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Qiu P, Liu T, Xu Y, Ye C, Zhang R, Wang Y, Jin Q. Multi-omic dissection of the cold resistance traits of white water lily. HORTICULTURE RESEARCH 2024; 11:uhae093. [PMID: 38840939 PMCID: PMC11151331 DOI: 10.1093/hr/uhae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/25/2024] [Indexed: 06/07/2024]
Abstract
The white water lily (Nymphaea candida), exemplifying nature's resilience, thrives in the high-altitude terrains of Xinjiang, China, serving as an ideal model for investigating cold adaptation mechanisms in aquatic plants. This study meticulously elucidates the complex cold adaptation mechanisms of the white water lily through a comprehensive and integrated methodological approach. We discovered that the water lily undergoes ecodormancy in winter, retaining high cellular viability and growth potential. During overwintering, the white water lily demonstrates effective resource reallocation, a process facilitated by morphological adjustments, thereby strengthening its resistance to cold temperatures. This enhancement is achieved particularly through the compartmentalization of large vacuoles, the accumulation of osmoregulatory substances, and an increased antioxidant capacity. We established the first exhaustive full-length transcriptome for the white water lily. A subsequent comprehensive analysis of the transcriptome, phytohormones, and metabolome uncovered a multifaceted regulatory network orchestrating cold adaptation. Our research spotlights phytohormone signaling, amino acid metabolism, and circadian rhythms as key elements in the water lily's defense against cold. The results emphasize the critical role of nitrogen metabolism, especially amino acid-related pathways, during cold stress. Metabolite profiling revealed the importance of compounds like myo-inositol and L-proline in enhancing cold tolerance. Remarkably, our study demonstrates that the white water lily notably diminishes the utilization of unsaturated fatty acids in its temperature regulation strategies. In conclusion, this research substantially enriches our understanding of the white water lily's intricate cold adaptation mechanisms, offering new perspectives on the adaptive strategies of aquatic plants and potential applications in agricultural advancement.
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Affiliation(s)
- Penghe Qiu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong Liu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingchun Xu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunxiu Ye
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Ran Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanjie Wang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qijiang Jin
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Li J, Sheng Y, Xu H, Li Q, Lin X, Zhou Y, Zhao Y, Song X, Wang J. Transcriptome and hormone metabolome reveal the mechanism of stem bending in water lily ( Nymphaea tetragona) cut-flowers. FRONTIERS IN PLANT SCIENCE 2023; 14:1195389. [PMID: 37746018 PMCID: PMC10515221 DOI: 10.3389/fpls.2023.1195389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Water lilies are popular ornamental cut-flowers with significant economic and cultural value. However, stem bending affects the preservation of cut-flowers during their vase life. To gain further insights into the molecular mechanisms of stem bending, transcriptome profiling, hormone measurement, and morphological analysis were performed using the stems of the 'Blue Bird' water lily. Transcriptome analysis revealed that 607 differentially expressed genes (DEGs) were associated with the dorsal and ventral stems of the water lily, of which 247 were up-regulated and 360 were down-regulated. Significant differences in genes associated with plant hormones, calcium ions, glucose metabolism, and photosynthesis pathways genes involved in the dorsal and ventral areas of the curved stem. In particular, DEGs were associated with the hormone synthesis, gravity response, starch granules, Ca2+ ions, and photosynthesis. The results of qRT-PCR were consistent with that of the transcriptome sequence analysis. A total of 12 hormones were detected, of which abscisic acid, indole-3-carboxaldehyde, indole-3-carboxaldehyde and jasmonic acid were significantly differentially expressed in the dorsal and ventral stems, and were significantly higher in the dorsal stem than in the ventral stem. The cell morphology in the dorsal and ventral areas of the curved stem clearly changed during vase life. The direction of starch granule settlement was consistent with the bending direction of the water lily stem, as well as the direction of gravity. In conclusion, stem bending in water lily cut-flowers is regulated by multiple factors and genes. This study provides an important theoretical basis for understanding the complex regulatory mechanism of water lily stem bending.
