1
|
Kerwin RE, Hart JE, Fiesel PD, Lou YR, Fan P, Jones AD, Last RL. Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster. Sci Adv 2024; 10:eadn3991. [PMID: 38657073 PMCID: PMC11094762 DOI: 10.1126/sciadv.adn3991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.
Collapse
Affiliation(s)
- Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jaynee E. Hart
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Wu J, Nan X, Zhang X, Xu W, Ma H, Yang Z, Wang C. The Identification and Analysis of the Self-Incompatibility Pollen Determinant Factor SLF in Lycium barbarum. Plants (Basel) 2024; 13:959. [PMID: 38611487 PMCID: PMC11013074 DOI: 10.3390/plants13070959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S2-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S2-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S2-LbSLF genes, and that there are two pairs of co-linear genes between S2-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S2-LbSLF members can be divided into six groups, and it was found that the 13 S2-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S2-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S2-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S2-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum.
Collapse
Affiliation(s)
- Jiali Wu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Xiongxiong Nan
- State Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, China
| | - Xin Zhang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
| | - Wendi Xu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
| | - Haijun Ma
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Ningxia Grape and Wine Innovation Center, North Minzu University, Yinchuan 750021, China
| | - Zijun Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Cuiping Wang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
| |
Collapse
|
3
|
Stirling SA, Guercio AM, Patrick RM, Huang XQ, Bergman ME, Dwivedi V, Kortbeek RWJ, Liu YK, Sun F, Tao WA, Li Y, Boachon B, Shabek N, Dudareva N. Volatile communication in plants relies on a KAI2-mediated signaling pathway. Science 2024; 383:1318-1325. [PMID: 38513014 DOI: 10.1126/science.adl4685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
Plants are constantly exposed to volatile organic compounds (VOCs) that are released during plant-plant communication, within-plant self-signaling, and plant-microbe interactions. Therefore, understanding VOC perception and downstream signaling is vital for unraveling the mechanisms behind information exchange in plants, which remain largely unexplored. Using the hormone-like function of volatile terpenoids in reproductive organ development as a system with a visual marker for communication, we demonstrate that a petunia karrikin-insensitive receptor, PhKAI2ia, stereospecifically perceives the (-)-germacrene D signal, triggering a KAI2-mediated signaling cascade and affecting plant fitness. This study uncovers the role(s) of the intermediate clade of KAI2 receptors, illuminates the involvement of a KAI2ia-dependent signaling pathway in volatile communication, and provides new insights into plant olfaction and the long-standing question about the nature of potential endogenous KAI2 ligand(s).
Collapse
Affiliation(s)
- Shannon A Stirling
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Angelica M Guercio
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Xing-Qi Huang
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Matthew E Bergman
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Varun Dwivedi
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ruy W J Kortbeek
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Fuai Sun
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Benoît Boachon
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Université Jean Monnet Saint-Etienne, CNRS, LBVpam UMR 5079, F-42023 Saint-Etienne, France
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA 95616, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
4
|
Zhang H, Liu Z, Geng R, Ren M, Cheng L, Liu D, Jiang C, Wen L, Xiao Z, Yang A. Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection. Genomics 2024; 116:110823. [PMID: 38492820 DOI: 10.1016/j.ygeno.2024.110823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
The TIFY gene family plays an essential role in plant development and abiotic and biotic stress responses. In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions. The TIFY gene family exhibited expansion and possessed gene redundancy resulting from tobacco ploidy change. In addition, most NtTIFYs equivalently expressed in roots, stems and leaves, while NtTIFY1, NtTIFY4, NtTIFY18 and NtTIFY30 preferentially expressed in roots. The JAZ III clade showed significant expression changes after inoculation with R. solanacearum, and the expression of NtTIFY7 in resistant varieties, compared with susceptible varieties, was more stably induced. Furthermore, NtTIFY7-silenced plants, compared with the control plants, were more susceptible to bacterial wilt. These results lay a foundation for exploring the evolutionary history of TIFY gene family and revealing gene function of NtTIFYs in tobacco bacterial wilt resistance.
Collapse
Affiliation(s)
- Huifen Zhang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhengwen Liu
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ruimei Geng
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Min Ren
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Lirui Cheng
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Dan Liu
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Caihong Jiang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Liuying Wen
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhiliang Xiao
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Aiguo Yang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| |
Collapse
|
5
|
Feng X, Chen Q, Wu W, Wang J, Li G, Xu S, Shao S, Liu M, Zhong C, Wu CI, Shi S, He Z. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nat Commun 2024; 15:1635. [PMID: 38388712 PMCID: PMC10884412 DOI: 10.1038/s41467-024-46080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
Collapse
Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Guohong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571100, Haikou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| |
Collapse
|
6
|
Zhang D, Li YY, Zhao X, Zhang C, Liu DK, Lan S, Yin W, Liu ZJ. Molecular insights into self-incompatibility systems: From evolution to breeding. Plant Commun 2024; 5:100719. [PMID: 37718509 PMCID: PMC10873884 DOI: 10.1016/j.xplc.2023.100719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Plants have evolved diverse self-incompatibility (SI) systems for outcrossing. Since Darwin's time, considerable progress has been made toward elucidating this unrivaled reproductive innovation. Recent advances in interdisciplinary studies and applications of biotechnology have given rise to major breakthroughs in understanding the molecular pathways that lead to SI, particularly the strikingly different SI mechanisms that operate in Solanaceae, Papaveraceae, Brassicaceae, and Primulaceae. These best-understood SI systems, together with discoveries in other "nonmodel" SI taxa such as Poaceae, suggest a complex evolutionary trajectory of SI, with multiple independent origins and frequent and irreversible losses. Extensive exploration of self-/nonself-discrimination signaling cascades has revealed a comprehensive catalog of male and female identity genes and modifier factors that control SI. These findings also enable the characterization, validation, and manipulation of SI-related factors for crop improvement, helping to address the challenges associated with development of inbred lines. Here, we review current knowledge about the evolution of SI systems, summarize key achievements in the molecular basis of pollen‒pistil interactions, discuss potential prospects for breeding of SI crops, and raise several unresolved questions that require further investigation.
Collapse
Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Weilun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
7
|
Song Y, Huang JP, Wang YJ, Huang SX. Chromosome level genome assembly of endangered medicinal plant Anisodus tanguticus. Sci Data 2024; 11:161. [PMID: 38307894 PMCID: PMC10837431 DOI: 10.1038/s41597-024-03007-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
Anisodus tanguticus is a medicinal herb that belongs to the Anisodus genus of the Solanaceae family. This endangered herb is mainly distributed in Qinghai-Tibet Plateau. In this study, we combined the Illumina short-read, Nanopore long-read and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to de novo assemble the A. tanguticus genome. A high-quality chromosomal-level genome assembly was obtained with a genome size of 1.26 Gb and a contig N50 of 25.07 Mb. Of the draft genome sequences, 97.47% were anchored to 24 pseudochromosomes with a scaffold N50 of 51.28 Mb. In addition, 842.14 Mb of transposable elements occupying 66.70% of the genome assembly were identified and 44,252 protein-coding genes were predicted. The genome assembly of A. tanguticus will provide genetic repertoire to understand the adaptation strategy of Anisodus species in the plateau, which will further promote the conservation of endangered A. tanguticus resources.
