regulate tepal morphogenesis. These findings further advance our understanding of the evolution of phylogenesis, expression, interaction and functions of AGL6 lineage genes from basal angiosperms, as well as the entire AGL6 lineage genes, and the significance of AGL6 lineage genes in the evolution and biological diversity.
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Affiliation(s)
- Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, PR China
| | - Shixin Deng
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Liyuan Chen
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Zhongkui Jia
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Ziyang Sang
- Forestry Bureau of Wufeng County, Wufeng, Hubei Province, PR China
| | - Zhonglong Zhu
- Wufeng Bo Ling Magnolia Wufengensis Technology Development Co., Ltd, Wufeng, Hubei Province, PR China
| | - Lvyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, PR China
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Shen G, Yang CH, Shen CY, Huang KS. Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms. Biol Res 2019; 52:25. [PMID: 31018872 PMCID: PMC6480507 DOI: 10.1186/s40659-019-0233-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The morphological diversity of flower organs is closely related to functional divergence within the MADS-box gene family. Bryophytes and seedless vascular plants have MADS-box genes but do not have ABCDE or AGAMOUS-LIKE6 (AGL6) genes. ABCDE and AGL6 genes belong to the subgroup of MADS-box genes. Previous works suggest that the B gene was the first ABCDE and AGL6 genes to emerge in plant but there are no mentions about the probable origin time of ACDE and AGL6 genes. Here, we collected ABCDE and AGL6 gene 381 protein sequences and 361 coding sequences from gymnosperms and angiosperms and reconstructed a complete Bayesian phylogeny of these genes. In this study, we want to clarify the probable origin time of ABCDE and AGL6 genes is a great help for understanding the role of the formation of the flower, which can decipher the forming order of MADS-box genes in the future. RESULTS These genes appeared to have been under purifying selection and their evolutionary rates are not significantly different from each other. Using the Bayesian evolutionary analysis by sampling trees (BEAST) tool, we estimated that: the mutation rate of the ABCDE and AGL6 genes was 2.617 × 10-3 substitutions/site/million years, and that B genes originated 339 million years ago (MYA), CD genes originated 322 MYA, and A genes shared the most recent common ancestor with E/AGL6 296 MYA, respectively. CONCLUSIONS The phylogeny of ABCDE and AGL6 genes subfamilies differed. The APETALA1 (AP1 or A gene) subfamily clustered into one group. The APETALA3/PISTILLATA (AP3/PI or B genes) subfamily clustered into two groups: the AP3 and PI clades. The AGAMOUS/SHATTERPROOF/SEEDSTICK (AG/SHP/STK or CD genes) subfamily clustered into a single group. The SEPALLATA (SEP or E gene) subfamily in angiosperms clustered into two groups: the SEP1/2/4 and SEP3 clades. The AGL6 subfamily clustered into a single group. Moreover, ABCDE and AGL6 genes appeared in the following order: AP3/PI → AG/SHP/STK → AGL6/SEP/AP1. In this study, we collected candidate sequences from gymnosperms and angiosperms. This study highlights important events in the evolutionary history of the ABCDE and AGL6 gene families and clarifies their evolutionary path.
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Affiliation(s)
- Gangxu Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Chih-Hui Yang
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chi-Yen Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
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11
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Peréz-Mesa P, Suárez-Baron H, Ambrose BA, González F, Pabón-Mora N. Floral MADS-box protein interactions in the early diverging angiosperm Aristolochia fimbriata Cham. (Aristolochiaceae: Piperales). Evol Dev 2019; 21:96-110. [PMID: 30734997 DOI: 10.1111/ede.12282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Floral identity MADS-box A, B, C, D, E, and AGL6 class genes are predominantly single copy in Magnoliids, and predate the whole genome duplication (WGD) events in monocots and eudicots. By comparison with the model species Arabidopsis thaliana, the expression patterns of B-, C-, and D-class genes in stamen, carpel, and ovules are conserved in Aristolochia fimbriata, whereas A-, E-class, and AGL6 genes have different expression patterns. Nevertheless, the interactions of these proteins that act through multimeric complexes remain poorly known in early divergent angiosperms. This study evaluates protein interactions among all floral MADS-box A. fimbriata proteins using the Yeast Two Hybrid System (Y2H). We found no homodimers and less heterodimers formed by AfimFUL when compared to AfimAGL6, which allowed us to suggest AGL6 homodimers in combination with AfimSEP2 as the most likely tetramer in sepal identity. We found AfimAP3-AfimPI obligate heterodimers and AfimAG-AfimSEP2 protein interactions intact suggesting conserved stamen and carpel tetrameric complexes in A. fimbriata. We observed a broader interaction partner set for AfimSEP2 than for its paralog AfimSEP1. We show conserved and exclusive MADS-box protein interactions in A. fimbriata in comparison with other eudicot and monocot model species in order to establish plesiomorphic MADS-box protein floral networks in angiosperms.
