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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Wu C, Cheng Z, Gao J. Mysterious Bamboo flowering phenomenon: A literature review and new perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168695. [PMID: 38000754 DOI: 10.1016/j.scitotenv.2023.168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Bamboo, a globally distributed non-timber forest resource, plays a critical role in local ecosystems and economies. Despite its significance, the understanding of bamboo's long and unpredictable flowering cycles remains limited. Our bibliometric analysis of bamboo flowering-related literature from the Web of Science database reveals an initial focus on regeneration studies, with a recent trend shifting towards microscopic and molecular perspectives. Furthermore, our narrative review emphasizes the importance of considering factors such as the proportion of flowering culms and the duration of flowering in classifying bamboo flowering phenomena. While numerous studies have endorsed the predator saturation hypothesis as a suitable explanation for the synchronicity of bamboo flowering, no existing theory explains bamboo's prolonged flowering cycles. We propose a new natural selection hypothesis as a potential explanation for these extraordinary cycles, underscoring the need for further research in this area. Despite the substantial volume of data accumulated on bamboo flowering, these resources have not been fully exploited in recent research. Future studies would benefit from more comprehensive data collection methods, encompassing field observations, satellite remote sensing data, and omics data. The convergence of traditional ecological studies with molecular techniques may pave the way for significant advancements in bamboo flowering research.
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Affiliation(s)
- Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China.
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Hu J, Chen Q, Idrees A, Bi W, Lai Z, Sun Y. Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:2929. [PMID: 37631141 PMCID: PMC10458798 DOI: 10.3390/plants12162929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral 'ABCE' model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations.
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Affiliation(s)
- Juan Hu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Atif Idrees
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs, Institute of Entomology, Guizhou University, Guiyang 550025, China;
| | - Wanjun Bi
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
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4
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Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C. Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model. BMC Genomics 2023; 24:447. [PMID: 37553575 PMCID: PMC10408238 DOI: 10.1186/s12864-023-09509-9] [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: 12/01/2022] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. RESULTS In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. CONCLUSION This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.
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Affiliation(s)
- Yi Lin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yan Wan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zequn Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailing Fang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Cheng Z, Mu C, Li X, Cheng W, Cai M, Wu C, Jiang J, Fang H, Bai Y, Zheng H, Geng R, Xu J, Xie Y, Dou Y, Li J, Mu S, Gao J. Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo ( Phyllostachys edulis). HORTICULTURE RESEARCH 2023; 10:uhad122. [PMID: 37554343 PMCID: PMC10405134 DOI: 10.1093/hr/uhad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/01/2023] [Indexed: 08/10/2023]
Abstract
Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1642 species worldwide. However, little is known about the transcriptional atlas that underpins root cell-type differentiation. Here, we set up a modified protocol for protoplast preparation and report single-cell transcriptomes of 14 279 filtered single cells derived from the basal root tips of moso bamboo. We identified four cell types and defined new cell-type-specific marker genes for the basal root. We reconstructed the developmental trajectories of the root cap, epidermis, and ground tissues and elucidated critical factors regulating cell fate determination. According to in situ hybridization and pseudotime trajectory analysis, the root cap and epidermis originated from a common initial cell lineage, revealing the particularity of bamboo basal root development. We further identified key regulatory factors for the differentiation of these cells and indicated divergent root developmental pathways between moso bamboo and rice. Additionally, PheWOX13a and PheWOX13b ectopically expressed in Arabidopsis inhibited primary root and lateral root growth and regulated the growth and development of the root cap, which was different from WOX13 orthologs in Arabidopsis. Taken together, our results offer an important resource for investigating the mechanism of root cell differentiation and root system architecture in perennial woody species of Bambusoideae.
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Affiliation(s)
- Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xiangyu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Miaomiao Cai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hui Fang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Ruiman Geng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Juan Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Shaohua Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
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Caperta AD, Fernandes I, Conceição SIR, Marques I, Róis AS, Paulo OS. Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae). Genes (Basel) 2023; 14:genes14040901. [PMID: 37107659 PMCID: PMC10137852 DOI: 10.3390/genes14040901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduction, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analysis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid-dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium sp.
