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Shi T, Zhou L, Ye Y, Yang X, Wang L, Yue Y. Characterization of YABBY transcription factors in Osmanthus fragrans and functional analysis of OfYABBY12 in floral scent formation and leaf morphology. BMC PLANT BIOLOGY 2024; 24:589. [PMID: 38902627 PMCID: PMC11191298 DOI: 10.1186/s12870-024-05047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/19/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND The plant-specific YABBY transcription factor family plays important roles in plant growth and development, particularly leaf growth, floral organ formation, and secondary metabolite synthesis. RESULTS Here, we identified a total of 13 OfYABBY genes from the Osmanthus fragrans genome. These 13 OfYABBY genes were divided into five subfamilies through phylogenetic analysis, and genes in the same subfamily showed similar gene structures and conserved protein motifs. Gene duplication promoted the expansion of the OfYABBY family in O. fragrans. Tissue-specific expression analysis showed that the OfYABBY family was mainly expressed in O. fragrans leaves and floral organs. To better understand the role of OfYABBY genes in plant growth and development, OfYABBY12 was selected for heterologous stable overexpression in tobacco, and OfYABBY12-overexpressing tobacco leaves released significantly fewer volatile organic compounds than wild-type tobacco leaves. Overexpression of OfYABBY12 led to the downregulation of NtCCD1/4 and decreased β-ionone biosynthesis. Correspondingly, a dual-luciferase assay showed that OfYABBY12 negatively regulated the expression of OfCCD4, which promotes β-ionone synthesis. Furthermore, tobacco leaves overexpressing OfYABBY12 were curled and wrinkled and had significantly reduced leaf thickness and leaf inclusions and significantly extended flower pistils (styles). CONCLUSION Overall, the results suggest that the OfYABBY gene family may influence the biosynthesis of the floral scent (especially β-ionone) in O. fragrans and may regulate leaf morphogenesis and lateral organs.
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Affiliation(s)
- Tingting Shi
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Ling Zhou
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Yunfang Ye
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiulian Yang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Lianggui Wang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yuanzheng Yue
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu Province, 210037, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
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Qiu H, Chen Y, Fu J, Zhang C. Expression of ethylene biosynthetic genes during flower senescence and in response to ethephon and silver nitrate treatments in Osmanthus fragrans. Genes Genomics 2024; 46:399-408. [PMID: 38319456 DOI: 10.1007/s13258-023-01489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Sweet osmanthus (Osmanthus fragrans) is an ornamental evergreen tree species in China, whose flowers are sensitive to ethylene. The synthesis of ethylene is controlled by key enzymes and restriction enzymes, 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), which are encoded by multigene families. However, the key synthase responsible for ethylene regulation in O. fragrans is still unknown. OBJECTIVE This study aims to screen the key ethylene synthase genes of sweet osmanthus flowers in response to ethylene regulation. METHODS In this study, we used the ACO and ACS sequences of Arabidopsis thaliana to search for homologous genes in the O. fragrans petal transcriptome database. These genes were also analyzed bioinformatically. Finally, the expression levels of O. fragrans were compared before and after senescence, as well as after ethephon and silver nitrate treatments. RESULTS The results showed that there are five ACO genes and one ACS gene in O. fragrans transcriptome database, and the phylogenetic tree revealed that the proteins encoded by these genes had high homology to the ACS and ACO proteins in plants. Sequence alignment shows that the OfACO1-5 proteins have the 2OG-Fe(II) oxygenase domain, while OfACS1 contains seven conserved domains, as well as conserved amino acids in transaminases and glutamate residues related to substrate specificity. Expression analysis revealed that the expression levels of OfACS1 and OfACO1-5 were significantly higher at the early senescence stage compared to the full flowering stage. The transcripts of the OfACS1, OfACO2, and OfACO5 genes were upregulated by treatment with ethephon. However, out of these three genes, only OfACO2 was significantly downregulated by treatment with AgNO3. CONCLUSION Our study found that OfACO2 is an important synthase gene in response to ethylene regulation in sweet osmanthus, which would provide valuable data for further investigation into the mechanisms of ethylene-induced senescence in sweet osmanthus flowers.
