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Fu R, Zhu Y, Liu Y, Yang Z, Lu R, Qiu Y, Lascoux M, Li P, Chen J. Shared xerophytic genes and their re-use in local adaptation to aridity in the desert plant Gymnocarpos przewalskii. Mol Ecol 2024; 33:e17380. [PMID: 38745400 DOI: 10.1111/mec.17380] [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: 08/22/2023] [Revised: 04/13/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
In order to thrive and survive, plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by parallel or convergent adaptation across species, and the latter by pronounced local adaptation among populations of the same species. In the present study, we generated a high-quality genome and re-sequenced 177 individuals for Gymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. We first focus on ancient adaptation to aridity at the molecular level by comparing the genomic data of 15 species that vary in their ability to withstand aridity. We found that a total of 118 genes were shared across xerophytic species but absent from non-xerophytic species. Of the 65 found in G. przewalskii, 63 were under purifying selection and two under positive selection. We then focused on local adaptation. Up to 20% of the G. przewalskii genome showed signatures of local adaptation to aridity during population divergence. Thirteen of the selected shared xerophytic genes were reused in local adaptation after population differentiation. Hence, only about 20% of the genes shared and specific to xerophytic species and associated with adaptation to aridity were later recruited for local adaptation in G. przewalskii.
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Affiliation(s)
- Ruirui Fu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxiang Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Aral, China
| | - Ruisen Lu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yingxiong Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Zhou S, Wu X, Yuan Y, Qiao X, Wang Z, Wu M, Qi K, Xie Z, Yin H, Zhang S. Evolutionary origin and gradual accumulation with plant evolution of the LACS family. BMC PLANT BIOLOGY 2024; 24:481. [PMID: 38816698 PMCID: PMC11140897 DOI: 10.1186/s12870-024-05194-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND LACS (long-chain acyl-CoA synthetase) genes are widespread in organisms and have multiple functions in plants, especially in lipid metabolism. However, the origin and evolutionary dynamics of the LACS gene family remain largely unknown. RESULTS Here, we identified 1785 LACS genes in the genomes of 166 diverse plant species and identified the clades (I, II, III, IV, V, VI) of six clades for the LACS gene family of green plants through phylogenetic analysis. Based on the evolutionary history of plant lineages, we found differences in the origins of different clades, with Clade IV originating from chlorophytes and representing the origin of LACS genes in green plants. The structural characteristics of different clades indicate that clade IV is relatively independent, while the relationships between clades (I, II, III) and clades (V, VI) are closer. Dispersed duplication (DSD) and transposed duplication (TRD) are the main forces driving the evolution of plant LACS genes. Network clustering analysis further grouped all LACS genes into six main clusters, with genes within each cluster showing significant co-linearity. Ka/Ks results suggest that LACS family genes underwent purifying selection during evolution. We analyzed the phylogenetic relationships and characteristics of six clades of the LACS gene family to explain the origin, evolutionary history, and phylogenetic relationships of different clades and proposed a hypothetical evolutionary model for the LACS family of genes in plants. CONCLUSIONS Our research provides genome-wide insights into the evolutionary history of the LACS gene family in green plants. These insights lay an important foundation for comprehensive functional characterization in future research.
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Affiliation(s)
- Siyuan Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yubo Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zewen Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mayan Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Yin
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
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Kushwaha A, Mishra V, Tripathi DK, Gupta R, Singh VP. Epigenetics governs senescence. PLANT REPRODUCTION 2024; 37:33-36. [PMID: 37594548 DOI: 10.1007/s00497-023-00479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023]
Abstract
Petal is one of the most esthetic and essential parts of a flower that fascinates the pollinators to enhance pollination. Petal senescence is a highly controlled and organized natural phenomenon assisted by phytohormones and gene regulation. It is an inelastically programmed event preceding to which petals give rise to color and scent that captivate pollinators, representing a flower's maturity for sexual reproduction. Till today, many genes involved in the petal senescence through genetic as well as epigenetic changes in response to hormones have been identified. In most of the species, petal senescence is controlled by ethylene, whereas others are independent of this hormone. It has also been proved that the increase in the carbohydrate contents like mannitol, inositol and trehalose delayed the senescence in tulips and Gladiolus. An increased sugar content prevents the biosynthesis of EIN3-like mRNA and further upregulates several senescence correlated genes. A wide range of different transcription factors as well as regulators are disparately expressed in ethylene insensitive and ethylene sensitive petal senescence. DcHB30, a downregulating factor, which upon linking physically to DcWRKY75 leads to the upregulation of ethylene promoting petal senescence. Here we describe the role of ethylene in petal senescence through epigenetic changes. Studies show that ethylene causes petal senescence through epigenetic changes. Feng et al. (Plant Physiol 192:546-564, 2023) observed that ARABIDOPSIS HOMOLOG OF TRITHORAX1 (DcATX1) promotes trimethylation of histone 3 (H3) at 4th lysine (H3K4me3) in Carnation. H3K4me3 further stimulates the expression of genes of ethylene biosynthesis and senescence, leading to senescence in Carnation.
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Affiliation(s)
- Ajayraj Kushwaha
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Vipul Mishra
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Durgesh Kumar Tripathi
- Crop Nanobiology and Molecular Stress Physiology Lab Amity, Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, 02707, South Korea.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India.
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Lan L, Leng L, Liu W, Ren Y, Reeve W, Fu X, Wu Z, Zhang X. The haplotype-resolved telomere-to-telomere carnation ( Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression. HORTICULTURE RESEARCH 2024; 11:uhad244. [PMID: 38225981 PMCID: PMC10788775 DOI: 10.1093/hr/uhad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/12/2023] [Indexed: 01/17/2024]
Abstract
Carnation (Dianthus caryophyllus) is one of the most valuable commercial flowers, due to its richness of color and form, and its excellent storage and vase life. The diverse demands of the market require faster breeding in carnations. A full understanding of carnations is therefore required to guide the direction of breeding. Hence, we assembled the haplotype-resolved gap-free carnation genome of the variety 'Baltico', which is the most common white standard variety worldwide. Based on high-depth HiFi, ultra-long nanopore, and Hi-C sequencing data, we assembled the telomere-to-telomere (T2T) genome to be 564 479 117 and 568 266 215 bp for the two haplotypes Hap1 and Hap2, respectively. This T2T genome exhibited great improvement in genome assembly and annotation results compared with the former version. The improvements were seen when different approaches to evaluation were used. Our T2T genome first informs the analysis of the telomere and centromere region, enabling us to speculate about specific centromere characteristics that cannot be identified by high-order repeats in carnations. We analyzed allele-specific expression in three tissues and the relationship between genome architecture and gene expression in the haplotypes. This demonstrated that the length of the genes, coding sequences, and introns, the exon numbers and the transposable element insertions correlate with gene expression ratios and levels. The insertions of transposable elements repress expression in gene regulatory networks in carnation. This gap-free finished T2T carnation genome provides a valuable resource to illustrate the genome characteristics and for functional genomics analysis in further studies and molecular breeding.