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Affiliation(s)
- Ana D Caperta
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Isabel Fernandes
- cE3c-Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sofia I R Conceição
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- LASIGE Computer Science and Engineering Research Centre, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Isabel Marques
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Forest Research Centre (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Ana S Róis
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- School of Psychology and Life Sciences, Universidade Lusófona de Humanidades e Tecnologias (ULHT), Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Octávio S Paulo
- cE3c-Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Pan X, Ouyang Y, Wei Y, Zhang B, Wang J, Zhang H. Genome-wide analysis of MADS-box families and their expressions in flower organs development of pineapple ( Ananas comosus (L.) Merr.). FRONTIERS IN PLANT SCIENCE 2022; 13:948587. [PMID: 36311063 PMCID: PMC9597317 DOI: 10.3389/fpls.2022.948587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
MADS-box genes play crucial roles in plant vegetative and reproductive growth, better development of inflorescences, flower, and fruit. Pineapple is a typical collective fruit, and a comprehensive analysis of the MADS-box gene family in the development of floral organs of pineapple is still lacking. In this study, the whole-genome survey and expression profiling of the MADS-box family in pineapple were introduced. Forty-four AcMADS genes were identified in pineapple, 39 of them were located on 18 chromosomes and five genes were distributed in five scaffolds. Twenty-two AcMADS genes were defined as 15 pairs of segmental duplication events. Most members of the type II subfamily of AcMADS genes had higher expression levels in floral organs compared with type I subfamily, thereby suggesting that AcMADS of type II may play more crucial roles in the development of floral organs of pineapple. Six AcMADS genes have significant tissue-specificity expression, thereby suggesting that they may participate in the formation of one or more floral organs. This study provides valuable insights into the role of MADS-box gene family in the floral organ development of pineapple.
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8
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Zhang Y, Chen Y, Zhou Y, Zhang J, Bai H, Zheng C. Comparative Transcriptome Reveals the Genes' Adaption to Herkogamy of Lumnitzera littorea (Jack) Voigt. Front Genet 2020; 11:584817. [PMID: 33363568 PMCID: PMC7753066 DOI: 10.3389/fgene.2020.584817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Lumnitzera littorea (Jack) Voigt is among the most endangered mangrove species in China. The morphology and evolution of L. littorea flowers have received substantial attention for their crucial reproductive functions. However, little is known about the genomic regulation of flower development in L. littorea. In this study, we characterized the morphology of two kinds of L. littorea flowers and performed comparative analyses of transcriptome profiles of the two different flowers. Morphological observation showed that some flowers have a column embedded in the petals while others produce a stretched flower style during petal unfolding in flowering. By using RNA-seq, we obtained 138,857 transcripts that were assembled into 82,833 unigenes with a mean length of 1055.48 bp. 82,834 and 34,997 unigenes were assigned to 52 gene ontology (GO) functional groups and 364 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 4,267 differentially expressed genes (DEGs), including 1,794 transcription factors (TFs), were identified between two types of flowers. These TFs are mainly involved in bHLH, B3, bZIP, MYB-related, and NAC family members. We further validated that 12 MADS-box genes, including 4 MIKC-type and 8 M-type TFs, were associated with the pollinate of L. littorea by herkogamy. Our current results provide valuable information for genetic analysis of L. littorea flowering and may be useful for illuminating its adaptive evolutionary mechanisms.