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Affiliation(s)
- Jie Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Yuhui Sheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
- College of Agricultural, Hengxing University, Qingdao, Shandong, China
| | - Huixian Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Qinxue Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Xiuya Lin
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Yang Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Ying Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Xiqiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
| | - Jian Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, Haikou, Hainan, China
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Zhang XH, Swait D, Jin XL, Vichyavichien P, Nifakos N, Kaplan N, Raymond L, Harlin JM. Evolutionary analysis of KED-rich proteins in plants. PLoS One 2023; 18:e0279772. [PMID: 36888590 PMCID: PMC9994729 DOI: 10.1371/journal.pone.0279772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/13/2022] [Indexed: 03/09/2023] Open
Abstract
During the course of evolution, organisms have developed genetic mechanisms in response to various environmental stresses including wounding from mechanical damage or herbivory-caused injury. A previous study of wounding response in the plant tobacco identified a unique wound-induced gene, aptly named KED due to its coding for a protein that has an unusually high content of amino acids lysine (K), glutamic acid (E) and aspartic acid (D). However, by far little is known about this intriguing gene. In this study, we investigated the evolutionary aspects of the KED-rich coding genes. We found that a consistent pattern of wound-induced KED gene expression is maintained across representative species of angiosperm and gymnosperm. KED genes can be identified in species from all groups of land plants (Embryophyta). All the KED proteins from vascular plants (Tracheophyta) including angiosperm, gymnosperm, fern and lycophyte share a conserved 19-amino acid domain near the C-terminus, whereas bryophytes (moss, liverwort and hornwort) possess KED-rich, multi-direct-repeat sequences that are distinct from the vascular plant KEDs. We detected KED-rich sequences in Charophyta species but not in Chlorophyta wherever genome sequences are available. Our studies suggest diverse and complex evolution pathways for land plant KED genes. Vascular plant KEDs exhibit high evolutionary conservation, implicating their shared function in response to wounding stress. The extraordinary enrichment of amino acids K, E and D in these groups of distinct and widely distributed proteins may reflect the structural and functional requirement for these three residues during some 600 million years of land plant evolution.
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Affiliation(s)
- Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
- * E-mail:
| | - David Swait
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Xiao-Lu Jin
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Paveena Vichyavichien
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Nicholas Nifakos
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Noah Kaplan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Lucwilerna Raymond
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - John M. Harlin
- Penta 5, USA, Sarasota, Florida, United States of America
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Xie Z, Yang C, Liu S, Li M, Gu L, Peng X, Zhang Z. Identification of AP2/ERF transcription factors in Tetrastigma hemsleyanum revealed the specific roles of ERF46 under cold stress. FRONTIERS IN PLANT SCIENCE 2022; 13:936602. [PMID: 36017255 PMCID: PMC9396264 DOI: 10.3389/fpls.2022.936602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Tetrastigma hemsleyanum (T. hemsleyanum) is a traditional medicinal plant that is widely used in China. Cultivated T. hemsleyanum usually encounters cold stress, limiting its growth and quality at key developmental stages. APETALA2 (AP2)/ethylene-responsive factor (ERF) transcription factors (TFs) comprise one of the largest gene superfamilies in plants and are widely involved in biotic and abiotic stresses. To reveal the roles of AP2/ERF TFs during T. hemsleyanum development, 70 AP2/ERF TFs were identified in T. hemsleyanum. Among them, 18 and 2 TFs were classified into the AP2 and RAV families, respectively. The other 50 TFs belonged to the ERF family and were further divided into the ERF and (dehydration reaction element binding factor) DREB subfamilies. The ERF subfamily contained 46 TFs, while the DREB subfamily contained 4 TFs. Phylogenetic analysis indicated that AP2/ERF TFs could be classified into five groups, in which 10 conserved motifs were confirmed. Several motifs were group- or subgroup-specific, implying that they were significant for the functions of the AP2/ERF TFs of these clades. In addition, 70 AP2/ERF TFs from the five groups were used for an expression pattern analysis under three low-temperature levels, namely, -4, 0, and 4°C. The majority of these AP2/ERF TFs exhibited a positive response to cold stress conditions. Specifically, ThERF5, ThERF31, ThERF46, and ThERF55 demonstrated a more sensitive response to cold stress. Moreover, AP2/ERF TFs exhibited specific expression patterns under cold stress. Transient overexpression and RNA interference indicated that ThERF46 has a specific tolerance to cold stress. These new insights provide the basis for further studies on the roles of AP2/ERF TFs in cold stress tolerance in T. hemsleyanum.