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Affiliation(s)
- Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Luhong Leng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
| | - Wayne Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Western Australia, Australia
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Jiang H, Qian Y, Zhang Z, Meng M, Deng Y, Wang G, He S, Yang L. Chromosome-level genome assembly and whole-genome resequencing of topmouth culter (Culter alburnus) provide insights into the intraspecific variation of its semi-buoyant and adhesive eggs. Mol Ecol Resour 2023; 23:1841-1852. [PMID: 37475144 DOI: 10.1111/1755-0998.13845] [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: 09/23/2022] [Revised: 04/24/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Topmouth culter (Culter alburnus) is an ecologically and economically important species belonging to the subfamily Culterinae that is native to and widespread in East Asia. Intraspecific variation of semi-buoyant and adhesive eggs in topmouth culter provides an ideal opportunity to investigate the genetic mechanisms of spawning habits underlying the adaptive radiation of cyprinids in East Asia. In this study, we present a chromosome-level genome assembly of topmouth culter and re-sequenced 158 individuals from six locations in China covering three geographical groups and two egg type variations. The topmouth culter genome size was 1.05 Gb, with a contig N50 length of 17.8 Mb and anchored onto 24 chromosomes. Phylogenetic analysis showed that the divergence time of the Culterinae was coinciding with the time of initiation of the Asian monsoon intensification. Gene family evolutionary analysis indicated that the expanded gene families in topmouth culter were associated with dietary adaptation. Population-level genetic analysis indicated clear differentiation among the six populations, which were clustered into three distinct clusters, consistent with their geographical divergence. The historical effective population size of topmouth culter correlated with the Tibetan Plateau uplifting according to the demographic history reconstruction. A selective sweep analysis between adhesive and semi-buoyant egg populations revealed the genes associated with the hydration and adhesiveness of eggs, indicating divergent selection towards different hydrological environments. This study offers a high-resolution genetic resource for further studies on evolutionary adaptation, genetic breeding and conservation of topmouth culter, providing insights into the molecular mechanisms for egg type variation of East Asian cyprinids.
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Affiliation(s)
- Haifeng Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuting Qian
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhi Zhang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Minghui Meng
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yu Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Life Science College, Hunan Normal University, Changsha, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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6
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He Z, Chao H, Zhou X, Ni Q, Hu Y, Yu R, Wang M, Li C, Chen J, Chen Y, Chen Y, Cui C, Zhang L, Chen M, Chen D. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development. HORTICULTURE RESEARCH 2023; 10:uhad196. [PMID: 38023476 PMCID: PMC10673659 DOI: 10.1093/hr/uhad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.
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Affiliation(s)
- Zhenxiang He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minghuai Wang
- Forest Protection Department, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Jingzhen Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yong Chen
- Xishan Forest Farm, Dazu District, Chongqing 402360, China
| | - Chunyi Cui
- Longshan Forest Farm, Lechang 512221, China
| | - Liangbo Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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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] [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.
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8
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Jiang H, Zhang X, Leng L, Gong D, Zhang X, Liu J, Peng D, Wu Z, Yang Y. A chromosome-scale and haplotype-resolved genome assembly of carnation ( Dianthus caryophyllus) based on high-fidelity sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1230836. [PMID: 37600187 PMCID: PMC10437072 DOI: 10.3389/fpls.2023.1230836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus 'Aili' at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in 'Aili' and previously published 'Francesco' and 'Scarlet Queen'. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.
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Affiliation(s)
- Heling Jiang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoni Zhang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Luhong Leng
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Desheng Gong
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaohui Zhang
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyang Liu
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Zhiqiang Wu
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingxue Yang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Nakayama M, Harada N, Murai A, Ueyama S, Harada T. Low-Oxygen Responses of Cut Carnation Flowers Associated with Modified Atmosphere Packaging. PLANTS (BASEL, SWITZERLAND) 2023; 12:2738. [PMID: 37514352 PMCID: PMC10386211 DOI: 10.3390/plants12142738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Gaseous factors affect post-harvest physiological processes in horticultural crops, including ornamental flowers. However, the molecular responses of cut flowers to the low-oxygen conditions associated with modified atmosphere packaging (MAP) have not yet been elucidated. Here, we show that storage of cut carnation flowers in a sealed polypropylene bag decreased the oxygen concentration in the bag to 3-5% and slowed flower opening. The vase life of carnation flowers after storage for seven days under MAP conditions was comparable to that without storage and was improved by the application of a commercial-quality preservative. The adenylate energy charge (AEC) was maintained at high levels in petals from florets stored under MAP conditions. This was accompanied by the upregulation of four hypoxia-related genes, among which the HYPOXIA-RESPONSIVE ETHYLENE RESPONSE FACTOR and PHYTOGLOBIN genes (DcERF19 and DcPGB1) were newly identified. These results suggest that hypoxia-responsive genes contribute to the maintenance of the energy status in carnation flowers stored under MAP conditions, making this gas-controlling technique potentially effective for maintaining cut flower quality without cooling.
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Affiliation(s)
- Misaki Nakayama
- School of Education, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Nao Harada
- School of Education, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Ai Murai
- School of Education, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Sayaka Ueyama
- School of Education, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Taro Harada
- Faculty of Education, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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10
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Leng L, Zhang X, Liu W, Wu Z. Genome-Wide Identification of the MYB and bHLH Families in Carnations and Expression Analysis at Different Floral Development Stages. Int J Mol Sci 2023; 24:ijms24119499. [PMID: 37298450 DOI: 10.3390/ijms24119499] [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: 05/06/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Carnations are one of the most popular ornamental flowers in the world with varied flower colors that have long attracted breeders and consumers alike. The differences in carnation flower color are mainly the result of the accumulation of flavonoid compounds in the petals. Anthocyanins are a type of flavonoid compound that produce richer colors. The expression of anthocyanin biosynthetic genes is mainly regulated by MYB and bHLH transcription factors. However, these TFs have not been comprehensively reported in popular carnation cultivars. Herein, 106 MYB and 125 bHLH genes were identified in the carnation genome. Gene structure and protein motif analyses show that members of the same subgroup have similar exon/intron and motif organization. Phylogenetic analysis combining the MYB and bHLH TFs from Arabidopsis thaliana separates the carnation DcaMYBs and DcabHLHs into 20 subgroups each. Gene expression (RNAseq) and phylogenetic analysis shows that DcaMYB13 in subgroup S4 and DcabHLH125 in subgroup IIIf have similar expression patterns to those of DFR, ANS, and GT/AT, which regulate anthocyanin accumulation, in the coloring of carnations, and in red-flowered and white-flowered carnations, DcaMYB13 and DcabHLH125 are likely the key genes responsible for the formation of red petals in carnations. These results lay a foundation for the study of MYB and bHLH TFs in carnations and provide valuable information for the functional verification of these genes in studies of tissue-specific regulation of anthocyanin biosynthesis.