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Affiliation(s)
- Pablo Peréz-Mesa
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | | | | | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Sede Bogotá, Colombia
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12
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Almeida AMR, Piñeyro-Nelson A, Yockteng RB, Specht CD. Comparative analysis of whole flower transcriptomes in the Zingiberales. PeerJ 2018; 6:e5490. [PMID: 30155368 PMCID: PMC6110254 DOI: 10.7717/peerj.5490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/30/2018] [Indexed: 01/14/2023] Open
Abstract
The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.
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Affiliation(s)
- Ana Maria R Almeida
- Department of Biological Sciences, California State University, Hayward, Hayward, CA, United States of America
| | - Alma Piñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, DF, Mexico
| | - Roxana B Yockteng
- Centro de Investigaciones Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá, Colombia.,Institut de Systématique, Evolution, Biodiversité-UMR-CNRS, National Museum of Natural History, Paris, France
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States of America
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13
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14
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Hui W, Yang Y, Wu G, Peng C, Chen X, Zayed MZ. Transcriptome profile analysis reveals the regulation mechanism of floral sex differentiation in Jatropha curcas L. Sci Rep 2017; 7:16421. [PMID: 29180629 PMCID: PMC5703882 DOI: 10.1038/s41598-017-16545-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/14/2017] [Indexed: 01/21/2023] Open
Abstract
The seeds of Jatropha curcas contain a high percentage of biodiesel. However, low seed yield which was limited by its poor female flowers was a bottleneck for its utilization. Here, we compared the transcriptomic profiles of five different samples during floral sex differentiation stages using Illumina Hiseq 4000. Our results showed that hundreds of differentially expressed genes (DEGs) were detected in floral sex initiation period, but thousands of DEGs were involved in the stamens and ovules development process. Moreover, the DEGs were mainly shown up-regulation in male floral initiation, but mainly down-regulation in female floral initiation. Male floral initiation was associated with the flavonoid biosynthesis pathway while female floral initiation was related to the phytohormone signal transduction pathway. Cytokinin (CTK) signaling triggered the initiation of female floral primordium, thereafter other phytohormones co-promoted the female floral development. In addition, the floral organ identity genes played important roles in floral sex differentiation process and displayed a general conservation of the ABCDE model in J. curcas. To the best of our knowledge, this data is the first comprehensive analysis of the underlying regulatory mechanism and the related genes during floral sex differentiation in J. curcas, which help in engineering high-yielding varieties of J. curcas.
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Affiliation(s)
- Wenkai Hui
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, P.R. China
| | - Yuantong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Changcao Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Xiaoyang Chen
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, P.R. China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China.
| | - Mohamed Zaky Zayed
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, P.R. China.,Forestry and Wood Technology Department, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria, Egypt
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15
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PIñeyro-Nelson A, Almeida AMRD, Sass C, Iles WJD, Specht CD. Change of Fate and Staminodial Laminarity as Potential Agents of Floral Diversification in the Zingiberales. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:41-54. [PMID: 28120453 DOI: 10.1002/jez.b.22724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Abstract
The evolution of floral morphology in the monocot order Zingiberales shows a trend in which androecial whorl organs are progressively modified into variously conspicuous "petaloid" structures with differing degrees of fertility. Petaloidy of androecial members results from extensive laminarization of an otherwise radially symmetric structure. The genetic basis of the laminarization of androecial members has been addressed through recent candidate gene studies focused on understanding the spatiotemporal expression patterns of genes known to be necessary to floral organ formation. Here, we explore the correlation between gene duplication events and floral and inflorescence morphological diversification across the Zingiberales by inferring ancestral character states and gene copy number using the most widely accepted phylogenetic hypotheses. Our results suggest that the duplication and differential loss of GLOBOSA (GLO) copies is correlated with a change in the degree of the laminarization of androecial members. We also find an association with increased diversification in most families. We hypothesize that retention of paralogs in flower development genes could have led to a developmental shift affecting androecial organs with potential adaptive consequences, thus favoring diversification in some lineages but not others.