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Affiliation(s)
- Hui Qiu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Yiwen Chen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Jianxin Fu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
| | - Chao Zhang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
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Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA. High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 2024; 7:54. [PMID: 38184717 PMCID: PMC10771460 DOI: 10.1038/s42003-023-05748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
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Affiliation(s)
- Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
| | - Crystal Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Nathan Backenstose
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Trevor Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
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Zhang H, Li Z, Wang M, Yang Y, Wang Y, Nie Q, Liang F, Qin H, Zhang Z. The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants. Int J Biol Macromol 2023; 253:127132. [PMID: 37778585 DOI: 10.1016/j.ijbiomac.2023.127132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.
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Affiliation(s)
- Hua Zhang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China.
| | - Zhiqi Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China
| | - Maoliang Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yipeng Yang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yongge Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Qiufeng Nie
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Fang Liang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Helan Qin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China; Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China.
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Ren J, Li W, Guo Z, Ma Z, Wan D, Lu S, Guo L, Gou H, Chen B, Mao J. Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious). BMC PLANT BIOLOGY 2023; 23:607. [PMID: 38030998 PMCID: PMC10688089 DOI: 10.1186/s12870-023-04631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4). RESULTS The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. CONCLUSIONS Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.
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Affiliation(s)
- Jiaxuan Ren
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zhigang Guo
- Tianshui Normal University, Tianshui, 741001, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Dongshi Wan
- College of Ecology, Lanzhou University, Lanzhou, 730000, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Lan Y, Zhang K, Wang L, Liang X, Liu H, Zhang X, Jiang N, Wu M, Yan H, Xiang Y. The R2R3-MYB transcription factor OfMYB21 positively regulates linalool biosynthesis in Osmanthus fragrans flowers. Int J Biol Macromol 2023; 249:126099. [PMID: 37543267 DOI: 10.1016/j.ijbiomac.2023.126099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/02/2023] [Accepted: 07/22/2023] [Indexed: 08/07/2023]
Abstract
Osmanthus fragrans is a well-known landscape ornamental tree species for its pleasing floral fragrance and abundance of flowers. Linalool, the core floral volatiles of O. fragrans, has tremendous economic value in the pharmaceuticals, cleaning products and cosmetics industries. However, the transcriptional regulatory network for the biosynthesis of linalool in O. fragrans remains unclear. Here, OfMYB21, a potential transcription factor regulating the linalool synthetase OfTPS2, was identified using RNA-seq data and qRT-PCR analysis. Yeast one-hybrid, dual-luciferase and EMSA showed that OfMYB21 directly binds to the promoter of OfTPS2 and activates its expression. Overexpression of OfMYB21 in the petals of O. fragrans led to up-regulation of OfTPS2 and increased accumulation of linalool, while silencing of OfMYB21 led to down-regulation of OfTPS2 and decreased biosynthesis of linalool. Subsequently, yeast two-hybrid, pull-down and BiFC experiments showed that OfMYB21 interacts with JA signaling factors OfJAZ2/3 and OfMYC2. Interestingly, the interaction between OfMYC2 and OfMYB21 further enhanced the transcription of OfTPS2, whereas OfJAZ3 attenuated this effect. Overall, our studies provided novel finding on the regulatory mechanisms responsible for the biosynthesis of the volatile monoterpenoid linalool in O. fragrans.
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Affiliation(s)
- Yangang Lan
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Kaimei Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Linna Wang
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyu Liang
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Honxia Liu
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyue Zhang
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Nianqin Jiang
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Min Wu
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Hanwei Yan
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Yan Xiang
- Laboratory of Tree Genetics and Molecular Breeding, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
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Xu X, Chen B, Zhang J, Lan S, Wu S. Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides. PeerJ 2023; 11:e16056. [PMID: 37744244 PMCID: PMC10512932 DOI: 10.7717/peerj.16056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.