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Affiliation(s)
- Luhong Leng
- 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 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- 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 518120, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiqiang Wu
- 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 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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11
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Feng S, Jiang X, Wang R, Tan H, Zhong L, Cheng Y, Bao M, Qiao H, Zhang F. Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation. PLANT PHYSIOLOGY 2023; 192:546-564. [PMID: 36623846 PMCID: PMC10152666 DOI: 10.1093/plphys/kiad008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 05/03/2023]
Abstract
Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, the involvement of histone methylation in regulating petal senescence remains poorly understood. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during ethylene-induced petal senescence in carnation (Dianthus caryophyllus L.). H3K4me3 levels were positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (DcACS1), and ACC oxidase (DcACO1), and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation ARABIDOPSIS HOMOLOG OF TRITHORAX1 (DcATX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delayed ethylene-induced petal senescence in carnation, which was associated with the down-regulated expression of DcWRKY75, DcACO1, and DcSAG12, whereas overexpression of DcATX1 exhibited the opposite effects. DcATX1 promoted the transcription of DcWRKY75, DcACO1, and DcSAG12 by elevating the H3K4me3 levels within their promoters. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1, DcSAG12 and potentially other downstream target genes by regulating H3K4me3 levels, thereby accelerating ethylene-induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence processes.
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Affiliation(s)
- Shan Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Jiang
- State key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruiming Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hualiang Tan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Linlin Zhong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Fan Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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12
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Zhu C, Huang Z, Sun Z, Feng S, Wang S, Wang T, Yuan X, Zhong L, Cheng Y, Bao M, Zhang F. The mutual regulation between DcEBF1/2 and DcEIL3-1 is involved in ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:636-650. [PMID: 36808165 DOI: 10.1111/tpj.16158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
Carnation (Dianthus caryophyllus L.) is a respiratory climacteric flower, comprising one of the most important cut flowers that is extremely sensitive to plant hormone ethylene. Ethylene signaling core transcription factor DcEIL3-1 plays a key role in ethylene induced petal senescence in carnation. However, how the dose of DcEIL3-1 is regulated in the carnation petal senescence process is still not clear. Here, we screened out two EBF (EIN3 Binding F-box) genes, DcEBF1 and DcEBF2, which showed quick elevation by ethylene treatment according to the ethylene induced carnation petal senescence transcriptome. Silencing of DcEBF1 and DcEBF2 accelerated, whereas overexpression of DcEBF1 and DcEBF2 delayed, ethylene induced petal senescence in carnation by influencing DcEIL3-1 downstream target genes but not DcEIL3-1 itself. Furthermore, DcEBF1 and DcEBF2 interact with DcEIL3-1 to degrade DcEIL3-1 via an ubiquitination pathway in vitro and in vivo. Finally, DcEIL3-1 binds to the promoter regions of DcEBF1 and DcEBF2 to activate their expression. In conclusion, the present study reveals the mutual regulation between DcEBF1/2 and DcEIL3-1 during ethylene induced petal senescence in carnation, which not only expands our understanding about ethylene signal regulation network in the carnation petal senescence process, but also provides potential targets with respect to breeding a cultivar of long-lived cut carnation.
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Affiliation(s)
- Chunlin Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiheng Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shan Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Siqi Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Teng Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyi Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linlin Zhong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fan Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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13
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Cheng G, Ye C, Zhang J, Li H, Jiang Y, Duan X. Water permeability of different aerial tissues of carnations is related to cuticular wax composition. PHYSIOLOGIA PLANTARUM 2023; 175:e13883. [PMID: 36840510 DOI: 10.1111/ppl.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Cuticular wax protects aerial plant tissues against uncontrolled water loss. To compare the differences among tissues, cultivars, and postharvest stages, we characterized the surface morphology, water permeability, and chemical composition of cuticular wax on the leaf, calyx, and petals of two carnation cultivars ('Master' and 'Lady green') at two postharvest stages. Obvious differences in these characteristics were found among tissues but not among cultivars or postharvest stages. The leaf surface was relatively smooth, whereas convex cells were observed on the petals. The mean minimum conductance of leaves was significantly higher than that of the calyx, followed by that of petals. It ranged between 8.8 × 10-4 m s-1 for 'Lady green' leaves at Stage II and 3.6 × 10-5 m s-1 for 'Master' petals at Stage I. Petal wax contained high concentrations of n-alkanes, whereas primary alcohols dominated in leaf wax. The weighted average chain length (ACL) was higher in petal wax than in leaf wax; it ranged from 19.6 in 'Lady green' leaves to 24.14 in 'Lady green' petals at Stage I. In conclusion, carnation petals are characterized by numerous convex cells on both the adaxial and abaxial surfaces, and their main cuticular wax components, alkanes, have a higher ACL than leaf cuticular wax, which contributes to their higher water barrier property. The results provide further evidence for the association between cuticular chemical composition and the physiological function of the cuticle in blocking water transpiration.
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Affiliation(s)
- Guiping Cheng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Changchun Ye
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jiajun Zhang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hongmei Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuewu Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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14
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Xu H, Wang S, Larkin RM, Zhang F. The transcription factors DcHB30 and DcWRKY75 antagonistically regulate ethylene-induced petal senescence in carnation (Dianthus caryophyllus). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7326-7343. [PMID: 36107792 DOI: 10.1093/jxb/erac357] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Although numerous transcription factors with antagonistic activities have been shown to contribute to growth and development, whether and how they regulate senescence in plants is largely unknown. In this study, we investigated the role of antagonistic transcription factors in petal senescence in carnation (Dianthus caryophyllus), one of the most common types of ethylene-sensitive cut flowers produced worldwide. We identified DcHB30 that encodes a ZF-HD transcription factor that is down-regulated in ethylene-treated petal transcriptomes. We found that silencing DcHB30 accelerated ethylene-induced petal senescence and that DcHB30 physically interacts with DcWRKY75, a positive regulator of ethylene-induced petal senescence. Phenotypic characterization and molecular evidence indicated that DcHB30 and DcWRKY75 competitively regulate the expression of their co-targeted genes DcACS1, DcACO1, DcSAG12, and DcSAG29 by reciprocally inhibiting the DNA-binding activity of each other on the gene promoters. This transcriptional regulation mechanism demonstrates that these transcription factors serve as positive and negative regulators in ethylene-induced petal senescence in carnation. Thus, our study provides insights into how antagonizing transcription factors regulate plant senescence.
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Affiliation(s)
- Han Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Siqi Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Fan Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Preservation, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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15
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Wang H, Xu D, Wang S, Wang A, Lei L, Jiang F, Yang B, Yuan L, Chen R, Zhang Y, Fan W. Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis. DNA Res 2022; 30:6880148. [PMID: 36473054 PMCID: PMC9847342 DOI: 10.1093/dnares/dsac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi-C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution.
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Affiliation(s)
| | | | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Rong Chen
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), 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
| | - Wei Fan
- To whom correspondence should be addressed. Tel. +86 18165787021.