Collapse
Affiliation(s)
- Yongli Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian-Ping Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Jiang Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Sheng-Xiong Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
8
|
Patrick RM, Huang XQ, Dudareva N, Li Y. Rhythmic histone acetylation acts in concert with day-night oscillation of the floral volatile metabolic network. New Phytol 2024; 241:1829-1839. [PMID: 38058220 DOI: 10.1111/nph.19447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
The biosynthesis of specialized metabolites is strictly regulated by environmental inputs such as the day-night cycle, but the underlying mechanisms remain elusive. In Petunia hybrida cv. Mitchell flowers, the biosynthesis and emission of volatile compounds display a diurnal pattern with a peak in the evening to attract nocturnal pollinators. Using petunia flowers as a model system, we found that chromatin level regulation, especially histone acetylation, plays an essential role in mediating the day-night oscillation of the biosynthetic gene network of specialized metabolites. By performing time-course chromatin immunoprecipitation assays for histone modifications, we uncovered that a specific group of genes involved in the regulation, biosynthesis, and emission of floral volatile compounds, which displays the greatest magnitude in day-night oscillating gene expression, is associated with highly dynamic histone acetylation marks H3K9ac and H3K27ac. Specifically, the strongest oscillating genes featured a drastic removal of histone acetylation marks at night, potentially to shut down the biosynthesis of floral volatile compounds during the morning when they are not needed. Inhibiting daytime histone acetylation led to a compromised evening induction of these genes. Overall, our study suggested an active role of chromatin modification in the diurnal oscillation of specialized metabolic network.
Collapse
Affiliation(s)
- Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xing-Qi Huang
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
9
|
Chopy M, Cavallini-Speisser Q, Chambrier P, Morel P, Just J, Hugouvieux V, Rodrigues Bento S, Zubieta C, Vandenbussche M, Monniaux M. Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petal morphogenesis in petunia. Plant Cell 2024; 36:324-345. [PMID: 37804091 PMCID: PMC10827313 DOI: 10.1093/plcell/koad258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Floral homeotic MADS-box transcription factors ensure the correct morphogenesis of floral organs, which are organized in different cell layers deriving from distinct meristematic layers. How cells from these distinct layers acquire their respective identities and coordinate their growth to ensure normal floral organ morphogenesis is unresolved. Here, we studied petunia (Petunia × hybrida) petals that form a limb and tube through congenital fusion. We identified petunia mutants (periclinal chimeras) expressing the B-class MADS-box gene DEFICIENS in the petal epidermis or in the petal mesophyll, called wico and star, respectively. Strikingly, wico flowers form a strongly reduced tube while their limbs are almost normal, while star flowers form a normal tube but greatly reduced and unpigmented limbs, showing that petunia petal morphogenesis is highly modular. These mutants highlight the layer-specific roles of PhDEF during petal development. We explored the link between PhDEF and petal pigmentation, a well-characterized limb epidermal trait. The anthocyanin biosynthesis pathway was strongly downregulated in star petals, including its major regulator ANTHOCYANIN2 (AN2). We established that PhDEF directly binds to the AN2 terminator in vitro and in vivo, suggesting that PhDEF might regulate AN2 expression and therefore petal epidermis pigmentation. Altogether, we show that cell layer-specific homeotic activity in petunia petals differently impacts tube and limb development, revealing the relative importance of the different cell layers in the modular architecture of petunia petals.
Collapse
Affiliation(s)
- Mathilde Chopy
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Quentin Cavallini-Speisser
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Patrice Morel
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Jérémy Just
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Suzanne Rodrigues Bento
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Michiel Vandenbussche
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Marie Monniaux
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| |
Collapse
|
10
|
Liu L, Xie Y, Yahaya BS, Wu F. GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms. Genes (Basel) 2024; 15:94. [PMID: 38254983 PMCID: PMC10815842 DOI: 10.3390/genes15010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.
Collapse
Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China;
| | - Yuxin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| |
Collapse
|
11
|
Zhou W, Wang C, Hao X, Chen F, Huang Q, Liu T, Xu J, Guo S, Liao B, Liu Z, Feng Y, Wang Y, Liao P, Xue J, Shi M, Maoz I, Kai G. A chromosome-level genome assembly of anesthetic drug-producing Anisodus acutangulus provides insights into its evolution and the biosynthesis of tropane alkaloids. Plant Commun 2024; 5:100680. [PMID: 37660252 PMCID: PMC10811374 DOI: 10.1016/j.xplc.2023.100680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Tropane alkaloids (TAs), which are anticholinergic agents, are an essential class of natural compounds, and there is a growing demand for TAs with anesthetic, analgesic, and spasmolytic effects. Anisodus acutangulus (Solanaceae) is a TA-producing plant that was used as an anesthetic in ancient China. In this study, we assembled a high-quality, chromosome-scale genome of A. acutangulus with a contig N50 of 7.4 Mb. A recent whole-genome duplication occurred in A. acutangulus after its divergence from other Solanaceae species, which resulted in the duplication of ADC1 and UGT genes involved in TA biosynthesis. The catalytic activities of H6H enzymes were determined for three Solanaceae plants. On the basis of evolution and co-expressed genes, AaWRKY11 was selected for further analyses, which revealed that its encoded transcription factor promotes TA biosynthesis by activating AaH6H1 expression. These findings provide useful insights into genome evolution related to TA biosynthesis and have potential implications for genetic manipulation of TA-producing plants.
Collapse
Affiliation(s)
- Wei Zhou
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Can Wang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Xiaolong Hao
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Fei Chen
- Sanya Nanfan Research Institute from Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Qikai Huang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Tingyao Liu
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhixiang Liu
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yue Feng
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yao Wang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Pan Liao
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Jiayu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Shi
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Itay Maoz
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Guoyin Kai
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China.
| |
Collapse
|
12
|
Skaliter O, Bednarczyk D, Shor E, Shklarman E, Manasherova E, Aravena-Calvo J, Kerzner S, Cna’ani A, Jasinska W, Masci T, Dvir G, Edelbaum O, Rimon B, Brotman Y, Cohen H, Vainstein A. The R2R3-MYB transcription factor EVER controls the emission of petunia floral volatiles by regulating epicuticular wax biosynthesis in the petal epidermis. Plant Cell 2023; 36:174-193. [PMID: 37818992 PMCID: PMC10734618 DOI: 10.1093/plcell/koad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
The epidermal cells of petunia (Petunia × hybrida) flowers are the main site of volatile emission. However, the mechanisms underlying the release of volatiles into the environment are still being explored. Here, using cell-layer-specific transcriptomic analysis, reverse genetics by virus-induced gene silencing and clustered regularly interspaced short palindromic repeat (CRISPR), and metabolomics, we identified EPIDERMIS VOLATILE EMISSION REGULATOR (EVER)-a petal adaxial epidermis-specific MYB activator that affects the emission of volatiles. To generate ever knockout lines, we developed a viral-based CRISPR/Cas9 system for efficient gene editing in plants. These knockout lines, together with transient-suppression assays, revealed EVER's involvement in the repression of low-vapor-pressure volatiles. Internal pools and annotated scent-related genes involved in volatile production and emission were not affected by EVER. RNA-Seq analyses of petals of ever knockout lines and EVER-overexpressing flowers revealed enrichment in wax-related biosynthesis genes. Liquid chromatography/gas chromatography-MS analyses of petal epicuticular waxes revealed substantial reductions in wax loads in ever petals, particularly of monomers of fatty acids and wax esters. These results implicate EVER in the emission of volatiles by fine-tuning the composition of petal epicuticular waxes. We reveal a petunia MYB regulator that interlinks epicuticular wax composition and volatile emission, thus unraveling a regulatory layer in the scent-emission machinery in petunia flowers.