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Affiliation(s)
- Xinyu Xu
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Bihua Chen
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
| | - Juan Zhang
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
| | - Siren Lan
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shasha Wu
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Wang Z, Farooq TH, He H, Shahani AAA, Hameed R, Fayyaz A, Yousaf MS, Wang J, Chen L. Cloning and functional analysis of the DXR gene and promoter region in Osmanthus fragrans var. semperflorens. Funct Integr Genomics 2023; 23:277. [PMID: 37603091 DOI: 10.1007/s10142-023-01214-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
The precise biological function and activity of the deoxylulose-5-phosphate reductoisomerase (DXR) gene and its promoter in Osmanthus fragrans var. semperflorens remain unclear, even though OfDXR is known as the crucial enzyme involved in plant terpenoid synthesis. This study aimed to shed light on the role and activity of the OfDXR gene and its promoter in O. fragrans var. semperflorens by employing RACE-PCR and Hi-TAIL-PCR techniques for the cloning of the gene and promoter sequence from the petal tissue. Subsequently, genetic transformation and histochemical staining methods were utilized to analyze their function and activity. The OfDXR gene exhibited a DNA sequence length of 5241 bp, encompassing 12 exons and 11 introns. The corresponding cDNA sequence of the OfDXR gene was 1629 bp, encoding 474 amino acid residues. Expression analysis revealed that the OfDXR gene was predominantly active in the petals during the early full blooming stage. Overexpression of the OfDXR gene in Arabidopsis plants at the primary or full blooming stage led to an augmentation in the total terpenoid content. Furthermore, the promoter sequence of the OfDXR gene spanned a length of 1174 bp and contained conserved regulatory/response elements, demonstrating functional activity. These findings indicate that the OfDXR gene plays a pivotal role in terpenoid synthesis, while its promoter exhibits robust activity.
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Affiliation(s)
- Zihan Wang
- College of Life Science and Technology, Central South University of Forestry and Technology, Hunan Changsha, 410004, China
| | - Taimoor Hassan Farooq
- College of Life Science and Technology, Central South University of Forestry and Technology, Hunan Changsha, 410004, China
- Bangor College China, a Joint Unit of Bangor University and Central South University of Forestry and Technology, Hunan Changsha, 410004, China
| | - Hanjie He
- College of Life Science and Technology, Central South University of Forestry and Technology, Hunan Changsha, 410004, China
| | - Aitzaz A A Shahani
- Key Laboratory of Crop Sciences and Plant Breeding Genetics, College of Agriculture, Yanbian University, Yanji, Jilin, China
| | - Rashida Hameed
- School of Environment and Safety Engineering, Institute of Environment and Ecology, Jiangsu University, Zhenjiang, China
| | - Amna Fayyaz
- Department of Plant Pathology, University of Davis, Davis, USA
| | | | - Jun Wang
- College of Life Science and Technology, Central South University of Forestry and Technology, Hunan Changsha, 410004, China.
| | - Lili Chen
- College of Life Science and Technology, Central South University of Forestry and Technology, Hunan Changsha, 410004, China.
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Ding H, Yang Z, Zai Z, Feng K, Wang L, Yue Y, Yang X. Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2346. [PMID: 37375971 DOI: 10.3390/plants12122346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans.
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Affiliation(s)
- Huifen Ding
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhandong Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhouying Zai
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Keyi Feng
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Ma W, Guan X, Miao Y, Zhang L. Whole Genome Resequencing Revealed the Effect of Helicase yqhH Gene on Regulating Bacillus thuringiensis LLP29 against Ultraviolet Radiation Stress. Int J Mol Sci 2023; 24:ijms24065810. [PMID: 36982883 PMCID: PMC10054049 DOI: 10.3390/ijms24065810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Bacillus thuringiensis (Bt) is a widely used microbial pesticide. However, its duration of effectiveness is greatly shortened due to the irradiation of ultraviolet rays, which seriously hinders the application of Bt preparations. Therefore, it is of great importance to study the resistance mechanism of Bt to UV at the molecular level to improve the UV-resistance of Bt strains. In order to know the functional genes in the UV resistance, the genome of UV-induced mutant Bt LLP29-M19 was re-sequenced and compared with the original strain Bt LLP29. It was shown that there were 1318 SNPs, 31 InDels, and 206 SV between the mutant strain and the original strain Bt LLP29 after UV irradiation, which were then analyzed for gene annotation. Additionally, a mutated gene named yqhH, a member of helicase superfamily II, was detected as an important candidate. Then, yqhH was expressed and purified successfully. Through the result of the enzymatic activity in vitro, yqhH was found to have ATP hydrolase and helicase activities. In order to further verify its function, the yqhH gene was knocked out and complemented by homologous recombinant gene knockout technology. The survival rate of the knockout mutant strain Bt LLP29-ΔyqhH was significantly lower than that of the original strain Bt LLP29 and the back-complemented strain Bt LLP29-ΔyqhH-R after treated with UV. Meanwhile, the total helicase activity was not significantly different on whether Bt carried yqhH or not. All of these greatly enrich important molecular mechanisms of Bt when it is in UV stress.