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16
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Astigueta FH, Baigorria AH, García MN, Delfosse VC, González SA, Pérez de la Torre MC, Moschen S, Lia VV, Heinz RA, Fernández P, Trupkin SA. Characterization and expression analysis of WRKY genes during leaf and corolla senescence of Petunia hybrida plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1765-1784. [PMID: 36387973 PMCID: PMC9636358 DOI: 10.1007/s12298-022-01243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Several families of transcription factors (TFs) control the progression of senescence. Many key TFs belonging to the WRKY family have been described to play crucial roles in the regulation of leaf senescence, mainly in Arabidopsis thaliana. However, little is known about senescence-associated WRKY members in floricultural species. Delay of senescence in leaves and petals of Petunia hybrida, a worldwide ornamental crop are highly appreciated traits. In this work, starting from 28 differentially expressed WRKY genes of A. thaliana during the progression of leaf senescence, we identified the orthologous in P. hybrida and explored the expression profiles of 20 PhWRKY genes during the progression of natural (age-related) leaf and corolla senescence as well as in the corollas of flowers undergoing pollination-induced senescence. Simultaneous visualization showed consistent and similar expression profiles of PhWRKYs during natural leaf and corolla senescence, although weak expression changes were observed during pollination-induced senescence. Comparable expression trends between PhWRKYs and the corresponding genes of A. thaliana were observed during leaf senescence, although more divergence was found in petals of pollinated petunia flowers. Integration of expression data with phylogenetics, conserved motif and cis-regulatory element analyses were used to establish a list of candidates that could regulate more than one senescence process. Our results suggest that several members of the WRKY family of TFs are tightly linked to the regulation of senescence in P. hybrida. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01243-y.
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Affiliation(s)
- Francisco H. Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Amilcar H. Baigorria
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Martín N. García
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Verónica C. Delfosse
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Sergio A. González
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
| | - Mariana C. Pérez de la Torre
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Sebastián Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, 4142 Tucumán, Argentina
| | - Verónica V. Lia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
- Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
| | - Ruth A. Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Paula Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Santiago A. Trupkin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
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17
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Li F, Gao Y, Jin C, Wen X, Geng H, Cheng Y, Qu H, Liu X, Feng S, Zhang F, Ruan J, Yang C, Zhang L, Wang J. The chromosome-level genome of Gypsophila paniculata reveals the molecular mechanism of floral development and ethylene insensitivity. HORTICULTURE RESEARCH 2022; 9:uhac176. [PMID: 36204200 PMCID: PMC9533222 DOI: 10.1093/hr/uhac176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the most famous worldwide cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history: an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ETHYLENE RESPONSE SENSOR (ERS) and the reduction of downstream ETHYLENE RESPONSE FACTOR (ERF) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.
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Affiliation(s)
- Fan Li
- Corresponding authors. E-mail: ; ;
| | | | | | | | - Huaiting Geng
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, 650200, Kunming, China
- School of Agriculture, Yunnan University, 650504, Kunming, China
| | - Ying Cheng
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, 650200, Kunming, China
- School of Agriculture, Yunnan University, 650504, Kunming, China
| | - Haoyue Qu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Shan Feng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
- National R&D Center for Citrus Postharvest Technology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Fan Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
- National R&D Center for Citrus Postharvest Technology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiwei Ruan
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, 650200, Kunming, China
| | - 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, 650200, Kunming, China
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18
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Yuan F, Wang X, Zhao B, Xu X, Shi M, Leng B, Dong X, Lu C, Feng Z, Guo J, Han G, Zhang H, Huang J, Chen M, Wang BS. The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution. MOLECULAR PLANT 2022; 15:1024-1044. [PMID: 35514085 DOI: 10.1016/j.molp.2022.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.
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Affiliation(s)
- Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Boqing Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xiaojing Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing, China
| | - Bingying Leng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xinxiu Dong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Chaoxia Lu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Zhongtao Feng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | | | | | - Min Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.
| | - Bao-Shan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.
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19
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Zhang X, Lin S, Peng D, Wu Q, Liao X, Xiang K, Wang Z, Tembrock LR, Bendahmane M, Bao M, Wu Z, Fu X. Integrated multi-omic data and analyses reveal the pathways underlying key ornamental traits in carnation flowers. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1182-1196. [PMID: 35247284 PMCID: PMC9129081 DOI: 10.1111/pbi.13801] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/09/2022] [Accepted: 02/19/2022] [Indexed: 05/20/2023]
Abstract
Carnation (Dianthus caryophyllus) is one of the most popular ornamental flowers in the world. Although numerous studies on carnations exist, the underlying mechanisms of flower color, fragrance, and the formation of double flowers remain unknown. Here, we employed an integrated multi-omics approach to elucidate the genetic and biochemical pathways underlying the most important ornamental features of carnation flowers. First, we assembled a high-quality chromosome-scale genome (636 Mb with contig N50 as 14.67 Mb) of D. caryophyllus, the 'Scarlet Queen'. Next, a series of metabolomic datasets was generated with a variety of instrumentation types from different parts of the flower at multiple stages of development to assess spatial and temporal differences in the accumulation of pigment and volatile compounds. Finally, transcriptomic data were generated to link genomic, biochemical, and morphological patterns to propose a set of pathways by which ornamental traits such as petal coloration, double flowers, and fragrance production are formed. Among them, the transcription factors bHLHs, MYBs, and a WRKY44 homolog are proposed to be important in controlling petal color patterning and genes such as coniferyl alcohol acetyltransferase and eugenol synthase are involved in the synthesis of eugenol. The integrated dataset of genomics, transcriptomics, and metabolomics presented herein provides an important foundation for understanding the underlying pathways of flower development and coloration, which in turn can be used for selective breeding and gene editing for the development of novel carnation cultivars.
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Affiliation(s)
- Xiaoni Zhang
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
- Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Dan Peng
- Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Quanshu Wu
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Xuezhu Liao
- Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Kunli Xiang
- Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Zehao Wang
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Luke R. Tembrock
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Mohammed Bendahmane
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
- Laboratoire Reproduction et Development des PlantesINRA‐CNRS‐Lyon1‐ENSEcole Normale Supérieure de LyonLyonFrance
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Zhiqiang Wu
- Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant BiologyCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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20
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Rodríguez-Parra A, Picazo-Aragonés J, Balao F. Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040518. [PMID: 35214851 PMCID: PMC8878694 DOI: 10.3390/plants11040518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 05/14/2023]
Abstract
Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.
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21
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Zheng Q, Majsec K, Katagiri F. Pathogen-driven coevolution across the CBP60 plant immune regulator subfamilies confers resilience on the regulator module. THE NEW PHYTOLOGIST 2022; 233:479-495. [PMID: 34610150 DOI: 10.1111/nph.17769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Components of the plant immune signaling network need mechanisms that confer resilience against fast-evolving pathogen effectors that target them. Among eight Arabidopsis CaM-Binding Protein (CBP) 60 family members, AtCBP60g and AtSARD1 are partially functionally redundant, major positive immune regulators, and AtCBP60a is a negative immune regulator. We investigated possible resilience-conferring evolutionary mechanisms among the CBP60a, CBP60g and SARD1 immune regulatory subfamilies. Phylogenetic analysis was used to investigate the times of CBP60 subfamily neofunctionalization. Then, using the pairwise distance rank based on the newly developed analytical platform Protein Evolution Analysis in a Euclidean Space (PEAES), hypotheses of specific coevolutionary mechanisms that could confer resilience on the regulator module were tested. The immune regulator subfamilies diversified around the time of angiosperm divergence and have been evolving very quickly. We detected significant coevolutionary interactions across the immune regulator subfamilies in all of 12 diverse core eudicot species lineages tested. The coevolutionary interactions were consistent with the hypothesized coevolution mechanisms. Despite their unusually fast evolution, members across the CBP60 immune regulator subfamilies have influenced the evolution of each other long after their diversification in a way that could confer resilience on the immune regulator module against fast-evolving pathogen effectors.