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Affiliation(s)
- Zhuomi Xie
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuyun Yang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siyi Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Peng
- Ningbo Municipal Hospital of TCM, Affiliated Hospital of Zhejiang Chinese Medical University, Ningbo, China
- Medicinal Plant Resource Center, Ningbo Research Institute of Traditional Chinese Medicine, Ningbo, China
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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Transcriptomic Insight into Viviparous Growth in Water Lily. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8445484. [PMID: 35845943 PMCID: PMC9283058 DOI: 10.1155/2022/8445484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/30/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Water lily is an important ornamental flower plant which is capable of viviparous plantlet development. But no study has been reported on the molecular basis of viviparity in water lily. Hence, we performed a comparative transcriptome study between viviparous water lily Nymphaea micrantha and a nonviviparous species Nymphaea colorata at four developmental stages. The higher expression of highly conserved AUX/IAA, ARF, GH3, and SAUR gene families in N. micrantha compared to N. colorata is predicted to have a major impact on the development and evolution of viviparity in water lily. Likewise, differential regulation of hormone signaling, brassinosteroid, photosynthesis, and energy-related pathways in the two species provide clues of their involvement in viviparity phenomenon. This study revealed the complex mechanism of viviparity trait in water lily. The transcriptomic signatures identified are important basis for future breeding and research of viviparity in water lily and other plant species.
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Wang X, Jain A, Chen B, Wang Y, Jin Q, Yugandhar P, Xu Y, Sun S, Hu F. Differential efficacy of water lily cultivars in phytoremediation of eutrophic water contaminated with phosphorus and nitrogen. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:139-146. [PMID: 34998101 DOI: 10.1016/j.plaphy.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Excessive inputs of phosphorus (P) and nitrogen (N) trigger eutrophication of the water bodies, which promotes the undesirable growth of algal bloom and deterioration of the water quality, and aquatic biodiversity. Macrophytes provide an environmentally benign and economically viable paradigm for the ecological restoration of eutrophic aquatic ecosystems. Water lily (Nymphaea) is largely used as ornamental plant for landscaping, and it has been documented that water lily possesses the potentiality in mitigating polluted aquatic environments. In the present study, water lily cultivars Nymphaea Texas Dawn (NTD), Nymphaea Colorado (NC), Nymphaea Madame Wilfron Gonnère (NMWG), and Nymphaea Sunshine Princess (NSP) were investigated for their potency in alleviating the eutrophication. The concentrations of total P and total N were significantly higher in the leaves of NC and NSP compared with NTD and NMWG. Therefore, NC and NSP were selected for subsequent studies to decipher their recuperation efficacy on eutrophic waters at different growth stages. NC and NSP significantly reduced the concentrations of eutrophication indicators i.e., total P, NH4+-N, and chemical oxygen demand in different gradients of the simulated eutrophic water in a growth-dependent manner. On the contrary, NC and NSP triggered a significant increase in the concentration of dissolved oxygen particularly at the seedling stage. Notably, the concentrations of total P (shoot and root) and total N (root) were relatively higher in NSP than NC. The study thus revealed a growth-dependent differential efficacy of NSP and NC in mitigating the different eutrophic waters.
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Affiliation(s)
- Xiaowen Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Bingqiong Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanjie Wang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qijiang Jin
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Yingchun Xu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shubin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Harms NE, Knight IA, Pratt PD, Reddy AM, Mukherjee A, Gong P, Coetzee J, Raghu S, Diaz R. Climate Mismatch between Introduced Biological Control Agents and Their Invasive Host Plants: Improving Biological Control of Tropical Weeds in Temperate Regions. INSECTS 2021; 12:insects12060549. [PMID: 34204761 PMCID: PMC8231509 DOI: 10.3390/insects12060549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/20/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Mismatched distributions between biological control agents and their host plants occur for a variety of reasons but are often linked to climate, specifically differences in their low-temperature tolerances. How to measure and use low-temperature tolerances of control agents to inform agent prioritization, selection for redistribution, or predict efficacy is vitally important, but has not been previously synthesized in a single source. We discuss causes of climate mismatches between agents and target weeds, the traditional and non-traditional approaches that could be used to decrease the degree of mismatch and improve control, and regulatory issues to consider when taking such approaches. We also discuss the variety of cold tolerance metrics, their measurement and ecological value, and the types of modeling that can be carried out to improve predictions about potential distributions of agents. We also briefly touch on molecular bases for cold tolerance and opportunities for improving cold tolerance of agents using modern molecular tools. Abstract Many weed biological control programs suffer from large-scale spatial variation in success due to restricted distributions or abundances of agents in temperate climates. For some of the world’s worst aquatic weeds, agents are established but overwintering conditions limit their survival in higher latitudes or elevations. The resulting need is for new or improved site- or region-specific biological control tools. Here, we review this challenge with a focus on low-temperature limitations of agents and propose a roadmap for improving success. Investigations across spatial scales, from global (e.g., foreign exploration), to local (selective breeding), to individual organisms (molecular modification), are discussed. A combination of traditional (foreign) and non-traditional (introduced range) exploration may lead to the discovery and development of better-adapted agent genotypes. A multivariate approach using ecologically relevant metrics to quantify and compare cold tolerance among agent populations is likely required. These data can be used to inform environmental niche modeling combined with mechanistic modeling of species’ fundamental climate niches and life histories to predict where, when, and at what abundance agents will occur. Finally, synthetic and systems biology approaches in conjunction with advanced modern genomics, gene silencing and gene editing technologies may be used to identify and alter the expression of genes enhancing cold tolerance, but this technology in the context of weed biological control has not been fully explored.