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Affiliation(s)
- Weibo Ma
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiong Guan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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11
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Liu G, Li Y, Sun X, Guo X, Jiang N, Fang Y, Chen J, Bao Z, Ma F. Association study of SNP locus for color related traits in herbaceous peony ( Paeonia lactiflora Pall.) using SLAF-seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1032449. [PMID: 36544869 PMCID: PMC9760751 DOI: 10.3389/fpls.2022.1032449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs.
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Affiliation(s)
- Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Ying Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xia Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xianfeng Guo
- College of Forestry, Shandong Agricultural University, Tai-An, Shandong, China
| | - Nannan Jiang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Yifu Fang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Junqiang Chen
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
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12
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Osmanthus Fragrans Loaded NIPAAM Hydrogel Promotes Osteogenic Differentiation of MC3T3-E1. Gels 2022; 8:gels8100659. [PMID: 36286160 PMCID: PMC9601630 DOI: 10.3390/gels8100659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
There is an urgent need to find long-acting, natural osteogenesis-promoting drug systems. In this study, first the potential targets and mechanism of osmanthus fragrans (O. fragrans) extract in regulating osteogenic differentiation based on autophagy were analyzed by network pharmacology and molecular docking. Then, osmanthus fragrans was extracted using the ethanol reflux method and an osmanthus fragrans extract loaded Poly N-isopropylacrylamide (OF/NIPAAM) hydrogel was prepared by electron beam radiation. The chemical components of the osmanthus fragrans extract and the microstructure of OF/NIPAAM hydrogels were characterized by ultraviolet-visible spectrophotometry (UV-Vis) and X-ray diffraction (XRD), respectively. Mouse embryonic osteoblast precursor cells MC3T3-E1 were cultured with different concentrations of OF/NIPAAM hydrogel to discover cell proliferation activity by CCK-8 assay. Alkaline phosphatase (ALP) staining and alizarin red staining were used to observe the differentiation and calcification. Through experimental exploration, we found that a total of 11 targets were predicted, which are TP53, CASP3, SIRT1, etc., and osmanthus fragrans had good binding activity to TP53. In vitro, except for proliferation promotion, OF/NIPAAM hydrogel enhanced ALP activity and formation of mineralized nodules of MC3T3-E1 cells at a concentration equal to or less than 62.5 μg/mL (p < 0.05). The addition of autophagy inhibitor 3-methyladenine (3-MA) reduced ALP activity and mineralized nodule formation.
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13
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Zhang C, Zhang K, Chai Z, Song Y, Wang X, Duan Y, Zhang M. Identification of miRNAs and Target Genes at Key Stages of Sexual Differentiation in Androdioecious Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms231810386. [PMID: 36142310 PMCID: PMC9499476 DOI: 10.3390/ijms231810386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022] Open
Abstract
Androdioecy is the crucial transition state in the evolutionary direction of hermaphroditism to dioecy, however, the molecular mechanisms underlying the formation of this sex system remain unclear. While popular in China for its ornamental and cultural value, Osmanthus fragrans has an extremely rare androdioecy breeding system, meaning that there are both male and hermaphroditic plants in a population. To unravel the mechanisms underlying the formation of androdioecy, we performed small RNA sequencing studies on male and hermaphroditic O. fragrans. A total of 334 miRNAs were identified, of which 59 were differentially expressed. Functional categorization revealed that the target genes of differentially expressed miRNAs were mainly involved in the biological processes of reproductive development and the hormone signal transduction pathway. We speculated that the miRNA160, miRNA167, miRNA393 and miRNA396 families may influence the sex differentiation in O. fragrans. Overall, our study is the first exploration of miRNAs in the growth and development process of O. fragrans, and is also the first study of androdioecious plants from the miRNA sequencing perspective. The analysis of miRNAs and target genes that may be involved in the sex differentiation process lay a foundation for the ultimate discovery of the androdioecious molecular mechanism in O. fragrans.