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Affiliation(s)
- Qi Zheng
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Kristina Majsec
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
| | - Fumiaki Katagiri
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, 55108, USA
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22
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Xu H, Luo D, Zhang F. DcWRKY75 promotes ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1473-1492. [PMID: 34587330 DOI: 10.1111/tpj.15523] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 05/09/2023]
Abstract
Carnation (Dianthus caryophyllus L.) is one of the most important and typical ethylene sensitive cut flowers worldwide, although how ethylene influences the petal senescence process in carnation remains largely unknown. Here, we screened out one of the key transcription factors, DcWRKY75, using a constructed ethylene induced petal senescence transcriptome in carnation and found that it shows quick induction by ethylene treatment. Silencing of DcWRKY75 delays ethylene induced petal senescence in carnation. Molecular evidence confirms that DcWRKY75 can bind to the promoter regions of two main ethylene biosynthetic genes (DcACS1 and DcACO1) and a couple of senescence associated genes (DcSAG12 and DcSAG29) to activate their expression. Furthermore, we show that DcWRKY75 is a direct target gene of DcEIL3-1, which is a homolog of the ethylene signaling core transcription factor EIN3 in Arabidopsis. DcEIL3-1 can physically interact with DcWRKY75 and silencing of DcEIL3-1 also delays ethylene induced petal senescence in carnation and inhibits the ethylene induced expression of DcWRKY75 and its target genes. The present study demonstrates that the transcriptional regulation network is vitally important for ethylene induced petal senescence process in carnation and potentially in other ethylene sensitive cut flowers.
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Affiliation(s)
- Han Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dan Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Fan Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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23
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Sun F, Sun S, Ye W, Duan C, Li B, Shan W, Zhu Z. Genome Sequence Data of Three Formae Speciales of Phytophthora vignae Causing Phytophthora Stem Rot on Different Vigna Species. PLANT DISEASE 2021; 105:3732-3735. [PMID: 34003033 DOI: 10.1094/pdis-11-20-2546-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora vignae is an important oomycete pathogen causing Phytophthora stem rot on some Vigna spp. Three P. vignae isolates obtained from mung bean, adzuki bean, and cowpea exhibited high similarities in morphology and physiology but are specialized to infect different hosts. Here, we report the first de novo assembly of the draft genomes of three P. vignae isolates, which were performed using the PacBio SMRT Sequel platform. This study will extend the genomic resource available for the Phytophthora genus and provide a good foundation for further research on comparative genomics of Phytophthora spp. and interaction mechanism between hosts and pathogens.
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Affiliation(s)
- Feifei Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Agronomy of Northwest Agriculture & Forestry University, Yangling, 712100, P. R. China
| | - Suli Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Benjin Li
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, P. R. China
| | - Weixing Shan
- College of Agronomy of Northwest Agriculture & Forestry University, Yangling, 712100, P. R. China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
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24
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Baiakhmetov E, Guyomar C, Shelest E, Nobis M, Gudkova PD. The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa. Sci Rep 2021; 11:15345. [PMID: 34321531 PMCID: PMC8319324 DOI: 10.1038/s41598-021-94068-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S. capillata, investigate the evolutionary history of the genus, demonstrate structural heteroplasmy of the chloroplast genome and announce for the first time the mitochondrial genome in Stipa. The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.
| | - Cervin Guyomar
- German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103, Leipzig, Germany.,Institute for Genetics, Environment and Plant Protection (IGEPP), Agrocampus Ouest, INRAE, University of Rennes 1, 35650, Le Rheu, France
| | - Ekaterina Shelest
- German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103, Leipzig, Germany.,Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., Tomsk, 634050, Russia.,Department of Biology, Altai State University, Lenin 61 Ave., Barnaul, Russia, 656049
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25
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Recent Progress in Enhancing Fungal Disease Resistance in Ornamental Plants. Int J Mol Sci 2021; 22:ijms22157956. [PMID: 34360726 PMCID: PMC8348885 DOI: 10.3390/ijms22157956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/19/2023] Open
Abstract
Fungal diseases pose a major threat to ornamental plants, with an increasing percentage of pathogen-driven host losses. In ornamental plants, management of the majority of fungal diseases primarily depends upon chemical control methods that are often non-specific. Host basal resistance, which is deficient in many ornamental plants, plays a key role in combating diseases. Despite their economic importance, conventional and molecular breeding approaches in ornamental plants to facilitate disease resistance are lagging, and this is predominantly due to their complex genomes, limited availability of gene pools, and degree of heterozygosity. Although genetic engineering in ornamental plants offers feasible methods to overcome the intrinsic barriers of classical breeding, achievements have mainly been reported only in regard to the modification of floral attributes in ornamentals. The unavailability of transformation protocols and candidate gene resources for several ornamental crops presents an obstacle for tackling the functional studies on disease resistance. Recently, multiomics technologies, in combination with genome editing tools, have provided shortcuts to examine the molecular and genetic regulatory mechanisms underlying fungal disease resistance, ultimately leading to the subsequent advances in the development of novel cultivars with desired fungal disease-resistant traits, in ornamental crops. Although fungal diseases constitute the majority of ornamental plant diseases, a comprehensive overview of this highly important fungal disease resistance seems to be insufficient in the field of ornamental horticulture. Hence, in this review, we highlight the representative mechanisms of the fungal infection-related resistance to pathogens in plants, with a focus on ornamental crops. Recent progress in molecular breeding, genetic engineering strategies, and RNAi technologies, such as HIGS and SIGS for the enhancement of fungal disease resistance in various important ornamental crops, is also described.
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26
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Chen JY, Xie FF, Cui YZ, Chen CB, Lu WJ, Hu XD, Hua QZ, Zhao J, Wu ZJ, Gao D, Zhang ZK, Jiang WK, Sun QM, Hu GB, Qin YH. A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis. HORTICULTURE RESEARCH 2021; 8:164. [PMID: 34230458 PMCID: PMC8260669 DOI: 10.1038/s41438-021-00612-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 05/03/2023]
Abstract
Pitaya (Hylocereus) is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide, and it has attracted significant attention because of its betalain-abundant fruits. Nonetheless, the lack of a pitaya reference genome significantly hinders studies focused on its evolution, as well as the potential for genetic improvement of this crop. Herein, we employed various sequencing approaches, namely, PacBio-SMRT, Illumina HiSeq paired-end, 10× Genomics, and Hi-C (high-throughput chromosome conformation capture) to provide a chromosome-level genomic assembly of 'GHB' pitaya (H. undatus, 2n = 2x = 22 chromosomes). The size of the assembled pitaya genome was 1.41 Gb, with a scaffold N50 of ~127.15 Mb. In total, 27,753 protein-coding genes and 896.31 Mb of repetitive sequences in the H. undatus genome were annotated. Pitaya has undergone a WGT (whole-genome triplication), and a recent WGD (whole-genome duplication) occurred after the gamma event, which is common to the other species in Cactaceae. A total of 29,328 intact LTR-RTs (~696.45 Mb) were obtained in H. undatus, of which two significantly expanded lineages, Ty1/copia and Ty3/gypsy, were the main drivers of the expanded genome. A high-density genetic map of F1 hybrid populations of 'GHB' × 'Dahong' pitayas (H. monacanthus) and their parents were constructed, and a total of 20,872 bin markers were identified (56,380 SNPs) for 11 linkage groups. More importantly, through transcriptomic and WGCNA (weighted gene coexpression network analysis), a global view of the gene regulatory network, including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis, was presented. Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution, as well as the modulation of betalain biosynthesis in edible fruits.