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Affiliation(s)
- Nathan E. Harms
- Aquatic Ecology and Invasive Species Branch, Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA;
- Correspondence: ; Tel.: +01-601-634-2976
| | - Ian A. Knight
- Aquatic Ecology and Invasive Species Branch, Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA;
| | - Paul D. Pratt
- Invasive Species and Pollinator Health Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA; (P.D.P.); (A.M.R.)
| | - Angelica M. Reddy
- Invasive Species and Pollinator Health Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA; (P.D.P.); (A.M.R.)
| | | | - Ping Gong
- Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA;
| | - Julie Coetzee
- Centre for Biological Control, Botany Department, Rhodes University, Grahamstown 6140, South Africa;
| | - S. Raghu
- CSIRO Health & Biosecurity, Brisbane 4001, Australia;
| | - Rodrigo Diaz
- Department of Entomology, Louisiana State University, Baton Rouge, LA 70803, USA;
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Nishiyama E, Nonogaki M, Yamazaki S, Nonogaki H, Ohshima K. Ancient and recent gene duplications as evolutionary drivers of the seed maturation regulators DELAY OF GERMINATION1 family genes. THE NEW PHYTOLOGIST 2021; 230:889-901. [PMID: 33454982 DOI: 10.1111/nph.17201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The DELAY OF GERMINATION1 (DOG1) family genes (DFGs) in Arabidopsis thaliana are involved in seed dormancy, reserve accumulation, and desiccation tolerance. Decoding the molecular evolution of DFGs is key to understanding how these seed programs evolved. This article demonstrates that DFGs have diverged in the four lineages DOG1, DOG1-LIKE4 (DOGL4), DOGL5 and DOGL6, whereas DOGL1, DOGL2 and DOGL3 arose separately within the DOG1 lineage. The systematic DFG nomenclature proposed in this article addresses the current issues of inconsistent DFG annotation and highlights DFG genomic synteny in angiosperms. DFG pseudogenes, or collapsed coding sequences, hidden in the genomes of early-diverging angiosperms are documented here. They suggest ancient birth and loss of DFGs over the course of angiosperm evolution. The proposed models suggest that the origin of DFG diversification dates back to the most recent common ancestor of living angiosperms. The presence of a single form of DFG in nonflowering plants is discussed. Phylogenetic analysis of gymnosperm, lycophyte, and liverwort DFGs and similar genes found in mosses and algae suggests that DFGs diverged from the TGACG motif-binding transcription factor genes before the divergence of the bryophyte lineage.
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Affiliation(s)
- Eri Nishiyama
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Mariko Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Satoru Yamazaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Kazuhiko Ohshima
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
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Nonogaki H, Nishiyama E, Ohshima K, Nonogaki M. Ancient Memories of Seeds: ABA-Dependent Growth Arrest and Reserve Accumulation. Trends Genet 2020; 36:464-473. [DOI: 10.1016/j.tig.2020.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
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10
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Song XM, Wang JP, Sun PC, Ma X, Yang QH, Hu JJ, Sun SR, Li YX, Yu JG, Feng SY, Pei QY, Yu T, Yang NS, Liu YZ, Li XQ, Paterson AH, Wang XY. Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization. HORTICULTURE RESEARCH 2020; 7:20. [PMID: 32133148 PMCID: PMC7035258 DOI: 10.1038/s41438-020-0253-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 05/04/2023]
Abstract
Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The cold-related regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.
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Affiliation(s)
- Xiao-Ming Song
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Jin-Peng Wang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Peng-Chuan Sun
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Xiao Ma
- Library, North China University of Science and Technology, Tangshan, 063210 China
| | - Qi-Hang Yang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Jing-Jing Hu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Sang-Rong Sun
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Yu-Xian Li
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
| | - Ji-Gao Yu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Shu-Yan Feng
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Qiao-Ying Pei
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Tong Yu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Nan-Shan Yang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Yin-Zhe Liu
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B 4Z7 Canada
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
| | - Xi-Yin Wang
- School of Life Science, North China University of Science and Technology, Tangshan, 063210 China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210 China
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