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14
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Ma B, Wu J, Shi TL, Yang YY, Wang WB, Zheng Y, Su SC, Yao YC, Xue WB, Porth I, El-Kassaby YA, Leng PS, Hu ZH, Mao JF. Lilac (Syringa oblata) genome provides insights into its evolution and molecular mechanism of petal color change. Commun Biol 2022; 5:686. [PMID: 35810211 PMCID: PMC9271065 DOI: 10.1038/s42003-022-03646-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac. A high-quality genome assembly for the lilac (Syringa oblata) provides insight into the evolution of this shrub and potential mechanisms underlying petal color change.
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Affiliation(s)
- Bo Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun-Yao Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Wen-Bo Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Shu-Chai Su
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun-Cong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Wen-Bo Xue
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ping-Sheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
| | - Zeng-Hui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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15
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Zhu M, Bin J, Ding H, Pan D, Tian Q, Yang X, Wang L, Yue Y. Insights into the trihelix transcription factor responses to salt and other stresses in Osmanthus fragrans. BMC Genomics 2022; 23:334. [PMID: 35488201 PMCID: PMC9055724 DOI: 10.1186/s12864-022-08569-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Osmanthus fragrans is an evergreen plant with high ornamental and economic values. However, they are easily injured by salt stress, which severely limits their use in high salinity areas. The trihelix transcription factor (TF) family, as one of the earliest discovered TF families in plants, plays an essential part in responses to different abiotic stresses, and it has potential functions in improving the salt-tolerance capability of O. fragrans. RESULTS In this study, 56 trihelix genes (OfGTs) were first identified in O. fragrans and then divided into five subfamilies in accordance with a phylogenetic tree analysis. The OfGTs were found to be located randomly on the 20 O. fragrans chromosomes, and an analysis of gene replication events indicated that the OfGT gene family underwent strong purification selection during the evolutionary process. The analysis of conserved motifs and gene structures implied that the OfGT members in the same subfamily have similar conserved motifs and gene structures. A promoter cis-elements analysis showed that all the OfGT genes contained multiple abiotic and hormonal stress-related cis-elements. The RNA-seq data suggested that the OfGTs have specific expression patterns in different tissues, and some were induced by salt stress. The qRT-PCR analysis of 12 selected OfGTs confirmed that OfGT1/3/21/33/42/45/46/52 were induced, with OfGT3/42/46 being the most highly expressed. In addition, OfGT42/OfGT46 had a co-expression pattern under salt-stress conditions. OfGT3/42/46 were mainly localized in the nuclei and exhibited no transcriptional activities based on the analysis of the subcellular localization and transcriptional activity assay. Furthermore, the expression levels of most of the selected OfGTs were induced by multiple abiotic and hormonal stresses, and the expression patterns of some OfGTs were also highly correlated with gibberellic acid and methyl jasmonate levels. Remarkably, the transient transformation results showed lower MDA content and increased expression of ROS-related genes NbAPX in transgenic plants, which implying OfGT3/42/46 may improve the salt tolerance of tobacco. CONCLUSIONS The results implied that the OfGT genes were related to abiotic and hormonal stress responses in O. fragrans, and that the OfGT3/42/46 genes in particular might play crucial roles in responses to salt stress. This study made a comprehensive summary of the OfGT gene family, including functions and co-expression patterns in response to salt and other stresses, as well as an evolutionary perspective. Consequently, it lays a foundation for further functional characterizations of these genes.