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Affiliation(s)
- Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Fang-Fang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Yan-Ze Cui
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Can-Bin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Xiao-di Hu
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Qing-Zhu Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi-Jiang Wu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, 530007, Nanning, Guangxi, China
| | - Dan Gao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi-Ke Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Wen-Kai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Qing-Ming Sun
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA)/Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, 510640, Guangzhou, China.
| | - Gui-Bing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China.
| | - Yong-Hua Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Lingnan Guangdong Laboratory of Modern Agriculture, College of Horticulture, South China Agricultural University, 510642, Guangzhou, Guangdong, China.
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Harada T, Horiguchi I, Ueyama S, Murai A, Tsuzuki C. Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.). PHYTOCHEMISTRY 2021; 185:112607. [PMID: 33774571 DOI: 10.1016/j.phytochem.2020.112607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Sucrose plays crucial roles in growth and responses of plants to the environment, including those in ornamental species. During post-harvest handling of cut flowers, sucrose degradation is an essential process of inter- and intra-cellular carbon partitioning affecting flower opening and senescence and, subsequently, flower quality. However, complete information about the molecular basis of sucrose degradation in ornamental flowers, which can be catalyzed by two kinds of sucrolytic enzymes, invertase (INV), and sucrose synthase (SUS), is not available from past reports. The present study shows that sucrose treatment of carnation (Dianthus caryophyllus L.) florets increased starch content in petals, accompanied by decreased vacuolar INV (VIN) activity and increased SUS activity. However, hypoxic treatment of carnation florets decreased sucrose content and cell-wall INV (CWIN) activity in petals. In silico analysis using the carnation genome database identified six CWIN, three VIN, eight cytoplasmic INV (CIN), and five SUS genes. Real-time RT-PCR analysis confirmed that these genes are differentially expressed in carnation petals in response to sucrose and hypoxic treatments, partially corresponding to the changes in enzyme activities. In contrast to DcSUS1 (Dca4507.1), a SUS gene already reported in carnation, which showed preferential expression under aerated conditions, the expression of DcSUS2 (Dca22218.1), an undescribed carnation SUS gene, was enhanced under hypoxia similarly to an alcohol dehydrogenase gene DcADH1 (Dca18671.1). These results suggest that sugar metabolism in carnation petals is regulated in response to environmental cues, accompanied by modulated activities and gene expression of a set of sucrolytic enzymes.
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Affiliation(s)
- Taro Harada
- Graduate School of Education, Okayama University, Okayama, 700-8530, Japan.
| | - Itsuku Horiguchi
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Sayaka Ueyama
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Ai Murai
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Chie Tsuzuki
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
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Yan L, Wang Z, Song W, Fan P, Kang Y, Lei Y, Wan L, Huai D, Chen Y, Wang X, Sudini H, Liao B. Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot. BMC Genomics 2021; 22:276. [PMID: 33863285 PMCID: PMC8052761 DOI: 10.1186/s12864-021-07534-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 03/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease of peanut. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect peanut stems, roots, pegs and pods, leading to varied yield losses. S. rolfsii strains GP3 and ZY collected from peanut in different provinces of China exhibited a significant difference in aggressiveness on peanut plants by artificial inoculation test. In this study, de-novo genome sequencing of these two distinct strains was performed aiming to reveal the genomic basis of difference in aggressiveness. RESULTS Scleotium rolfsii strains GP3 and ZY, with weak and high aggressiveness on peanut plants, exhibited similar growth rate and oxalic acid production in laboratory. The genomes of S. rolfsii strains GP3 and ZY were sequenced by Pacbio long read technology and exhibited 70.51 Mb and 70.61 Mb, with contigs of 27 and 23, and encoded 17,097 and 16,743 gene models, respectively. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires, which might be associated with aggressiveness, differed between GP3 and ZY. There were 58 and 45 unique pathogen-host interaction (PHI) genes in GP3 and ZY, respectively. The ZY strain had more carbohydrate-active enzymes (CAZymes) in its secretome than GP3, especially in the glycoside hydrolase family (GH), the carbohydrate esterase family (CBM), and the polysaccharide lyase family (PL). GP3 and ZY also had different effector candidates and putative secondary metabolite synthetic gene clusters. These results indicated that differences in PHI, secreted CAZymes, effectors and secondary metabolites may play important roles in aggressive difference between these two strains. CONCLUSIONS The data provided a further understanding of the S. rolfsii genome. Genomic comparison provided clues to the difference in aggressiveness of S. rolfsii strains.
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Affiliation(s)
- Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Wanduo Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Pengmin Fan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Liyun Wan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Hari Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324 India
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Zheng T, Li P, Li L, Zhang Q. Research advances in and prospects of ornamental plant genomics. HORTICULTURE RESEARCH 2021; 8:65. [PMID: 33790259 PMCID: PMC8012582 DOI: 10.1038/s41438-021-00499-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.
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Affiliation(s)
- Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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30
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Giovannini A, Laura M, Nesi B, Savona M, Cardi T. Genes and genome editing tools for breeding desirable phenotypes in ornamentals. PLANT CELL REPORTS 2021; 40:461-478. [PMID: 33388891 PMCID: PMC7778708 DOI: 10.1007/s00299-020-02632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/27/2020] [Indexed: 05/05/2023]
Abstract
We review the main genes underlying commercial traits in cut flower species and critically discuss the possibility to apply genome editing approaches to produce novel variation and phenotypes. Promoting flowering and flower longevity as well as creating novelty in flower structure, colour range and fragrances are major objectives of ornamental plant breeding. The novel genome editing techniques add new possibilities to study gene function and breed new varieties. The implementation of such techniques, however, relies on detailed information about structure and function of genomes and genes. Moreover, improved protocols for efficient delivery of editing reagents are required. Recent results of the application of genome editing techniques to elite ornamental crops are discussed in this review. Enabling technologies and genomic resources are reviewed in relation to the implementation of such approaches. Availability of the main gene sequences, underlying commercial traits and in vitro transformation protocols are provided for the world's best-selling cut flowers, namely rose, lily, chrysanthemum, lisianthus, tulip, gerbera, freesia, alstroemeria, carnation and hydrangea. Results obtained so far are described and their implications for the improvement of flowering, flower architecture, colour, scent and shelf-life are discussed.