Collapse
Affiliation(s)
- Oded Skaliter
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Dominika Bednarczyk
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ekaterina Shor
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Elena Shklarman
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ekaterina Manasherova
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Javiera Aravena-Calvo
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Shane Kerzner
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Alon Cna’ani
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Weronika Jasinska
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Tania Masci
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Gony Dvir
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Orit Edelbaum
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ben Rimon
- Department of Ornamental Horticulture and Biotechnology, The Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion 7505101, Israel
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Hagai Cohen
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| |
Collapse
|
13
|
Yang J, Wu Y, Zhang P, Ma J, Yao YJ, Ma YL, Zhang L, Yang Y, Zhao C, Wu J, Fang X, Liu J. Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family. Nat Commun 2023; 14:8457. [PMID: 38114555 PMCID: PMC10730914 DOI: 10.1038/s41467-023-44246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.
Collapse
Affiliation(s)
- Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Jun Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Lin Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, Ningxia, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Changmin Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jihua Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| |
Collapse
|
14
|
Zepeda B, Marcelis LFM, Kaiser E, Verdonk JC. Petunia as a model for MYB transcription factor action under salt stress. Front Plant Sci 2023; 14:1286547. [PMID: 38155855 PMCID: PMC10753185 DOI: 10.3389/fpls.2023.1286547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Salinity is a current and growing problem, affecting crops worldwide by reducing yields and product quality. Plants have different mechanisms to adapt to salinity; some crops are highly studied, and their salinity tolerance mechanisms are widely known. However, there are other crops with commercial importance that still need characterization of their molecular mechanisms. Usually, transcription factors are in charge of the regulation of complex processes such as the response to salinity. MYB-TFs are a family of transcription factors that regulate various processes in plant development, and both central and specialized metabolism. MYB-TFs have been studied extensively as mediators of specialized metabolism, and some are master regulators. The influence of MYB-TFs on highly orchestrated mechanisms, such as salinity tolerance, is an attractive research target. The versatility of petunia as a model species has allowed for advances to be made in multiple fields: metabolomic pathways, quality traits, stress resistance, and signal transduction. It has the potential to be the link between horticultural crops and lab models, making it useful in translating discoveries related to the MYB-TF pathways into other crops. We present a phylogenetic tree made with Petunia axillaris and Petunia inflata R2R3-MYB subfamily sequences, which could be used to find functional conservation between different species. This work could set the foundations to improve salinity resistance in other commercial crops in later studies.
Collapse
Affiliation(s)
| | | | | | - Julian C. Verdonk
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
15
|
Turchetto C, Silvério ADC, Waschburger EL, Lacerda MEG, Quintana IV, Turchetto-Zolet AC. Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230142. [PMID: 38048778 PMCID: PMC10695626 DOI: 10.1590/1415-4757-gmb-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 12/06/2023] Open
Abstract
The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.
Collapse
Affiliation(s)
- Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Ariadne de Castro Silvério
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
| | - Edgar Luis Waschburger
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Maria Eduarda Gonçalves Lacerda
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Isadora Vieira Quintana
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| |
Collapse
|
16
|
Pezzi PH, Gonçalves LT, Deprá M, Freitas LBD. Evolution and diversification of the O-methyltransferase (OMT) gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230121. [PMID: 37948506 PMCID: PMC10637433 DOI: 10.1590/1678-4685-gmb-2023-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/30/2023] [Indexed: 11/12/2023] Open
Abstract
O-methyltransferases (OMTs) are a group of enzymes involved in several fundamental biological processes in plants, including lignin biosynthesis, pigmentation, and aroma production. Despite the intensive investigation of the role of OMTs in plant secondary metabolism, the evolution and diversification of this gene family in Solanaceae remain poorly understood. Here, we conducted a genome-wide survey of OMT genes in six Solanaceae species, reconstructing gene phylogenetic trees, predicting the potential involvement in biological processes, and investigating the exon/intron structure and chromosomal location. We identified 57 caffeoyl-CoA OMTs (CCoAOMTs) and 196 caffeic acid OMTs (COMTs) in the studied species. We observed a conserved gene block on chromosome 2 that consisted of tandem duplicated copies of OMT genes. Our results suggest that the expansion of the OMT gene family in Solanaceae was driven by whole genome duplication, segmental duplication, and tandem duplication, with multiple genes being retained by neofunctionalization and subfunctionalization. This study represents an essential first step in unraveling the evolutionary history of OMTs in Solanaceae. Our findings deepen our understanding of the crucial role of OMTs in several biological processes and highlight their significance as potential biotechnological targets.
Collapse
Affiliation(s)
- Pedro Henrique Pezzi
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | | | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Porto Alegre, RS, Brazil
| | | |
Collapse
|
17
|
Rezaei H, Mirzaie-asl A, Abdollahi MR, Tohidfar M. Enhancing petunia tissue culture efficiency with machine learning: A pathway to improved callogenesis. PLoS One 2023; 18:e0293754. [PMID: 37922261 PMCID: PMC10624318 DOI: 10.1371/journal.pone.0293754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/18/2023] [Indexed: 11/05/2023] Open
Abstract
The important feature of petunia in tissue culture is its unpredictable and genotype-dependent callogenesis, posing challenges for efficient regeneration and biotechnology applications. To address this issue, machine learning (ML) can be considered a powerful tool to analyze callogenesis data, extract key parameters, and predict optimal conditions for petunia callogenesis, facilitating more controlled and productive tissue culture processes. The study aimed to develop a predictive model for callogenesis in petunia using ML algorithms and to optimize the concentrations of phytohormones to enhance callus formation rate (CFR) and callus fresh weight (CFW). The inputs for the model were BAP, KIN, IBA, and NAA, while the outputs were CFR and CFW. Three ML algorithms, namely MLP, RBF, and GRNN, were compared, and the results revealed that GRNN (R2≥83) outperformed MLP and RBF in terms of accuracy. Furthermore, a sensitivity analysis was conducted to determine the relative importance of the four phytohormones. IBA exhibited the highest importance, followed by NAA, BAP, and KIN. Leveraging the superior performance of the GRNN model, a genetic algorithm (GA) was integrated to optimize the concentration of phytohormones for maximizing CFR and CFW. The genetic algorithm identified an optimized combination of phytohormones consisting of 1.31 mg/L BAP, 1.02 mg/L KIN, 1.44 mg/L NAA, and 1.70 mg/L IBA, resulting in 95.83% CFR. To validate the reliability of the predicted results, optimized combinations of phytohormones were tested in a laboratory experiment. The results of the validation experiment indicated no significant difference between the experimental and optimized results obtained through the GA. This study presents a novel approach combining ML, sensitivity analysis, and GA for modeling and predicting callogenesis in petunia. The findings offer valuable insights into the optimization of phytohormone concentrations, facilitating improved callus formation and potential applications in plant tissue culture and genetic engineering.