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Affiliation(s)
- Alma PIñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, Mexico
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Ana Maria Rocha De Almeida
- Programa de Pós-Graduação em Genética e Biodiversidade, Universidade Federal da Bahia, Rua Barão de Geremoabo, Salvador/BA, Brazil
- Department of Biological Sciences, California State University East Bay (CSUEB), Hayward, California
| | - Chodon Sass
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - William James Donaldson Iles
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Chelsea Dvorak Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
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16
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Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes. Sci Rep 2016; 6:39031. [PMID: 27966614 PMCID: PMC5155217 DOI: 10.1038/srep39031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/16/2016] [Indexed: 01/19/2023] Open
Abstract
Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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17
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Soza VL, Snelson CD, Hewett Hazelton KD, Di Stilio VS. Partial redundancy and functional specialization of E-class SEPALLATA genes in an early-diverging eudicot. Dev Biol 2016; 419:143-155. [DOI: 10.1016/j.ydbio.2016.07.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/05/2016] [Accepted: 07/26/2016] [Indexed: 11/16/2022]
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18
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Tian X, Yu Q, Liu H, Liao J. Temporal-Spatial Transcriptome Analyses Provide Insights into the Development of Petaloid Androecium in Canna indica. FRONTIERS IN PLANT SCIENCE 2016; 7:1194. [PMID: 27582744 PMCID: PMC4987385 DOI: 10.3389/fpls.2016.01194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Canna indica (Zingiberales) is one of the most important ornamental species characterized with beautiful petaloid staminodes, which are considered to evolve from stamens. However, the genetic basis for the development of petaloid staminodes remains unclear largely because the genomic sequences are not available. By using RNA-Seq, we sequenced the transcripts in the flower of C. indica, and quantified the temporal gene expressions in flower primordium and differentiated flower, as well as the spatial gene expressions in petal and petaloid staminode. In total, 118,869 unigenes were assembled, among which 67,299 unigenes were annotated. Quantification analysis identified the differentially expressed genes in the temporal and spatial two comparisons, based on which, Gene Ontology enrichment analysis highlighted the representative terms in each sample, such as specification of organ number in flower primordium, growth in differentiated flower, secondary cell wall biogenesis in petal and cell division in petaloid staminode. Among the 51 analyzed MADS-box unigenes, 37 were up-regulated in differentiated flower compared with those in flower primordium. A-class unigenes were expressed higher in petal than in petaloid staminode, and C-class unigenes were expressed oppositely, whereas B-class unigenes demonstrated close expression levels in these two organs, indicating that petaloid staminode retains stamen identity to some degree. In situ hybridization provided more detailed expression patterns of these unigenes, and revealed the extended expression of B-class to the carpel at later stages when the style turned flat. These results constitute a preliminary basis for the study of flower development in C. indica and can be applied in further study of the evolution of Zingiberales.