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Affiliation(s)
- A. Giovannini
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - M. Laura
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - B. Nesi
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Via dei Fiori 8, 51017 Pescia, Italy
| | - M. Savona
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - T. Cardi
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
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31
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Yamada Y, Hirakawa H, Hori K, Minakuchi Y, Toyoda A, Shitan N, Sato F. Comparative analysis using the draft genome sequence of California poppy (Eschscholzia californica) for exploring the candidate genes involved in benzylisoquinoline alkaloid biosynthesis. Biosci Biotechnol Biochem 2021; 85:851-859. [DOI: 10.1093/bbb/zbaa091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022]
Abstract
ABSTRACT
Genome characterization of California poppy (Eschscholzia californica cv. “Hitoezaki”), which produces pharmaceutically important benzylisoquinoline alkaloids (BIAs), was carried out using the draft genome sequence. The numbers of tRNA and rRNA genes were close to those of the other plant species tested, whereas the frequency of repetitive sequences was distinct from those species. Comparison of the predicted genes with those of Amborella trichopoda, Nelumbo nucifera, Solanum lycopersicum, and Arabidopsis thaliana, and analyses of gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway indicated that the enzyme genes involved in BIA biosynthesis were highly enriched in the California poppy genome. Further comparative analysis using the genome information of Papaver somniferum and Aquilegia coerulea, both BIA-producing plants, revealed that many genes encoding BIA biosynthetic enzymes, transcription factors, transporters, and candidate proteins, possibly related to BIA biosynthesis, were specifically distributed in these plant species.
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Affiliation(s)
- Yasuyuki Yamada
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Japan
| | | | - Kentaro Hori
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | | | - Nobukazu Shitan
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Japan
| | - Fumihiko Sato
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Graduate School of Science, Osaka Prefecture University, Sakai, Japan
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32
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Morimoto H, Narumi-Kawasaki T, Takamura T, Fukai S. Flower color mutation caused by spontaneous cell layer displacement in carnation (Dianthus caryophyllus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110598. [PMID: 32900436 DOI: 10.1016/j.plantsci.2020.110598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
A change of layer arrangement of shoot apical meristem (SAM) organized by three cell layers (L1, L2 and L3) is thought to be one of the provocations of bud sport, which often induces changes in phenotypic colors in periclinal chimeras. This paper describes a cell layer rearrangement which is the cause of spontaneous flower color mutation by using two carnation (Dianthus caryophyllus L.) cultivars that are presumably periclinal chimeras, 'Feminine Minami' (deep pink flower) and its recessive sport 'Tommy Minami' (pinkish red flower). The genotype of the acyl-glucose-dependent anthocyanin 5-glucosyltransferase (AA5GT) which is responsible for the color change of red to pink, in each cell layer was deduced by genomic analysis using tissues originated from specific cell layer and investigation of partial petal color mutations. In the results, the genotype of the L1 of 'Feminine Minami' was heterozygous for functional AA5GT and non-functional AA5GT carrying retrotransposon Ty1dic1 (AA5GT-Ty1dic1), and its inner cell layer hid red flower genotype, whereas AA5GT-Ty1dic1 of the L1 of 'Tommy Minami' became homogenic in absence of the insertion of a new Ty1dic1. Our outcomes concluded that the L1 of 'Tommy Minami' harboring the recessive AA5GT alleles are attributed to the inner cell layer of 'Feminine Minami' possessing red flower genotype.
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Affiliation(s)
- Hayato Morimoto
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama 790-8566, Japan
| | - Takako Narumi-Kawasaki
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama 790-8566, Japan; Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Takejiro Takamura
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama 790-8566, Japan; Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Seiichi Fukai
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama 790-8566, Japan; Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan.
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33
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Iijima L, Kishimoto S, Ohmiya A, Yagi M, Okamoto E, Miyahara T, Tsujimoto T, Ozeki Y, Uchiyama N, Hakamatsuka T, Kouno T, Cano EA, Shimizu M, Nishihara M. Esterified carotenoids are synthesized in petals of carnation (Dianthus caryophyllus) and accumulate in differentiated chromoplasts. Sci Rep 2020; 10:15256. [PMID: 32938985 PMCID: PMC7495429 DOI: 10.1038/s41598-020-72078-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
Although yellow and orange petal colors are derived from carotenoids in many plant species, this has not yet been demonstrated for the order Caryophyllales, which includes carnations. Here, we identified a carnation cultivar with pale yellow flowers that accumulated carotenoids in petals. Additionally, some xanthophyll compounds were esterified, as is the case for yellow flowers in other plant species. Ultrastructural analysis showed that chromoplasts with numerous plastoglobules, in which flower-specific carotenoids accumulate, were present in the pale yellow petals. RNA-seq and RT-qPCR analyses indicated that the expression levels of genes for carotenoid biosynthesis and esterification in pale yellow and pink petals (that accumulate small amounts of carotenoids) were similar or lower than in green petals (that accumulate substantial amounts of carotenoids) and white petals (that accumulate extremely low levels of carotenoids). Pale yellow and pink petals had a considerably lower level of expression of genes for carotenoid degradation than white petals, suggesting that reduced degradation activity caused accumulation of carotenoids. Our results indicate that some carnation cultivars can synthesize and accumulate esterified carotenoids. By manipulating the rate of biosynthesis and esterification of carotenoids in these cultivars, it should be feasible to produce novel carnation cultivars with vivid yellow flowers.
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Affiliation(s)
- Luna Iijima
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Sanae Kishimoto
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan.
| | - Akemi Ohmiya
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-0852, Japan
| | - Emi Okamoto
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Taira Miyahara
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Takashi Tsujimoto
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Yoshihiro Ozeki
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takashi Hakamatsuka
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takanobu Kouno
- Japan Agribio Company Limited, 110-5 Itayamachi, Naka-ku, Hamamatsu, Shizuoka, 430-0928, Japan
| | - Emilio A Cano
- Barberet & Blanc S. A., Camino Viejo 205, 30890, Puerto Lumbreras, Murcia, Spain
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan
| | - Masahiro Nishihara
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan
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Ren L, Shang Y, Yang L, Wang S, Wang X, Chen S, Bao Z, An D, Meng F, Cai J, Guo Y. Chromosome-level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies. Mol Ecol Resour 2020; 21:251-262. [PMID: 32853451 DOI: 10.1111/1755-0998.13246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 01/29/2023]
Abstract
Sarcophaga peregrina is considered to be of great ecological, medical and forensic significance, and has unusual biological characteristics such as an ovoviviparous reproductive pattern and adaptation to feed on carrion. The availability of a high-quality genome will help to further reveal the mechanisms underlying these charcateristics. Here we present a de novo-assembled genome at chromosome scale for S. peregrina. The final assembled genome was 560.31 Mb with contig N50 of 3.84 Mb. Hi-C scaffolding reliably anchored six pseudochromosomes, accounting for 97.76% of the assembled genome. Moreover, 45.70% of repeat elements were identified in the genome. A total of 14,476 protein-coding genes were functionally annotated, accounting for 92.14% of all predicted genes. Phylogenetic analysis indicated that S. peregrina and S. bullata diverged ~ 7.14 million years ago. Comparative genomic analysis revealed expanded and positively selected genes related to biological features that aid in clarifying its ovoviviparous reproduction and carrion-feeding adaptations, such as lipid metabolism, olfactory receptor activity, antioxidant enzymes, proteolysis and serine-type endopeptidase activity. Protein-coding genes associated with ovoviparity, such as yolk proteins, transferrin and acid sphingomyelinase, were identified. This study provides a valuable genomic resource for S. peregrina, and sheds insight into further revealing the underlying molecular mechanisms of adaptive evolution.