Collapse
Affiliation(s)
- Hamed Rezaei
- Department of Plant Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Asghar Mirzaie-asl
- Department of Plant Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Reza Abdollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran
| |
Collapse
|
18
|
Drummond RSM, Lee HW, Luo Z, Dakin JF, Janssen BJ, Snowden KC. Varying the expression pattern of the strigolactone receptor gene DAD2 results in phenotypes distinct from both wild type and knockout mutants. Front Plant Sci 2023; 14:1277617. [PMID: 37900765 PMCID: PMC10600376 DOI: 10.3389/fpls.2023.1277617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023]
Abstract
The action of the petunia strigolactone (SL) hormone receptor DAD2 is dependent not only on its interaction with the PhMAX2A and PhD53A proteins, but also on its expression patterns within the plant. Previously, in a yeast-2-hybrid system, we showed that a series of a single and double amino acid mutants of DAD2 had altered interactions with these binding partners. In this study, we tested the mutants in two plant systems, Arabidopsis and petunia. Testing in Arabidopsis was enabled by creating a CRISPR-Cas9 knockout mutant of the Arabidopsis strigolactone receptor (AtD14). We produced SL receptor activity in both systems using wild type and mutant genes; however, the mutants had functions largely indistinguishable from those of the wild type. The expression of the wild type DAD2 from the CaMV 35S promoter in dad2 petunia produced plants neither quite like the dad2 mutant nor the V26 wild type. These plants had greater height and leaf size although branch number and the plant shape remained more like those of the mutant. These traits may be valuable in the context of a restricted area growing system such as controlled environment agriculture.
Collapse
Affiliation(s)
- Revel S. M. Drummond
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | | | | | | | | | - Kimberley C. Snowden
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| |
Collapse
|
19
|
Alisawi O, Richert-Pöggeler KR, Heslop-Harrison J(P, Schwarzacher T. The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes. Front Plant Sci 2023; 14:1232588. [PMID: 37868307 PMCID: PMC10587573 DOI: 10.3389/fpls.2023.1232588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
Introduction The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Methods Raw reads from available genomic assemblies and survey sequences of P. axillaris N (PaxiN), P. inflata S6, (PinfS6), P. hybrida (PhybR27) and the here sequenced P. parodii S7 (PparS7) were used for graph and k-mer based cluster analysis of TAREAN and RepeatExplorer. Analysis of repeat specific monomer lengths and sequence heterogeneity of the major tandem repeat families with more than 0.01% genome proportion were complemented by fluorescent in situ hybridization (FISH) using consensus sequences as probes to chromosomes of all four species. Results Seven repeat families, PSAT1, PSAT3, PSAT4, PSAT5 PSAT6, PSAT7 and PSAT8, shared high consensus sequence similarity and organisation between the four genomes. Additionally, many degenerate copies were present. FISH in P. hybrida and in the three wild petunias confirmed the bioinformatics data and gave corresponding signals on all or some chromosomes. PSAT1 is located at the ends of all chromosomes except the 45S rDNA bearing short arms of chromosomes II and III, and we classify it as a telomere associated sequence (TAS). It is the most abundant satellite repeat with over 300,000 copies, 0.2% of the genomes. PSAT3 and the variant PSAT7 are located adjacent to the centromere or mid-arm of one to three chromosome pairs. PSAT5 has a strong signal at the end of the short arm of chromosome III in P. axillaris and P.inflata, while in P. hybrida additional interstitial sites were present. PSAT6 is located at the centromeres of chromosomes II and III. PSAT4 and PSAT8 were found with only short arrays. Discussion These results demonstrate that (i) repeat families occupy distinct niches within chromosomes, (ii) they differ in the copy number, cluster organization and homogenization events, and that (iii) the recent genome hybridization in breeding P. hybrida preserved the chromosomal position of repeats but affected the copy number of repetitive DNA.
Collapse
Affiliation(s)
- Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
| | - Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J.S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
20
|
Li G, Michaelis DF, Huang J, Serek M, Gehl C. New insights into the genetic manipulation of the R2R3-MYB and CHI gene families on anthocyanin pigmentation in Petunia hybrida. Plant Physiol Biochem 2023; 203:108000. [PMID: 37683585 DOI: 10.1016/j.plaphy.2023.108000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Several R2R3-MYB genes control anthocyanin pigmentation in petunia, and ANTHOCYANIN-2 (AN2) is treated as the main player in petal limbs. However, the actual roles of R2R3-MYBs in the coloration of different floral tissues in the so called "darkly-veined" petunias are still not clear. The genetic background and expression of AN2 paralogs from various petunias with different color patterns were identified. All "darkly-veined" genotypes have the identical mutation in the AN2 gene, but express a different functional paralog - ANTHOCYANIN-4 (AN4) - abundantly in flowers. Constitutive overexpression of PhAN4 in this petunia resulted not only in a fully colored flower but also in a clearly visible pigmentation in the green tissue and roots, which can be rapidly increased by stress conditions. Suppression of AN4 gene resulted in discolored petals and whitish anthers. Interestingly, when a similar white flower phenotype was achieved by knockout of an essential structural gene of anthocyanin biosynthesis - CHALCONE ISOMERASE-A (CHI-A) - the plant responded directly by upregulating of another paralogs - DEEP PURPLE (DPL) and PURPLE HAZE (PHZ). Moreover, we also found that CHI-B can partially substitute for CHI-A in anthers, but not in vegetative tissues. Further, no significant effects on the longevity of white or enhanced colored flowers were observed compared with the wild type. We concluded that endogenous up-regulation of AN4 leads to the restoration of petal color in the "darkly-veined" phenotypes as a result of the breeding process under human selection, and CHI-B is a backup for CHI-A acitvity in some floral tissues.
Collapse
Affiliation(s)
- Guo Li
- Institute of Horticultural Production Systems, Floriculture, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Dietz Felix Michaelis
- Institute of Horticultural Production Systems, Floriculture, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Junjie Huang
- Institute of Horticultural Production Systems, Floriculture, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Margrethe Serek
- Institute of Horticultural Production Systems, Floriculture, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Christian Gehl
- Institute of Horticultural Production Systems, Floriculture, Faculty of Natural Sciences, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| |
Collapse
|
21
|
Shoji T, Sugawara S, Mori T, Kobayashi M, Kusano M, Saito K. Induced production of specialized steroids by transcriptional reprogramming in Petunia hybrida. PNAS Nexus 2023; 2:pgad326. [PMID: 37920550 PMCID: PMC10619512 DOI: 10.1093/pnasnexus/pgad326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023]
Abstract
Plants produce specialized metabolites with defensive properties that are often synthesized through the coordinated regulation of metabolic genes by transcription factors in various biological contexts. In this study, we investigated the regulatory function of the transcription factor PhERF1 from petunia (Petunia hybrida), which belongs to a small group of ETHYLENE RESPONSE FACTOR (ERF) family members that regulate the biosynthesis of bioactive alkaloids and terpenoids in various plant lineages. We examined the effects of transiently overexpressing PhERF1 in petunia leaves on the transcriptome and metabolome, demonstrating the production of a class of specialized steroids, petuniolides, and petuniasterones in these leaves. We also observed the activation of many metabolic genes, including those involved in sterol biosynthesis, as well as clustered genes that encode new metabolic enzymes, such as cytochrome P450 oxidoreductases, 2-oxoglutarate-dependent dioxygenases, and BAHD acyltransferases. Furthermore, we determined that PhERF1 transcriptionally induces downstream metabolic genes by recognizing specific cis-regulatory elements in their promoters. This study highlights the potential of evolutionarily conserved transcriptional regulators to induce the production of specialized products through transcriptional reprogramming.