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Affiliation(s)
- Xueyi Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Qianxia Yu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Huanfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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19
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Arango-Ocampo C, González F, Alzate JF, Pabón-Mora N. The developmental and genetic bases of apetaly in Bocconia frutescens (Chelidonieae: Papaveraceae). EvoDevo 2016; 7:16. [PMID: 27489612 DOI: 10.1186/s1322701600546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/19/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Bocconia and Macleaya are the only genera of the poppy family (Papaveraceae) lacking petals; however, the developmental and genetic processes underlying such evolutionary shift have not yet been studied. RESULTS We studied floral development in two species of petal-less poppies Bocconia frutescens and Macleaya cordata as well as in the closely related petal-bearing Stylophorum diphyllum. We generated a floral transcriptome of B. frutescens to identify MADS-box ABCE floral organ identity genes expressed during early floral development. We performed phylogenetic analyses of these genes across Ranunculales as well as RT-PCR and qRT-PCR to assess loci-specific expression patterns. We found that petal-to-stamen homeosis in petal-less poppies occurs through distinct developmental pathways. Transcriptomic analyses of B. frutescens floral buds showed that homologs of all MADS-box genes are expressed except for the APETALA3-3 ortholog. Species-specific duplications of other ABCE genes in B. frutescens have resulted in functional copies with expanded expression patterns than those predicted by the model. CONCLUSIONS Petal loss in B. frutescens is likely associated with the lack of expression of AP3-3 and an expanded expression of AGAMOUS. The genetic basis of petal identity is conserved in Ranunculaceae and Papaveraceae although they have different number of AP3 paralogs and exhibit dissimilar floral groundplans.
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Affiliation(s)
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Fernando Alzate
- Centro de Secuenciación Genómica Nacional (CSGN), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
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20
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Arango-Ocampo C, González F, Alzate JF, Pabón-Mora N. The developmental and genetic bases of apetaly in Bocconia frutescens (Chelidonieae: Papaveraceae). EvoDevo 2016; 7:16. [PMID: 27489612 PMCID: PMC4971710 DOI: 10.1186/s13227-016-0054-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Bocconia and Macleaya are the only genera of the poppy family (Papaveraceae) lacking petals; however, the developmental and genetic processes underlying such evolutionary shift have not yet been studied. Results We studied floral development in two species of petal-less poppies Bocconiafrutescens and Macleayacordata as well as in the closely related petal-bearing Stylophorum diphyllum. We generated a floral transcriptome of B. frutescens to identify MADS-box ABCE floral organ identity genes expressed during early floral development. We performed phylogenetic analyses of these genes across Ranunculales as well as RT-PCR and qRT-PCR to assess loci-specific expression patterns. We found that petal-to-stamen homeosis in petal-less poppies occurs through distinct developmental pathways. Transcriptomic analyses of B. frutescens floral buds showed that homologs of all MADS-box genes are expressed except for the APETALA3-3 ortholog. Species-specific duplications of other ABCE genes in B. frutescens have resulted in functional copies with expanded expression patterns than those predicted by the model. Conclusions Petal loss in B. frutescens is likely associated with the lack of expression of AP3-3 and an expanded expression of AGAMOUS. The genetic basis of petal identity is conserved in Ranunculaceae and Papaveraceae although they have different number of AP3 paralogs and exhibit dissimilar floral groundplans. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0054-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Fernando Alzate
- Centro de Secuenciación Genómica Nacional (CSGN), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
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21
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Janssens SB, Vandelook F, De Langhe E, Verstraete B, Smets E, Vandenhouwe I, Swennen R. Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia. THE NEW PHYTOLOGIST 2016; 210:1453-65. [PMID: 26832306 PMCID: PMC5066818 DOI: 10.1111/nph.13856] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/07/2015] [Indexed: 05/20/2023]
Abstract
Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.