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Affiliation(s)
- Meilin Zhu
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Jing Bin
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Huifen Ding
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Duo Pan
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Qingyin Tian
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
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16
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Han Y, Lu M, Yue S, Li K, Dong M, Liu L, Wang H, Shang F. Comparative methylomics and chromatin accessibility analysis in Osmanthus fragrans uncovers regulation of genic transcription and mechanisms of key floral scent production. HORTICULTURE RESEARCH 2022; 9:uhac096. [PMID: 35795393 PMCID: PMC9250655 DOI: 10.1093/hr/uhac096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/07/2022] [Indexed: 06/12/2023]
Abstract
Linalool and ionone are two important aromatic components in sweet osmanthus petals, and the regulatory mechanisms that produce these two components remain unclear. In this study, we employed whole-genome methylation sequencing and ATAC-seq technology to analyze the genomic DNA methylation status and chromatin accessibility of the sweet osmanthus cultivars 'Zaohuang' and 'Chenghong Dangui'. Results showed that the promoter region of TPS2, a key gene in the linalool synthesis pathway, was less methylated in 'Chenghong Dangui' than in 'Zaohuang'. The chromatin was more accessible in 'Chenghong Dangui' than in 'Zaohuang', which resulted in a much stronger expression of this gene in 'Chenghong Dangui' than in 'Zaohuang'. This eventually led to a high quantity of linalool and its oxides in the petals of 'Chenghong Dangui', but there were lower levels present in the petals of 'Zaohuang'. These results suggest that DNA methylation and chromatin accessibility play major roles in linalool synthesis in sweet osmanthus. The methylation level of the promoter region of CCD4, a key gene for ionone synthesis, was higher in 'Zaohuang' than in 'Chenghong Dangui'. The chromatin accessibility was lower in 'Zaohuang' than in 'Chenghong Dangui', although the expression of this gene was significantly higher in 'Zaohuang' than in 'Chenghong Dangui'. ChIP-seq analysis and a series of experiments showed that the differential expression of CCD4 and CCD1 in the two cultivars may predominantly be the result of regulation by ERF2 and other transcription factors. However, a 183-bp deletion involving the CCD4 promoter region in 'Chenghong Dangui' may be the main reason for the low expression of this gene in its petals. This study provides an important theoretical basis for improving selective breeding of key floral fragrance components in sweet osmanthus.
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Affiliation(s)
| | - Miaomiao Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shumin Yue
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Ke Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Meifang Dong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Luxian Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Hongyun Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
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17
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Zhou Y, Yin M, Abbas F, Sun Y, Gao T, Yan F, Li X, Yu Y, Yue Y, Yu R, Fan Y. Classification and Association Analysis of Gerbera ( Gerbera hybrida) Flower Color Traits. FRONTIERS IN PLANT SCIENCE 2022; 12:779288. [PMID: 35145530 PMCID: PMC8824200 DOI: 10.3389/fpls.2021.779288] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/31/2021] [Indexed: 05/17/2023]
Abstract
Floral color plays a crucial role in plant life such as plant-pollinator interactions and modifying the abiotic environment of reproductive structures. In the current study, 123 gerbera accessions were divided into six color groups (white, yellow, orange, pink, red, and purple), based on Royal Horticultural Society Color Chart calibration and colorimeter measurement. Partial least squares discriminant analysis showed that the white group was mainly affected by L* value, a* value, C value, and total anthocyanin contents, while the yellow group was positively correlated with L* value, b* value, and total anthocyanin contents. Similarly, the orange group was mainly affected by b* value and total carotenoid contents, whereas the pink group was positively correlated with L* and h values. Furthermore, the red group was affected by L* value, a* value, C value, and total anthocyanin contents, whilst the purple group was mainly distributed by L* value, a* value, b* value, and total anthocyanin contents. Based on 'Jin Xiang' transcriptome data, 14,106 expressed sequence tag (EST)-SSR markers were identified and 48 pairs of primers (19 newly developed primers) were screened. Population genetic structure, neighbor-joining clustering, and principal coordinate analysis showed that 123 gerbera accessions could be divided into two groups. EST-SSR-based association analysis showed that 1, 1, 2, 1, 1, 2, and 1 significant loci were related to L*, a*, b*, C, and h, total carotenoid, and total anthocyanin contents, respectively. These results provide an important reference for flower color classification and genetic improvement of gerbera.