Collapse
Affiliation(s)
- Tsubasa Shoji
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Institute of Natural Medicine, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Satoko Sugawara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
22
|
Rogers HJ. How far can omics go in unveiling the mechanisms of floral senescence? Biochem Soc Trans 2023; 51:1485-1493. [PMID: 37387359 PMCID: PMC10586764 DOI: 10.1042/bst20221097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Floral senescence is of fundamental interest in understanding plant developmental regulation, it is of ecological and agricultural interest in relation to seed production, and is of key importance to the production of cut flowers. The biochemical changes occurring are well-studied and involve macromolecular breakdown and remobilisation of nutrients to developing seeds or other young organs in the plant. However, the initiation and regulation of the process and inter-organ communication remain to be fully elucidated. Although ethylene emission, which becomes autocatalytic, is a key regulator in some species, in other species it appears not to be as important. Other plant growth regulators such as cytokinins, however, seem to be important in floral senescence across both ethylene sensitive and insensitive species. Other plant growth regulators are also likely involved. Omics approaches have provided a wealth of data especially in ornamental species where genome data is lacking. Two families of transcription factors: NAC and WRKY emerge as major regulators, and omics information has been critical in understanding their functions. Future progress would greatly benefit from a single model species for understanding floral senescence; however, this is challenging due to the diversity of regulatory mechanisms. Combining omics data sets can be powerful in understanding different layers of regulation, but in vitro biochemical and or genetic analysis through transgenics or mutants is still needed to fully verify mechanisms and interactions between regulators.
Collapse
|
23
|
Vainio J, Mattila S, Abdou SM, Sipari N, Teeri TH. Petunia dihydroflavonol 4-reductase is only a few amino acids away from producing orange pelargonidin-based anthocyanins. Front Plant Sci 2023; 14:1227219. [PMID: 37645465 PMCID: PMC10461392 DOI: 10.3389/fpls.2023.1227219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Anthocyanins are responsible for the color spectrum of both ornamental and natural flowers. However, not all plant species produce all colors. For example, roses are not blue because they do not naturally possess a hydroxylase that opens the pathway for delphinidin and its derivatives. It is more intriguing why some plants do not carry orange or scarlet red flowers with anthocyanins based on pelargonidin, because the precursor for these anthocyanins should be available if anthocyanins are made at all. The key to this is the substrate specificity of dihydroflavonol 4-reductase (DFR), an enzyme located at the branch point between flavonols and anthocyanins. The most common example is petunia, which does not bear orange flowers unless the enzyme is complemented by biotechnology. We changed a few amino acids in the active site of the enzyme and showed that the mutated petunia DFR started to favor dihydrokaempferol, the precursor to orange pelargonidin, in vitro. When transferred to petunia, it produced an orange hue and dramatically more pelargonidin-based anthocyanins in the flowers.
Collapse
Affiliation(s)
- Jere Vainio
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Saku Mattila
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Sara M. Abdou
- Horticulture and Product Physiology Group, Wageningen University, Wageningen, Netherlands
| | - Nina Sipari
- Viikki Metabolomics Unit, University of Helsinki, Helsinki, Finland
| | - Teemu H. Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Viikki Metabolomics Unit, University of Helsinki, Helsinki, Finland
| |
Collapse
|
24
|
Wang S, Gao J, Li Z, Chen K, Pu W, Feng C. Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana. Front Plant Sci 2023; 14:1205683. [PMID: 37575947 PMCID: PMC10421670 DOI: 10.3389/fpls.2023.1205683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Introduction Nicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking. Methods In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species. Results The incongruence among gene trees showed that the formation of N. sylvestris involved incomplete lineage sorting. The nuclear-plastid discordance and nuclear introgression absence indicated that organelle capture from section Trigonophyllae was involved in forming section Petunioides. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections Nicotiana, Repandae, Rusticae, Polydicliae, and Suaveolentes. Notably, we provide novel insights into the hybridization event of section Polydicliae and Suaveolentes. The section Polydicliae formed from a single hybridization event between maternal progenitor N. attenuata and paternal progenitor N. undulata; the N. sylvestris (paternal progenitor) and the N. glauca (maternal progenitor) were involved in the formation of section Suaveolentes. Discussion This study represents the first exploration of Nicotiana polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in Nicotiana and other related species.
Collapse
Affiliation(s)
- Shuaibin Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Zhaowu Li
- Puai Medical College, Shaoyang University, Shaoyang, China
| | - Kai Chen
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Chen Feng
- Jiangxi Provincial Key Laboratory of ex-situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| |
Collapse
|
25
|
Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
Collapse
|
26
|
Shor E, Skaliter O, Sharon E, Kitsberg Y, Bednarczyk D, Kerzner S, Vainstein D, Tabach Y, Vainstein A. Developmental and temporal changes in petunia petal transcriptome reveal scent-repressing plant-specific RING-kinase-WD40 protein. Front Plant Sci 2023; 14:1180899. [PMID: 37360732 PMCID: PMC10286513 DOI: 10.3389/fpls.2023.1180899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/05/2023] [Indexed: 06/28/2023]
Abstract
In moth-pollinated petunias, production of floral volatiles initiates when the flower opens and occurs rhythmically during the day, for optimal flower-pollinator interaction. To characterize the developmental transcriptomic response to time of day, we generated RNA-Seq databases for corollas of floral buds and mature flowers in the morning and in the evening. Around 70% of transcripts accumulating in petals demonstrated significant changes in expression levels in response to the flowers' transition from a 4.5-cm bud to a flower 1 day postanthesis (1DPA). Overall, 44% of the petal transcripts were differentially expressed in the morning vs. evening. Morning/evening changes were affected by flower developmental stage, with a 2.5-fold larger transcriptomic response to daytime in 1DPA flowers compared to buds. Analyzed genes known to encode enzymes in volatile organic compound biosynthesis were upregulated in 1DPA flowers vs. buds-in parallel with the activation of scent production. Based on analysis of global changes in the petal transcriptome, PhWD2 was identified as a putative scent-related factor. PhWD2 is a protein that is uniquely present in plants and has a three-domain structure: RING-kinase-WD40. Suppression of PhWD2 (termed UPPER - Unique Plant PhEnylpropanoid Regulator) resulted in a significant increase in the levels of volatiles emitted from and accumulated in internal pools, suggesting that it is a negative regulator of petunia floral scent production.
Collapse
Affiliation(s)
- Ekaterina Shor
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oded Skaliter
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Elad Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaarit Kitsberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dominika Bednarczyk
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shane Kerzner
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Danny Vainstein
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Tabach
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Vainstein
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
27
|
Wong DCJ, Pichersky E, Peakall R. Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant-pollinator interactions. Curr Opin Plant Biol 2023; 73:102332. [PMID: 36652780 DOI: 10.1016/j.pbi.2022.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 06/10/2023]
Abstract
Flowering plants have evolved extraordinarily diverse metabolites that underpin the floral visual and olfactory signals enabling plant-pollinator interactions. In some cases, these metabolites also provide unusual rewards that specific pollinators depend on. While some metabolites are shared by most flowering plants, many have evolved in restricted lineages in response to the specific selection pressures encountered within different niches. The latter are designated as specialized metabolites. Recent investigations continue to uncover a growing repertoire of unusual specialized metabolites. Increased accessibility to cutting-edge multi-omics technologies (e.g. genome, transcriptome, proteome, metabolome) is now opening new doors to simultaneously uncover the molecular basis of their synthesis and their evolution across diverse plant lineages. Drawing upon the recent literature, this perspective discusses these aspects and, where known, their ecological and evolutionary relevance. A primer on omics-guided approaches to discover the genetic and biochemical basis of functional specialized metabolites is also provided.