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Affiliation(s)
| | | | - Edmond De Langhe
- Laboratory of Tropical Crop ImprovementWillem de Croylaan 42LeuvenBE‐3001Belgium
| | | | - Erik Smets
- Plant Conservation and Population BiologyKU LeuvenKasteelpark Arenberg 31PO Box 2435LeuvenBE‐3001Belgium
- Naturalis Biodiversity CenterLeiden UniversityPO Box 9517Leiden2300RAthe Netherlands
| | - Ines Vandenhouwe
- Bioversity InternationalWillem De Croylaan 42LeuvenBE‐3001Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop ImprovementWillem de Croylaan 42LeuvenBE‐3001Belgium
- Bioversity InternationalWillem De Croylaan 42LeuvenBE‐3001Belgium
- International Institute of Tropical AgriculturePO Box 10, DulutiArushaTanzania
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22
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Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among clades in the homeobox region. Dev Genes Evol 2016; 226:259-68. [PMID: 27150824 DOI: 10.1007/s00427-016-0545-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 04/10/2016] [Indexed: 10/21/2022]
Abstract
Gene families have been shown to play important roles in plant evolution and are associated with diversification and speciation. Genes of WUSCHEL-related homeobox family of transcription factors have important functions in plant development and are correlated with the appearance of evolutionary novelties. There are several published studies related to this family, but little is known about the relationships among the main clades in the phylogeny and the molecular evolution of the family. In this study, we obtained a well-resolved Bayesian phylogenetic tree establishing the relationships among the main clades and determining the position of Selaginella moellendorffii WOX genes. Moreover, a correlation was identified between the number of genes in the genomes and the events of whole-genome duplications. The intron-exon structure is more consistent across the modern clade, which appeared more recently in the WOX evolutionary history, and coincides with the development of higher complexity in plant species. No positive selection was detected among sites through the branches in the tree. However, with regard to the main clades, functional divergence among certain amino acids in the homeodomain region was found. Relaxed purifying selection could be the main driving force in the evolution of these genes and in agreement with some genes have been demonstrated to be functionally redundant.
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23
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Sass C, Iles WJD, Barrett CF, Smith SY, Specht CD. Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage. PeerJ 2016; 4:e1584. [PMID: 26819846 PMCID: PMC4727956 DOI: 10.7717/peerj.1584] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
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Affiliation(s)
- Chodon Sass
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
| | - William J D Iles
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
| | - Craig F Barrett
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States; Department of Biology, California State University, Los Angeles, Los Angeles, CA, United States
| | - Selena Y Smith
- Department of Earth & Environmental Sciences and the Museum of Paleontology, University of Michigan , Ann Arbor, MI , United States
| | - Chelsea D Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
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Yu X, Duan X, Zhang R, Fu X, Ye L, Kong H, Xu G, Shan H. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution. FRONTIERS IN PLANT SCIENCE 2016; 7:598. [PMID: 27200066 PMCID: PMC4852290 DOI: 10.3389/fpls.2016.00598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.
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Affiliation(s)
- Xianxian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Lingling Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Guixia Xu
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Hongyan Shan
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Kubota S, Kanno A. Analysis of the floral MADS-box genes from monocotyledonous Trilliaceae species indicates the involvement of SEPALLATA3-like genes in sepal-petal differentiation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:266-276. [PMID: 26706077 DOI: 10.1016/j.plantsci.2015.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/20/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
The evolution of greenish sepals from petaloid outer tepals has occurred repeatedly in various lineages of non-grass monocots. Studies in distinct monocot species showed that the evolution of sepals could be explained by the ABC model; for example, the defect of B-class function in the outermost whorl was linked to the evolution of sepals. Here, floral MADS-box genes from three sepal-bearing monocotyledonous Trilliaceae species, Trillium camschatcense, Paris verticillata, and Kinugasa japonica were examined. Unexpectedly, expression of not only A- but also B-class genes was detected in the sepals of all three species. Although the E-class gene is generally expressed across all floral whorls, no expression was detected in sepals in the three species examined here. Overexpression of the E-class SEPALLATA3-like gene from T. camschatcense (TcamSEP) in Arabidopsis thaliana produced phenotypes identical to those reported for orthologs in other monocots. Additionally, yeast hybrid experiments indicated that TcamSEP could form a higher-order complex with an endogenous heterodimer of B-class APETALA3/DEFICIENS-like (TcamDEF) and PISTILLATA/GLOBOSA-like (TcamGLO) proteins. These results suggest a conserved role for Trilliaceae SEPALLATA3-like genes in functionalization of the B-class genes, and that a lack of SEPALLATA3-like gene expression in the outermost whorl may be related to the formation of greenish sepals.