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Affiliation(s)
- Yiwei Zhou
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Mao Yin
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yue Sun
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting Gao
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Fulong Yan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xinyue Li
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yunyi Yu
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yuechong Yue
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
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18
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Zeng Z, Chen S, Xu M, Wang M, Chen Z, Wang L, Pang J. Cloning, Expression, and Tobacco Overexpression Analyses of a PISTILLATA/ GLOBOSA-like ( OfGLO1) Gene from Osmanthus fragrans. Genes (Basel) 2021; 12:1748. [PMID: 34828354 PMCID: PMC8623234 DOI: 10.3390/genes12111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
GLOBOSA (GLO), a B-class MADS-box gene, is involved in floral organ determination but has rarely been studied in Osmanthus fragrans, which is a very popular ornamental tree species in China. Here, the full-length cDNA of a homologous GLO1 gene (named OfGLO1) was cloned from a flower bud of O. fragrans using the RACE technique. The OfGLO1 has a 645 bp open reading frame, encoding 214 amino acids. Similar to other PI/GLO proteins, OfGLO1 has two conserved domains, MADS MEF2-like and K-box, and a 16-amino-acid PI motif in the C terminal region. Our phylogeny analysis classified OfGLO1 as a PI-type member of the B-class MADS-box gene family. The qRT-PCR assay showed that the expression of OfGLO1 in O. fragrans was continuously upregulated from the tight bud stage to the full flowering stage but barely expressed in the pistils, sepals, and non-floral organs, such as root, leaf, and stem. The genetic effect of OfGLO1 was assayed by ectopic expression in tobacco plants. Compared with the wild-type, OfGLO1 transformants showed reduced plant size, earlier flowering, shorter stamens, and lower seed setting rates. Furthermore, some stamens were changed into petal-like structures. These findings indicate that OfGLO1 plays an important role in the regulation of flower development. This study improved our understanding of class B gene function in woody plants.
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Affiliation(s)
| | | | | | | | | | | | - Jiliang Pang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; (Z.Z.); (S.C.); (M.X.); (M.W.); (Z.C.); (L.W.)
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Zhou XJ, Li JT, Wang HL, Han JW, Zhang K, Dong SW, Zhang YZ, Ya HY, Cheng YW, Sun SS. The chromosome-scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense. Mol Ecol Resour 2021; 22:988-1001. [PMID: 34652864 DOI: 10.1111/1755-0998.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023]
Abstract
Rhododendron henanense subsp. lingbaoense (hereafter referred to as R. henanense) is an endemic species naturally distributed in the Henan province, China, with high horticultural, ornamental and medicinal value. Herein, we report a de novo genome assembly for R. henanense using a combination of PacBio long read and Illumina short read sequencing technologies. In total, we assembled 634.07 Mb with a contig N50 of 2.5 Mb, representing ~96.93% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of R. henanense genome were assembled, covering ~98.21% of the genome assembly. The genome was composed of ~65.76% repetitive sequences and 31,098 protein-coding genes, 88.77% of which could be functionally annotated. Rhododendron henanense displayed a high level of synteny with other Rhododendron species from the Hymenanthes subgenus. Our data also suggests that R. henanense genes related to stress responses have undergone expansion, which may underly the unique abiotic and biotic stress resistance of the species. This alpine Rhododendron chromosome-scale genome assembly provides fundamental molecular resources for germplasm conservation, breeding efforts, evolutionary studies, and elucidating the unique biological characteristics of R. henanense.
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Affiliation(s)
- Xiao-Jun Zhou
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Jian-Tao Li
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, China
| | - Hai-Liang Wang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Jun-Wang Han
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Kai Zhang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Shuai-Wei Dong
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Yan-Zhao Zhang
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Hui-Yuan Ya
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Yan-Wei Cheng
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Shan-Shan Sun
- Life Science College, Luoyang Normal University, Luoyang, China
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