Collapse
Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
28
|
Shor E, Ravid J, Sharon E, Skaliter O, Masci T, Vainstein A. SCARECROW-like GRAS protein PES positively regulates petunia floral scent production. Plant Physiol 2023; 192:409-425. [PMID: 36760164 PMCID: PMC10152688 DOI: 10.1093/plphys/kiad081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 05/03/2023]
Abstract
Emission of scent volatiles by flowers is important for successful pollination and consequently, reproduction. Petunia (Petunia hybrida) floral scent is formed mainly by volatile products of the phenylpropanoid pathway. We identified and characterized a regulator of petunia scent production: the GRAS protein PHENYLPROPANOID EMISSION-REGULATING SCARECROW-LIKE (PES). Its expression increased in petals during bud development and was highest in open flowers. Overexpression of PES increased the production of floral volatiles, while its suppression resulted in scent reduction. We showed that PES upregulates the expression of genes encoding enzymes of the phenylpropanoid and shikimate pathways in petals, and of the core regulator of volatile biosynthesis ODORANT1 by activating its promoter. PES is an ortholog of Arabidopsis (Arabidopsis thaliana) PHYTOCHROME A SIGNAL TRANSDUCTION 1, involved in physiological responses to far-red (FR) light. Analyses of the effect of nonphotosynthetic irradiation (low-intensity FR light) on petunia floral volatiles revealed FR light as a scent-activating factor. While PHYTOCHROME A regulated scent-related gene expression and floral scent production under FR light, the influence of PES on volatile production was not limited by FR light conditions.
Collapse
Affiliation(s)
- Ekaterina Shor
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Jasmin Ravid
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Elad Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Oded Skaliter
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Tania Masci
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Alexander Vainstein
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| |
Collapse
|
29
|
Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 2023; 186:2313-2328.e15. [PMID: 37146612 DOI: 10.1016/j.cell.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
Collapse
Affiliation(s)
- Yaoyao Wu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Dawei Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Hu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Hongbo Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, Denmark
| | - Shaoqun Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xinyan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhigui Bao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Yu Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; School of Agriculture, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yao Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100094, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Edeline Gagnon
- Technische Universität München, TUM School of Life Sciences, Emil-Ramann-Strasse 2, 85354 Freising, Germany
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chunzhi Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Thomas Städler
- Institute of Integrative Biology and Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Ithaca, NY 14853, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| |
Collapse
|
30
|
Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. Plant Physiol 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
Collapse
Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
31
|
Hartig N, Seibt KM, Heitkam T. How to start a LINE: 5' switching rejuvenates LINE retrotransposons in tobacco and related Nicotiana species. Plant J 2023. [PMID: 36965091 DOI: 10.1111/tpj.16208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
By contrast to their conserved mammalian counterparts, plant long interspersed nuclear elements (LINEs) are highly variable, splitting into many low-copy families. Curiously, LINE families from the retrotransposable element (RTE) clade retain a stronger sequence conservation and hence reach higher copy numbers. The cause of this RTE-typical property is not yet understood, but would help clarify why some transposable elements are removed quickly, whereas others persist in plant genomes. Here, we bring forward a detailed study of RTE LINE structure, diversity and evolution in plants. For this, we argue that the nightshade family is the ideal taxon to follow the evolutionary trajectories of RTE LINEs, given their high abundance, recent activity and partnership to non-autonomous elements. Using bioinformatic, cytogenetic and molecular approaches, we detect 4029 full-length RTE LINEs across the Solanaceae. We finely characterize and manually curate a core group of 458 full-length LINEs in allotetraploid tobacco, show an integration event after polyploidization and trace hybridization by RTE LINE composition of parental genomes. Finally, we reveal the role of the untranslated regions (UTRs) as causes for the unique RTE LINE amplification and evolution pattern in plants. On the one hand, we detected a highly conserved motif at the 3' UTR, suggesting strong selective constraints acting on the RTE terminus. On the other hand, we observed successive rounds of 5' UTR cycling, constantly rejuvenating the promoter sequences. This interplay between exchangeable promoters and conserved LINE bodies and 3' UTR likely allows RTE LINEs to persist and thrive in plant genomes.
Collapse
Affiliation(s)
- Nora Hartig
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Tony Heitkam
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| |
Collapse
|
32
|
Huang J, Xu W, Zhai J, Hu Y, Guo J, Zhang C, Zhao Y, Zhang L, Martine C, Ma H, Huang CH. Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants. Plant Commun 2023:100595. [PMID: 36966360 PMCID: PMC10363554 DOI: 10.1016/j.xplc.2023.100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.
Collapse
Affiliation(s)
- Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
33
|
Strazzer P, Verbree B, Bliek M, Koes R, Quattrocchio FM. The Amsterdam petunia germplasm collection: A tool in plant science. Front Plant Sci 2023; 14:1129724. [PMID: 37025133 PMCID: PMC10070740 DOI: 10.3389/fpls.2023.1129724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Petunia hybrida is a plant model system used by many researchers to investigate a broad range of biological questions. One of the reasons for the success of this organism as a lab model is the existence of numerous mutants, involved in a wide range of processes, and the ever-increasing size of this collection owing to a highly active and efficient transposon system. We report here on the origin of petunia-based research and describe the collection of petunia lines housed in the University of Amsterdam, where many of the existing genotypes are maintained.
Collapse
|
34
|
Binaghi M, Esfeld K, Mandel T, Freitas LB, Roesti M, Kuhlemeier C. Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species. BMC Biol 2023; 21:58. [PMID: 36941631 PMCID: PMC10029178 DOI: 10.1186/s12915-023-01561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. RESULTS Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. CONCLUSIONS Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype-phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection.
Collapse
Affiliation(s)
- Marta Binaghi
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland.
| |
Collapse
|
35
|
Zhang F, Qiu F, Zeng J, Xu Z, Tang Y, Zhao T, Gou Y, Su F, Wang S, Sun X, Xue Z, Wang W, Yang C, Zeng L, Lan X, Chen M, Zhou J, Liao Z. Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family. Nat Commun 2023; 14:1446. [PMID: 36922496 PMCID: PMC10017790 DOI: 10.1038/s41467-023-37133-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
Tropane alkaloids (TAs) are widely distributed in the Solanaceae, while some important medicinal tropane alkaloids (mTAs), such as hyoscyamine and scopolamine, are restricted to certain species/tribes in this family. Little is known about the genomic basis and evolution of TAs biosynthesis and specialization in the Solanaceae. Here, we present chromosome-level genomes of two representative mTAs-producing species: Atropa belladonna and Datura stramonium. Our results reveal that the two species employ a conserved biosynthetic pathway to produce mTAs despite being distantly related within the nightshade family. A conserved gene cluster combined with gene duplication underlies the wide distribution of TAs in this family. We also provide evidence that branching genes leading to mTAs likely have evolved in early ancestral Solanaceae species but have been lost in most of the lineages, with A. belladonna and D. stramonium being exceptions. Furthermore, we identify a cytochrome P450 that modifies hyoscyamine into norhyoscyamine. Our results provide a genomic basis for evolutionary insights into the biosynthesis of TAs in the Solanaceae and will be useful for biotechnological production of mTAs via synthetic biology approaches.
Collapse
Affiliation(s)
- Fangyuan Zhang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Fei Qiu
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Junlan Zeng
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Zhichao Xu
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Yueli Tang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Tengfei Zhao
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Yuqin Gou
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Fei Su
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Shiyi Wang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Xiuli Sun
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Zheyong Xue
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunxian Yang
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Lingjiang Zeng
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China.,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, Tibetan Collaborative Innovation Centre of Agricultural and Animal Husbandry Resources, Xizang Agricultural and Animal Husbandry College, Nyingchi, Tibet, 860000, China
| | - Min Chen
- College of Pharmaceutical Sciences, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Ministry of Education), Southwest University, Chongqing, 400715, China
| | - Junhui Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhihua Liao
- State Key Laboratory of Silkworm Genome Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China. .,Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
36
|
Kurotani KI, Hirakawa H, Shirasawa K, Tanizawa Y, Nakamura Y, Isobe S, Notaguchi M. Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms. Plant Cell Physiol 2023; 64:248-257. [PMID: 36755428 PMCID: PMC9977260 DOI: 10.1093/pcp/pcac168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/28/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant-microbe interactions. In terms of plant-plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.