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Affiliation(s)
- Shosei Kubota
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
| | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
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Hu Y, Liang W, Yin C, Yang X, Ping B, Li A, Jia R, Chen M, Luo Z, Cai Q, Zhao X, Zhang D, Yuan Z. Interactions of OsMADS1 with Floral Homeotic Genes in Rice Flower Development. MOLECULAR PLANT 2015; 8:1366-84. [PMID: 25917758 DOI: 10.1016/j.molp.2015.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/05/2015] [Accepted: 04/16/2015] [Indexed: 05/23/2023]
Abstract
During reproductive development, rice plants develop unique flower organs which determine the final grain yield. OsMADS1, one of SEPALLATA-like MADS-box genes, has been unraveled to play critical roles in rice floral organ identity specification and floral meristem determinacy. However, the molecular mechanisms underlying interactions of OsMADS1 with other floral homeotic genes in regulating flower development remains largely elusive. In this work, we studied the genetic interactions of OsMADS1 with B-, C-, and D-class genes along with physical interactions among their proteins. We show that the physical and genetic interactions between OsMADS1 and OsMADS3 are essential for floral meristem activity maintenance and organ identity specification; while OsMADS1 physically and genetically interacts with OsMADS58 in regulating floral meristem determinacy and suppressing spikelet meristem reversion. We provided important genetic evidence to support the neofunctionalization of two rice C-class genes (OsMADS3 and OsMADS58) during flower development. Gene expression profiling and quantitative RT-PCR analyses further revealed that OsMADS1 affects the expression of many genes involved in floral identity and hormone signaling, and chromatin immunoprecipitation (ChIP)-PCR assay further demonstrated that OsMADS17 is a direct target gene of OsMADS1. Taken together, these results reveal that OsMADS1 has diversified regulatory functions in specifying rice floral organ and meristem identity, probably through its genetic and physical interactions with different floral homeotic regulators.
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Affiliation(s)
- Yun Hu
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Changsong Yin
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xuelian Yang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Baozhe Ping
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Anxue Li
- Shanghai Ocean University, Shanghai 201306, China
| | - Ru Jia
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Mingjiao Chen
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Zhijing Luo
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xiangxiang Zhao
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian 223300, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Zheng Yuan
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China.
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27
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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28
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Rocha de Almeida AM, Yockteng R, Specht CD. Evolution of petaloidy in the zingiberales: An assessment of the relationship between ultrastructure and gene expression patterns. Dev Dyn 2015; 244:1121-1132. [DOI: 10.1002/dvdy.24280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 01/26/2023] Open
Affiliation(s)
- Ana Maria Rocha de Almeida
- Programa de Pós-Graduação em Genética e Biodiversidade, Universidade Federal da Bahia; Campus Ondina Salvador/BA Brazil
- Departments of Plant and Microbial Biology and Integrative Biology and the University and Jepson Herbaria; University of California; Berkeley California
| | - Roxana Yockteng
- Departments of Plant and Microbial Biology and Integrative Biology and the University and Jepson Herbaria; University of California; Berkeley California
- Corporación Colombiana de Investigación (CORPOICA); Bogotá Colombia
| | - Chelsea D. Specht
- Departments of Plant and Microbial Biology and Integrative Biology and the University and Jepson Herbaria; University of California; Berkeley California
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29
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Specht CD, Howarth DG. Adaptation in flower form: a comparative evodevo approach. THE NEW PHYTOLOGIST 2015; 206:74-90. [PMID: 25470511 DOI: 10.1111/nph.13198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/15/2014] [Indexed: 05/10/2023]
Abstract
Evolutionary developmental biology (evodevo) attempts to explain how the process of organismal development evolves, utilizing a comparative approach to investigate changes in developmental pathways and processes that occur during the evolution of a given lineage. Evolutionary genetics uses a population approach to understand how organismal changes in form or function are linked to underlying genetics, focusing on changes in gene and genotype frequencies within populations and the fixation of genotypic variation into traits that define species or evoke speciation events. Microevolutionary processes, including mutation, genetic drift, natural selection and gene flow, can provide the foundation for macroevolutionary patterns observed as morphological evolution and adaptation. The temporal element linking microevolutionary processes to macroevolutionary patterns is development: an organism's genotype is converted to phenotype by ontogenetic processes. Because selection acts upon the phenotype, the connection between evolutionary genetics and developmental evolution becomes essential to understanding adaptive evolution in organismal form and function. Here, we discuss how developmental genetic studies focused on key developmental processes could be linked within a comparative framework to study the developmental genetics of adaptive evolution, providing examples from research on two key processes of plant evodevo - floral symmetry and organ fusion - and their role in the adaptation of floral form.