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Affiliation(s)
- Ying Zhang
- School of Life Sciences and Technology, Lingnan Normal University, Zhanjiang, China.,National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yan Zhou
- School of Life Sciences and Technology, Lingnan Normal University, Zhanjiang, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - He Bai
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Chunfang Zheng
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
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9
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Li SY, Zhang Q, Jin YH, Zou JX, Zheng YS, Li DD. A MADS-box gene, EgMADS21, negatively regulates EgDGAT2 expression and decreases polyunsaturated fatty acid accumulation in oil palm (Elaeis guineensis Jacq.). PLANT CELL REPORTS 2020; 39:1505-1516. [PMID: 32804247 DOI: 10.1007/s00299-020-02579-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/06/2020] [Indexed: 05/13/2023]
Abstract
EgMADS21 regulates PUFA accumulation in oil palm. Oil palm (Elaeis guineensis Jacq.) is the most productive world oil crop, accounting for 36% of world plant oil production. However, the molecular mechanism of the transcriptional regulation of fatty acid accumulation and lipid synthesis in the mesocarp of oil palm by up- or downregulating the expression of genes involved in related pathways remains largely unknown. Here, an oil palm MADS-box gene, EgMADS21, was screened in a yeast one-hybrid assay using the EgDGAT2 promoter sequence as bait. EgMADS21 is preferentially expressed in early mesocarp developmental stages in oil palm fruit and presents a negative correlation with EgDGAT2 expression. The direct binding of EgMADS21 to the EgDGAT2 promoter was confirmed by electrophoretic mobility shift assay. Subsequently, transient expression of EgMADS21 in oil palm protoplasts revealed that EgMADS21 not only binds to the EgDGAT2 promoter but also negatively regulates the expression of EgDGAT2. Furthermore, EgMADS21 was stably overexpressed in transgenic oil palm embryoids by Agrobacterium-mediated transformation. In three independent transgenic lines, EgDGAT2 expression was significantly suppressed by the expression of EgMADS21. The content of linoleic acid (C18:2) in the three transgenic embryoids was significantly decreased, while that of oleic acid (C18:1) was significantly increased. Combined with the substrate preference of EgDGAT2 identified in previous research, the results demonstrate the molecular mechanism by which EgMADS21 regulates EgDGAT2 expression and ultimately affects fatty acid accumulation in the mesocarp of oil palm.
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Affiliation(s)
- Si-Yu Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Qing Zhang
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yuan-Hang Jin
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Ji-Xin Zou
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yu-Sheng Zheng
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dong-Dong Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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Xie L, Cai M, Li X, Zheng H, Xie Y, Cheng Z, Bai Y, Li J, Mu S, Gao J. Overexpression of PheNAC3 from moso bamboo promotes leaf senescence and enhances abiotic stress tolerance in Arabidopsis. PeerJ 2020; 8:e8716. [PMID: 32266114 PMCID: PMC7120055 DOI: 10.7717/peerj.8716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/10/2020] [Indexed: 11/20/2022] Open
Abstract
The NAC family is one of the largest transcription factor families unique to plants, which regulates the growth and development, biotic and abiotic stress responses, and maturation and senescence in plants. In this study, PheNAC3, a NAC gene, was isolated and characterized from moso bamboo (Phyllostachys edulis). PheNAC3 belong to the NAC1 subgroup and has a conserved NAC domain on the N-terminus, which with 88.74% similarity to ONAC011 protein. PheNAC3 localized in the nucleus and exhibited transactivation activity. PheNAC3 was upregulated during the process of senescence of leaves and detected shoots. PheNAC3 was also induced by ABA, MeJA, NaCl and darkness, but it had no remarkable response to PEG and SA treatments. Overexpression of PheNAC3 could cause precocious senescence in Arabidopsis. Transgenic Arabidopsis displayed faster seed germination, better seedling growth, and a higher survival rate than the wild-type under salt or drought stress conditions. Moreover, AtSAG12 associated with senescence and AtRD29A and AtRD29b related to ABA were upregulated by PheNAC3 overexpression, but AtCAB was inhibited. These findings show that PheNAC3 may participate in leaf senescence and play critical roles in the salt and drought stress response.
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Affiliation(s)
- Lihua Xie
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China.,Pingdingshan University, Pingdingshan, Henan, China
| | - Miaomiao Cai
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Xiangyu Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Huifang Zheng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Yali Xie
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Zhanchao Cheng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Yucong Bai
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Juan Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Shaohua Mu
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing, China
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Cheng Z, Hou D, Ge W, Li X, Xie L, Zheng H, Cai M, Liu J, Gao J. Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo. PLANT & CELL PHYSIOLOGY 2020; 61:76-87. [PMID: 31550004 DOI: 10.1093/pcp/pcz179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/06/2019] [Indexed: 05/11/2023]
Abstract
A flower is an essential organ for sexual reproduction in flowering plants, which has been extensively studied in model plants. In this study, we used transcriptomic, small RNA and degradome analyses to characterize key microRNAs (miRNAs) and their targets in floral organs of moso bamboo. In total, we identified 13,051 differentially expressed genes and 109 known miRNAs from 26 miRNA families. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as novel miRNAs. Sixteen conserved miRNAs were specifically and highly expressed in stamens, including miRNA159 and miRNA166. In situ hybridization shows that miRNA159 plays a key role in the regulation of stamen development, and the expression levels of its targets PheMYB98 and PheMYB42 were low. Furthermore, Phe-MIRNA159 partially recovers phenotypes of mir159ab double mutant. Overexpression of Phe-MIR159 could cause failure in anther dehisce, and the mature pollens could not be dispersed and further reduce fertility in Arabidopsis. Semi-thin section result shows that anther endothelial layer of Phe-MIRNA159 overexpressing lines is lack of secondary thickening, resulting in limited force for anther opening. Phe-miR159 may regulate the expression of genes related to secondary thickening through negative regulation of AtMYB33, affecting the anther dehiscence. Taken together, this study provides insights regarding molecular networks underlying floral organs development of moso bamboo.