Collapse
Affiliation(s)
- Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Yasuhiro Tanizawa
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Yasukazu Nakamura
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Sachiko Isobe
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
| | - Michitaka Notaguchi
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
| |
Collapse
|
37
|
Li G, Serek M, Gehl C. Physiological changes besides the enhancement of pigmentation in Petunia hybrida caused by overexpression of PhAN2, an R2R3-MYB transcription factor. Plant Cell Rep 2023; 42:609-627. [PMID: 36690873 DOI: 10.1007/s00299-023-02983-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Ectopic expression of PhAN2 in vegetative tissue can improve regeneration and adventitious rooting but inhibit axillary bud outgrowth of petunia, while overexpression specifically in flowers could shorten longevity. Anthocyanin 2 has been only treated as a critical positive regulation factor of anthocyanin biosynthesis in petunia flowers. To determine if this gene had other functions in plant growth, we overexpressed this gene in an an2 mutant petunia cultivar driven by promoters with different strengths or tissue specificity. Various physiological processes of transformants in different growth stages and environments were analyzed. Besides the expected pigmentation improvement in different tissues, the results also showed that ectopic expression of AN2 could improve the regeneration skill but inhibit the axillary bud germination of in vitro plants. Moreover, the rooting ability of shoot tips of transformants was significantly improved, while some transgenic lines' flower longevity was shortened. Gene expression analysis showed that the transcripts level of AN2, partner genes anthocyanin 1 (AN1), anthocyanin 11 (AN11), and target gene dihydroflavonol 4-reductase (DFR) was altered in the different transgenic lines. In addition, ethylene biosynthesis-related genes 1-aminocyclopropane-1-carboxylic acid synthase (ACS1) and ACC oxidase (ACO1) were upregulated in rooting and flower senescence processes but at different time points. Overall, our data demonstrate that the critical role of this AN2 gene in plant growth physiology may extend beyond that of a single activator of anthocyanin biosynthesis.
Collapse
Affiliation(s)
- Guo Li
- Faculty of Natural Sciences, Institute of Horticultural Production Systems, Floriculture, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Margrethe Serek
- Faculty of Natural Sciences, Institute of Horticultural Production Systems, Floriculture, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Christian Gehl
- Faculty of Natural Sciences, Institute of Horticultural Production Systems, Floriculture, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| |
Collapse
|
38
|
Sun L, Cao S, Zheng N, Kao TH. Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots. Plant Cell 2023; 35:673-699. [PMID: 36478090 PMCID: PMC9940881 DOI: 10.1093/plcell/koac357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1-Cullin1-F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.
Collapse
Affiliation(s)
- Linhan Sun
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shiyun Cao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Teh-hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
39
|
Tomaszewska P, Vorontsova MS, Renvoize SA, Ficinski SZ, Tohme J, Schwarzacher T, Castiblanco V, de Vega JJ, Mitchell RAC, Heslop-Harrison JS(P. Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species. Ann Bot 2023; 131:87-108. [PMID: 34874999 PMCID: PMC9904353 DOI: 10.1093/aob/mcab147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/06/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. METHODS Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. KEY RESULTS Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. CONCLUSIONS We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.
Collapse
Affiliation(s)
| | | | | | | | - Joseph Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | - J S (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
40
|
Heslop-Harrison JS(P, Schwarzacher T, Liu Q. Polyploidy: its consequences and enabling role in plant diversification and evolution. Ann Bot 2023; 131:1-10. [PMID: 36282971 PMCID: PMC9904344 DOI: 10.1093/aob/mcac132] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. SCOPE World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. CONCLUSION Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
Collapse
Affiliation(s)
- J S (Pat) Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | |
Collapse
|
41
|
Choi JW, Choi HH, Park YS, Jang MJ, Kim S. Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae. BMC Plant Biol 2023; 23:48. [PMID: 36683040 PMCID: PMC9869560 DOI: 10.1186/s12870-022-04017-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking. RESULTS Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups. CONCLUSIONS Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.
Collapse
Affiliation(s)
- Jin-Wook Choi
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Hyeon Ho Choi
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Young-Soo Park
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
| |
Collapse
|
42
|
Liao P, Maoz I, Shih ML, Lee JH, Huang XQ, Morgan JA, Dudareva N. Emission of floral volatiles is facilitated by cell-wall non-specific lipid transfer proteins. Nat Commun 2023; 14:330. [PMID: 36658137 DOI: 10.1038/s41467-023-36027-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
For volatile organic compounds (VOCs) to be released from the plant cell into the atmosphere, they have to cross the plasma membrane, the cell wall, and the cuticle. However, how these hydrophobic compounds cross the hydrophilic cell wall is largely unknown. Using biochemical and reverse-genetic approaches combined with mathematical simulation, we show that cell-wall localized non-specific lipid transfer proteins (nsLTPs) facilitate VOC emission. Out of three highly expressed nsLTPs in petunia petals, which emit high levels of phenylpropanoid/benzenoid compounds, only PhnsLTP3 contributes to the VOC export across the cell wall to the cuticle. A decrease in PhnsLTP3 expression reduces volatile emission and leads to VOC redistribution with less VOCs reaching the cuticle without affecting their total pools. This intracellular build-up of VOCs lowers their biosynthesis by feedback downregulation of phenylalanine precursor supply to prevent self-intoxication. Overall, these results demonstrate that nsLTPs are intrinsic members of the VOC emission network, which facilitate VOC diffusion across the cell wall.
Collapse
|
43
|
He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. Plant Cell 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
Collapse
Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
44
|
Jin C, Dong L, Wei C, Wani MA, Yang C, Li S, Li F. Creating novel ornamentals via new strategies in the era of genome editing. Front Plant Sci 2023; 14:1142866. [PMID: 37123857 PMCID: PMC10140431 DOI: 10.3389/fpls.2023.1142866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Ornamental breeding has traditionally focused on improving novelty, yield, quality, and resistance to biotic or abiotic stress. However, achieving these goals has often required laborious crossbreeding, while precise breeding techniques have been underutilized. Fortunately, recent advancements in plant genome sequencing and editing technology have opened up exciting new frontiers for revolutionizing ornamental breeding. In this review, we provide an overview of the current state of ornamental transgenic breeding and propose four promising breeding strategies that have already proven successful in crop breeding and could be adapted for ornamental breeding with the help of genome editing. These strategies include recombination manipulation, haploid inducer creation, clonal seed production, and reverse breeding. We also discuss in detail the research progress, application status, and feasibility of each of these tactics.
Collapse
Affiliation(s)
- Chunlian Jin
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Liqing Dong
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Chang Wei
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Muneeb Ahmad Wani
- Department of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Chunmei Yang
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Shenchong Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
| | - Fan Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
| |
Collapse
|
45
|
Conant GC. POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics. Methods Mol Biol 2023; 2545:77-90. [PMID: 36720808 DOI: 10.1007/978-1-0716-2561-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Thirteen years ago, we described an evolutionary modeling tool that could resolve the orthology relationships among the homologous genomic regions created by a whole-genome duplication. This tool, which we subsequently named POInT (the Polyploid Orthology Inference Tool), was originally only useful for studying a genome duplication known from bakers' yeast and its relatives. Now, with hundreds of genome sequences that contain the relicts of ancient polyploidy available, POInT can be used to study dozens of different polyploidies, asking both questions about the history of individual events and about the commonalities and differences seen between those events. In this chapter, I give a brief history of the development of POInT as an illustration of the interconnected nature of computational biology research. I then further describe how POInT operates and some of the strengths and drawbacks of its structure. I close with a few examples of discoveries we have made using it.