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Affiliation(s)
- Chelsea D Specht
- Departments of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Dianella G Howarth
- Department of Biological Sciences, St John's University, 8000 Utopia Pkwy, Jamaica, NY, 11439, USA
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30
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Lombardo F, Yoshida H. Interpreting lemma and palea homologies: a point of view from rice floral mutants. FRONTIERS IN PLANT SCIENCE 2015; 6:61. [PMID: 25741351 PMCID: PMC4331672 DOI: 10.3389/fpls.2015.00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/24/2015] [Indexed: 05/04/2023]
Abstract
In contrast to eudicot flowers which typically exhibit sepals and petals at their periphery, the flowers of grasses are distinguished by the presence of characteristic outer organs. In place of sepals, grasses have evolved the lemma and the palea, two bract-like structures that partially or fully enclose the inner reproductive organs. With little morphological similarities to sepals, whether the lemma and palea are part of the perianth or non-floral organs has been a longstanding debate. In recent years, comparative studies of floral mutants as well as the availability of whole genome sequences in many plant species have provided strong arguments in favor of the hypothesis of lemma and palea being modified sepals. In rice, a feature of the palea is the bending of its lateral region into a hook-shaped marginal structure. This allows the palea to lock into the facing lemma region, forming a close-fitting lemma-palea enclosure. In this article, we focus on the rice lemma and palea and review some of the key transcription factors involved in their development and functional specialization. Alternative interpretations of these organs are also addressed.
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Affiliation(s)
| | - Hitoshi Yoshida
- *Correspondence: Hitoshi Yoshida, Rice Biotechnology Research Project, Rice Research Division, National Agriculture and Food Research Organization (NARO) Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. e-mail:
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31
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Li X, Fan T, Song J, Sun W, Xia K, Liao J, Zhang M. Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis. PLoS One 2014; 9:e114134. [PMID: 25461565 PMCID: PMC4252096 DOI: 10.1371/journal.pone.0114134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022] Open
Abstract
Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.
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Affiliation(s)
- Xiumei Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juanjuan Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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32
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Rensing SA. Gene duplication as a driver of plant morphogenetic evolution. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:43-8. [PMID: 24507493 DOI: 10.1016/j.pbi.2013.11.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 05/19/2023]
Abstract
Most duplicated genes (paralogs) are quickly erased during evolution, and only some are retained. Yet, gene and genome duplications are connected to the evolution of genetic and, in turn, morphological complexity. Plants are especially prone to experience polyploidizations and to enhance their gene repertoire after such events. Genes encoding proteins involved in transcriptional regulation are of especial interest since they are correlated with the occurrence of genome duplication events and with the rise of plant morphological complexity. Here, I review what we know about paralog retention as a driver for morphogenetic evolution of plants. The main focus is on the evolution of plant genes controlling development (morphogenetic transcription factors).
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Affiliation(s)
- Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
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33
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Yockteng R, Almeida AMR, Yee S, Andre T, Hill C, Specht CD. A method for extracting high-quality RNA from diverse plants for next-generation sequencing and gene expression analyses. APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1300070. [PMID: 25202509 PMCID: PMC4103122 DOI: 10.3732/apps.1300070] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/18/2013] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues. • METHODS AND RESULTS Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at -80°C. Extractions were performed and quality was measured for yield and purity. • CONCLUSIONS This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR) and semiquantitative reverse transcription PCR (RT-PCR).
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Affiliation(s)
- Roxana Yockteng
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California 94720 USA ; Origine, Structure et Evolution de la Diversité (UMR 7205 CNRS), Muséum National d'Histoire Naturelle, CP39, 16 rue Buffon, 75231 Paris Cedex 05, France
| | - Ana M R Almeida
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California 94720 USA
| | - Stephen Yee
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California 94720 USA
| | - Thiago Andre
- Laboratório de Taxonomia Vegetal e Biologia Reprodutiva, Departamento de Botânica, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Colin Hill
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California 94720 USA
| | - Chelsea D Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California 94720 USA
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