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Affiliation(s)
- Zhanchao Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Dan Hou
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Wei Ge
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
| | - Xiangyu Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Lihua Xie
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Huifang Zheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Miaomiao Cai
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jun Liu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
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13
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Jiao Y, Hu Q, Zhu Y, Zhu L, Ma T, Zeng H, Zang Q, Li X, Lin X. Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens). BMC Bioinformatics 2019; 20:687. [PMID: 31874613 PMCID: PMC6929269 DOI: 10.1186/s12859-019-3261-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is still unclear. RESULTS In this study, three successive stages of flowering buds and the corresponding vegetative buds (non-flowering stage) from Lei bamboo (Phyllostachys violascens) were collected for transcriptome analysis using Illumina RNA-Seq method. We generated about 442 million clean reads from the above samples, and 132,678 unigenes were acquired with N50 of 1080 bp. A total of 7266 differentially expressed genes (DEGs) were determined. According to expression profile and gene function analysis, some environmental stress responsive and plant hormone-related DEGs were highly expressed in the inflorescence meristem formation stage (TF_1) while some floral organ development related genes were up-regulated significantly in floral organs determination stage (TF_2) and floral organs maturation (TF_3) stage, implying the essential roles of these DEGs in flower induction and maturation of Lei bamboo. Additionally, a total of 25 MADS-box unigenes were identified. Based on the expression profile, B, C/D and E clade genes were more related to floral organs development compared with A clade genes in Lei bamboo. CONCLUSIONS This transcriptome data presents fundamental information about the genes and pathways involved in flower induction and development of Lei bamboo. Moreover, a critical sampling method is provided which could be benefit for bamboo flowering mechanism study.
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Affiliation(s)
- Yulian Jiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China
| | - Qiutao Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Longfei Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Haiyong Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Qiaolu Zang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'An, 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Lin'an, 311300, Zhejiang, China.
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Identification and characterization of the MADS-box genes highly expressed in the laticifer cells of Hevea brasiliensis. Sci Rep 2019; 9:12673. [PMID: 31481699 PMCID: PMC6722073 DOI: 10.1038/s41598-019-48958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/16/2019] [Indexed: 11/08/2022] Open
Abstract
MADS-box transcription factors possess many functions in plant reproduction and development. However, few MADS-box genes related to secondary metabolites regulation have been identified. In Hevea brasiliensis, natural rubber is a representative cis-polyisoprenoids in secondary metabolism which occurs in the rubber laticifer cells, the molecular regulation basis of natural rubber biosynthesis is not clear. Here, a total of 24 MADS-box genes including 4 type I MADS-box genes and 20 type II MADS-box genes were identified in the transcriptome of rubber tree latex. The phylogenetic analysis was performed to clarify the evolutionary relationships of all the 24 rubber tree MADS-box proteins with MADS-box transcription factors from Arabidopsis thaliana and Oryza sativa. Four type I MADS-box genes were subdivided into Mα (3 genes) and Mβ (1 gene). Twenty type II MADS-box genes were subclassified into MIKC* (8 genes) and MIKCc (12 genes). Eight MADS-box genes (HblMADS3, 5, 6, 7, 9, 13, 23, 24) were predominant expression in laticifers. ABA up-regulated the expression of HblMADS9, and the expression of HblMADS3, HblMADS5, HblMADS24 were up-regulated by MeJA. The function of HblMADS24 was elucidated. HblMADS24 bound HbFPS1 promoter in yeast and HblMADS24 activated HbFPS1 promoter in tobacco plants. Moreover, we proposed that HblMADS24 is a transcription activator of HbFPS1 which taking part in natural rubber biosynthesis.