Collapse
Affiliation(s)
- Gavin C Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
- Program in Genetics, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
46
|
Rezaei H, Mirzaie-Asl A, Abdollahi MR, Tohidfar M. Comparative analysis of different artificial neural networks for predicting and optimizing in vitro seed germination and sterilization of petunia. PLoS One 2023; 18:e0285657. [PMID: 37167278 PMCID: PMC10174541 DOI: 10.1371/journal.pone.0285657] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
The process of optimizing in vitro seed sterilization and germination is a complicated task since this process is influenced by interactions of many factors (e.g., genotype, disinfectants, pH of the media, temperature, light, immersion time). This study investigated the role of various types and concentrations of disinfectants (i.e., NaOCl, Ca(ClO)2, HgCl2, H2O2, NWCN-Fe, MWCNT) as well as immersion time in successful in vitro seed sterilization and germination of petunia. Also, the utility of three artificial neural networks (ANNs) (e.g., multilayer perceptron (MLP), radial basis function (RBF), and generalized regression neural network (GRNN)) as modeling tools were evaluated to analyze the effect of disinfectants and immersion time on in vitro seed sterilization and germination. Moreover, non‑dominated sorting genetic algorithm‑II (NSGA‑II) was employed for optimizing the selected prediction model. The GRNN algorithm displayed superior predictive accuracy in comparison to MLP and RBF models. Also, the results showed that NSGA‑II can be considered as a reliable multi-objective optimization algorithm for finding the optimal level of disinfectants and immersion time to simultaneously minimize contamination rate and maximize germination percentage. Generally, GRNN-NSGA-II as an up-to-date and reliable computational tool can be applied in future plant in vitro culture studies.
Collapse
Affiliation(s)
- Hamed Rezaei
- Department of Plant Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Asghar Mirzaie-Asl
- Department of Plant Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Reza Abdollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran
| |
Collapse
|
47
|
Chen L, Xia B, Li Z, Liu X, Bai Y, Yang Y, Gao W, Meng Q, Xu N, Sun Y, Li Q, Yue L, He M, Zhou Y. Syringa oblata genome provides new insights into molecular mechanism of flower color differences among individuals and biosynthesis of its flower volatiles. Front Plant Sci 2022; 13:1078677. [PMID: 36618636 PMCID: PMC9811319 DOI: 10.3389/fpls.2022.1078677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Syringa oblata is a high ornamental value tree owing to its elegant colors, unique aromas and wide adaptability, however, studies on the molecular mechanism underlying the formation of its ornamental traits are still lacking. Here, we presented a chromosome-scale genome assembly of S. oblata and the final genome size was 1.11 Gb with a contig N50 of 4.75 Mb, anchored on 23 chromosomes and was a better reference for S. oblata transcriptome assembly. Further by integrating transcriptomic and metabolic data, it was concluded that F3H, F3'H, 4CL and PAL, especially the F3'H, were important candidates involved in the formation of floral color differences among S. oblata individuals. Genome-wide identification and analysis revealed that the TPS-b subfamily was the most abundant subfamily of TPS family in S. oblata, which together with the CYP76 family genes determined the formation of the major floral volatiles of S. oblata. Overall, our results provide an important reference for mechanistic studies on the main ornamental traits and molecular breeding in S. oblata.
Collapse
Affiliation(s)
- Lifei Chen
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Xiaowei Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yun Bai
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Wenjie Gao
- School of Ecological Technology and Engineering, Shanghai Institute of Technology University, Shanghai, China
| | - Qingran Meng
- School of Perfume and Aroma Technology, Shanghai Institute of Technology University, Shanghai, China
| | - Ning Xu
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Sun
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Qiang Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Liran Yue
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Changchun, China
| |
Collapse
|
48
|
Beltrame LC, Thompson CE, Freitas LB. Molecular evolution and structural analyses of proteins involved in metabolic pathways of volatile organic compounds in Petunia hybrida (Solanaceae). Genet Mol Biol 2022; 46:e20220114. [PMID: 36534952 PMCID: PMC9762610 DOI: 10.1590/1678-4685-gmb-2022-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
The association between plants and their pollinators is essential for increasing the diversity in angiosperms. Morphological and physiological traits, mainly floral scent, can influence the pollination dynamics and select pollinators for each plant species. In this work, we studied two proteins involved in producing volatile organic compounds in plants, conyferyl alcohol acyltransferase (CFAT) and benzoyl-CoA:benzyl alcohol/phenyl ethanol benzoyl transferase (BPBT) genes. We aimed to understand these proteins with respect to evolutionary and structural aspects and functions in Solanaceae using phylogenetic methods and comparative molecular modeling. We used Bayesian inference to describe the proteins' evolutionary history using Petunia x hybrida as a query to search for homologs in the Solanaceae family. Theoretical 3D models were obtained for both proteins using Panicum virgatum as a template. The phylogenetic tree included several different enzymes with diverse biological roles in Solanaceae, displaying the transferase domain. We identified only one sequence of CFAT in the databases, which belongs to Petunia x hybrida, and found several BPBT sequences from the genera Nicotiana, Solanum, and Capsicum. The 3D structures of CFAT and BPBT have two different domains, and we have identified the amino acid residues essential for the enzymatic activity and interaction with substrates.
Collapse
Affiliation(s)
- Lucas C. Beltrame
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Claudia E. Thompson
- Universidade Federal de Ciências da Saúde de Porto Alegre, Departamento de Farmacociências, Porto Alegre, RS, Brazil
| | - Loreta B. Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| |
Collapse
|
49
|
Vassilieff H, Haddad S, Jamilloux V, Choisne N, Sharma V, Giraud D, Wan M, Serfraz S, Geering ADW, Teycheney PY, Maumus F. CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mob DNA 2022; 13:31. [PMID: 36463202 PMCID: PMC9719215 DOI: 10.1186/s13100-022-00288-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.
Collapse
Affiliation(s)
- Héléna Vassilieff
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Sana Haddad
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.460789.40000 0004 4910 6535Present Address: Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Véronique Jamilloux
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.507621.7Present Address: Université Paris-Saclay, INRAE, PROSE, 92160 Antony, France
| | - Nathalie Choisne
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Vikas Sharma
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France ,grid.8385.60000 0001 2297 375XPresent Address: Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Delphine Giraud
- UMR AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, 20230 San Giuliano, France
| | - Mariène Wan
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Saad Serfraz
- grid.413016.10000 0004 0607 1563CABB, University of Agriculture Faisalabad, Faisalabad, 38000 Pakistan
| | - Andrew D. W. Geering
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 Australia
| | | | - Florian Maumus
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| |
Collapse
|
50
|
Chen D, Zhang T, Chen Y, Ma H, Qi J. Tree2GD: a phylogenomic method to detect large-scale gene duplication events. Bioinformatics 2022; 38:5317-5321. [PMID: 36218394 DOI: 10.1093/bioinformatics/btac669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/11/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy. RESULTS Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications. AVAILABILITY AND IMPLEMENTATION Tree2GD is written in Python and C++ and is available at https://github.com/Dee-chen/Tree2gd. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Duoyuan Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hong Ma
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| |
Collapse
|