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Transcriptome and digital gene expression analysis unravels the novel mechanism of early flowering in Angelica sinensis. Sci Rep 2019; 9:10035. [PMID: 31296928 PMCID: PMC6624268 DOI: 10.1038/s41598-019-46414-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Angelica sinensis (Oliv.) Diels is a widely used medicinal plant mainly originated in Gansu, China. Angelica sinensis is greatly demanded in the clinical practice of Chinese medicine due to its broad pharmacological activities of hematopoietic and anti-inflammatory properties. But, the percentage of early flowering in Angelica sinensis arrives to 20%~30%, which severely affects its quality and quantity. Here, transcriptome profiling and digital gene expression analysis were applied to study the mechanism of early flowering in Angelica sinensis. A total of 49,183,534 clean reads were obtained and assembled into 68,262 unigenes, and 49,477 unigenes (72.5%) could be annotated to a minimum of one database in the Nr, Nt, Swiss-Pro, GO, COG and KEGG. Taking the above transcriptome data as a reference, digital gene expression result showed that 5,094 genes expression level were significant changed during early flowering. These annotated genes offered much information promoting that the biosynthesis of secondary metabolites pathway, the hormone signal transduction pathway, and the transcription regulation system may be closely related to the early flowering phenomenon of Angelica sinensis. Further expression patterns of key genes contribute to early flowering were analyzed using quantitative real-time PCR. The transcriptome result offered important gene expression information about early flowering in Angelica sinensis.
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Liu J, Cheng Z, Li X, Xie L, Bai Y, Peng L, Li J, Gao J. Expression Analysis and Regulation Network Identification of the CONSTANS-Like Gene Family in Moso Bamboo ( Phyllostachys edulis) Under Photoperiod Treatments. DNA Cell Biol 2019; 38:607-626. [PMID: 31210530 DOI: 10.1089/dna.2018.4611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CONSTANS (CO)/CONSTANS-like (COL) genes that have been studied in annual model plants such as Arabidopsis thaliana and Oryza sativa play key roles in the photoperiodic flowering pathway. Moso bamboo is a perennial plant characterized by a long vegetative stage and flowers synchronously followed by widespread death. However, the characteristics of COL in moso bamboo remain unclear. In view of this, we performed a genome-wide identification and expression analysis of the COL gene family in moso bamboo. Fourteen nonredundant PheCOL genes were identified, and we analyzed gene structures, phylogeny, and subcellular location predictions. Phylogenetic analyses indicated that 14 PheCOLs could be clustered into three groups, and each clade was well supported by conserved intron/exon structures and motifs. A number of light-related and tissue-specific cis-elements were randomly distributed within the promoter sequences of the PheCOLs. The expression profiling of PheCOL genes in various tissues and developmental stages revealed that most of PheCOL genes were most highly expressed in the leaves and took part in moso bamboo flower development and rapid shoot growth. In addition, the transcription of PheCOLs exhibited a clear diurnal oscillation in both long-day and short-day conditions. Most of the PheCOL genes were inhibited under light treatment and upregulated in dark conditions. PheCOLs can interact with each other. Subcellular localization result showed that PheCOL14 encoded a cell membrane protein, and it bound to the promoter of PheCOL3. Taken together, the results of this study will be useful not only as they contribute to comprehensive information for further analyses of the molecular functions of the PheCOL gene family, but also will provide a theoretical foundation for the further construction of moso bamboo photoperiod regulation networks.
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Affiliation(s)
- Jun Liu
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Zhanchao Cheng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Xiangyu Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Lihua Xie
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Yucong Bai
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Lixin Peng
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Juan Li
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry Administration, Beijing, People's Republic of China
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17
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Ning K, Han Y, Chen Z, Luo C, Wang S, Zhang W, Li L, Zhang X, Fan S, Wang Q. Genome-wide analysis of MADS-box family genes during flower development in lettuce. PLANT, CELL & ENVIRONMENT 2019; 42:1868-1881. [PMID: 30680748 DOI: 10.1111/pce.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 05/08/2023]
Abstract
Lettuce (Lactuca sativa L.) is an important leafy vegetable consumed worldwide. Heat-induced bolting and flowering greatly limit lettuce production during the summer. Additionally, MADS-box transcription factors are important for various aspects of plant development and architecture (e.g., flowering and floral patterning). However, there has been no comprehensive study of lettuce MADS-box family genes. In this study, we identified 82 MADS-box family genes in lettuce, including 23 type I genes and 59 type II genes. Transcriptome profiling revealed that LsMADS gene expression patterns differ among the various floral stages and organs. Moreover, heat-responsive cis-elements were detected in the promoter regions of many LsMADS genes. An in situ hybridization assay of 10 homologs of flower-patterning genes and a yeast two-hybrid assay of the encoded proteins revealed that the ABC model is conserved in lettuce. Specifically, the APETALA1 (AP1) homolog in lettuce, LsMADS55, is responsive to heat and is specifically expressed in the inflorescence meristem and pappus bristles. The overexpression of LsMADS55 results in early flowering in Arabidopsis thaliana. Furthermore, we observed that the heat shock factor LsHSFB2A-1 can bind to the LsMADS55 promoter in lettuce. Therefore, a model was proposed for the LsMADS-regulated floral organ specification and heat-induced flowering in lettuce.
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Affiliation(s)
- Kang Ning
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Yingyan Han
- Plant Science and Technology College, Beijing University of Agriculture/New Technological Laboratory in Agriculture Application in Beijing, Beijing, 102206, China
| | - Zijing Chen
- College of Horticulture Science and Engineering/State Key Laboratory of Crop Biology, Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huanghuaihai Region, Shan Dong Agricultural University, Taian, Shandong, 271018, China
| | - Chen Luo
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Shenglin Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Wenjing Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Ling Li
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Shuangxi Fan
- Plant Science and Technology College, Beijing University of Agriculture/New Technological Laboratory in Agriculture Application in Beijing, Beijing, 102206, China
| | - Qian Wang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
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He C, Si C, Teixeira da Silva JA, Li M, Duan J. Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid. BMC PLANT BIOLOGY 2019; 19:223. [PMID: 31138149 PMCID: PMC6540398 DOI: 10.1186/s12870-019-1836-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. RESULTS Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. CONCLUSIONS MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | | | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210014 China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
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Zhou B, Wang J, Lou H, Wang H, Xu Q. Comparative transcriptome analysis of dioecious, unisexual floral development in Ribes diacanthum pall. Gene 2019; 699:43-53. [DOI: 10.1016/j.gene.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 01/09/2023]
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20
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Hou D, Cheng Z, Xie L, Li X, Li J, Mu S, Gao J. The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs. FRONTIERS IN PLANT SCIENCE 2018; 9:738. [PMID: 30042769 PMCID: PMC6048295 DOI: 10.3389/fpls.2018.00738] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/15/2018] [Indexed: 05/04/2023]
Abstract
The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.
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Affiliation(s)
| | | | | | | | | | | | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, International Center for Bamboo and Rattan, Beijing, China
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21
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Yuan JL, Yue JJ, Gu XP, Lin CS. Flowering of Woody Bamboo in Tissue Culture Systems. FRONTIERS IN PLANT SCIENCE 2017; 8:1589. [PMID: 28959269 PMCID: PMC5603696 DOI: 10.3389/fpls.2017.01589] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/30/2017] [Indexed: 05/29/2023]
Abstract
Flowering and subsequent seed set are not only normal activities in the life of most plants, but constitute the very reason for their existence. Woody bamboos can take a long time to flower, even over 100 years. This makes it difficult to breed bamboo, since flowering time cannot be predicted and passing through each generation takes too long. Another unique characteristic of woody bamboo is that a bamboo stand will often flower synchronously, both disrupting the supply chain within the bamboo industry and affecting local ecology. Therefore, an understanding of the mechanism that initiates bamboo flowering is important not only for biology research, but also for the bamboo industry. Induction of flowering in vitro is an effective way to both shorten the flowering period and control the flowering time, and has been shown for several species of bamboo. The use of controlled tissue culture systems allows investigation into the mechanism of bamboo flowering and facilitates selective breeding. Here, after a brief introduction of flowering in bamboo, we review the research on in vitro flowering of bamboo, including our current understanding of the effects of plant growth regulators and medium components on flower induction and how in vitro bamboo flowers can be used in research.
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Affiliation(s)
- Jin-Ling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China
| | - Xiao-Ping Gu
- Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia SinicaTaipei, Taiwan
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