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Affiliation(s)
- Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Li Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Shiwen Wang
- Department of Forensic Science, School of Basic Medical Sciences, Xinjiang Medical University, Ürümqi, China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Shan Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | | | - Dong An
- OE biotech Co. Ltd, Shanghai, China
| | - Fanming Meng
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
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Liu C, Shi X, Wu F, Ren M, Gao G, Wu Q. Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera. BMC Genomics 2020; 21:477. [PMID: 32652928 PMCID: PMC7354681 DOI: 10.1186/s12864-020-06891-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
Background Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China. Result The 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production. Conclusion The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Ahn CH, Ramya M, An HR, Park PM, Kim YJ, Lee SY, Jang S. Progress and Challenges in the Improvement of Ornamental Plants by Genome Editing. PLANTS 2020; 9:plants9060687. [PMID: 32481726 PMCID: PMC7356337 DOI: 10.3390/plants9060687] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023]
Abstract
Biotechnological approaches have been used to modify the floral color, size, and fragrance of ornamental plants, as well as to increase disease resistance and vase life. Together with the advancement of whole genome sequencing technologies, new plant breeding techniques have rapidly emerged in recent years. Compared to the early versions of gene editing tools, such as meganucleases (MNs), zinc fingers (ZFNs), and transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) is capable of altering a genome more efficiently and with higher accuracy. Most recently, new CRISPR systems, including base editors and prime editors, confer reduced off-target activity with improved DNA specificity and an expanded targeting scope. However, there are still controversial issues worldwide for the recognition of genome-edited plants, including whether genome-edited plants are genetically modified organisms and require a safety evaluation process. In the current review, we briefly summarize the current progress in gene editing systems and also introduce successful/representative cases of the CRISPR system application for the improvement of ornamental plants with desirable traits. Furthermore, potential challenges and future prospects in the use of genome-editing tools for ornamental plants are also discussed.
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Affiliation(s)
- Chang Ho Ahn
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Yae-Jin Kim
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Su Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
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Aalifar M, Aliniaeifard S, Arab M, Zare Mehrjerdi M, Dianati Daylami S, Serek M, Woltering E, Li T. Blue Light Improves Vase Life of Carnation Cut Flowers Through Its Effect on the Antioxidant Defense System. FRONTIERS IN PLANT SCIENCE 2020; 11:511. [PMID: 32670299 PMCID: PMC7326070 DOI: 10.3389/fpls.2020.00511] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/06/2020] [Indexed: 05/27/2023]
Abstract
Improving marketability and extension of vase life of cut flowers has practical significance for the development of the cut flower industry. Although considerable efforts have been made over many years to improve the vase life of cut flowers through controlling the immediate environment and through post-harvest use of floral preservatives, the impact of lighting environment on vase life has been largely overlooked. In the current study, the effect of three LED light spectra [white (400-730 nm), blue (peak at 460 nm), and red (peak at 660 nm)] at 150 μmol m-2 s-1 on vase life and on physiological and biochemical characteristics of carnation cut flowers was investigated. Exposure to blue light (BL) considerably delayed senescence and improved vase life over that of flowers exposed to red light (RL) and white light (WL). H2O2 and malondialdehyde (MDA) contents in petals gradually increased during vase life; the increase was lowest in BL-exposed flowers. As a consequence, BL-exposed flowers maintained a higher membrane stability index (MSI) compared to RL- and WL-exposed flowers. A higher activity of antioxidant enzymes [superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX)] was detected in petals of BL-exposed flowers, compared to their activities in RL- and WL-exposed flowers. In BL-exposed flowers, the decline in petal carotenoid contents was delayed in comparison to RL- and WL-exposed flowers. Maximum quantum efficiency of photosystem II (Fv/Fm) and a higher percentage of open stomata were observed in leaves of BL-exposed flowers. Sucrose and glucose contents accumulated in petals during vase life; sugar concentrations were higher in BL-exposed flowers than in RL- and WL-exposed flowers. It is concluded that BL exposure improves the vase life of carnation cut flowers through its effect on the antioxidant defense system in petals and on photosynthetic performance in the leaves.
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Affiliation(s)
- Mostafa Aalifar
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, Tehran, Iran
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, Tehran, Iran
| | - Mostafa Arab
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, Tehran, Iran
| | - Mahboobeh Zare Mehrjerdi
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, Tehran, Iran
| | - Shirin Dianati Daylami
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, Tehran, Iran
| | - Margrethe Serek
- Faculty of Natural Sciences, Institute of Horticultural Production Systems, Floriculture, Leibniz University Hannover, Hannover, Germany
| | - Ernst Woltering
- Wageningen Food & Biobased Research, Wageningen, Netherlands
- Horticulture and Product Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Tao Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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Gattolin S, Cirilli M, Chessa S, Stella A, Bassi D, Rossini L. Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2585-2595. [PMID: 31960023 PMCID: PMC7210751 DOI: 10.1093/jxb/eraa032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 05/04/2023]
Abstract
The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.
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Affiliation(s)
- Stefano Gattolin
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
- PTP Science Park, Lodi, Italy
- Correspondence: or
| | - Marco Cirilli
- Università degli Studi di Milano – DiSAA, Milano, Italy
| | - Stefania Chessa
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Alessandra Stella
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Daniele Bassi
- Università degli Studi di Milano – DiSAA, Milano, Italy
| | - Laura Rossini
- Università degli Studi di Milano – DiSAA, Milano, Italy
- Correspondence: or
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Gattolin S, Cirilli M, Chessa S, Stella A, Bassi D, Rossini L. Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots. JOURNAL OF EXPERIMENTAL BOTANY 2020. [PMID: 31960023 DOI: 10.1093/jxb/eraa032/5710789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.
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Affiliation(s)
- Stefano Gattolin
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
- PTP Science Park, Lodi, Italy
| | - Marco Cirilli
- Università degli Studi di Milano - DiSAA, Milano, Italy
| | - Stefania Chessa
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Alessandra Stella
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Milano, Italy
| | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Milano, Italy
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Meng F, Liu Z, Han H, Finkelbergs D, Jiang Y, Zhu M, Wang Y, Sun Z, Chen C, Guo Y, Cai J. Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly. Gigascience 2020; 9:giaa020. [PMID: 32191812 PMCID: PMC7081965 DOI: 10.1093/gigascience/giaa020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/26/2019] [Accepted: 02/14/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Blowflies (Diptera: Calliphoridae) are the most commonly found entomological evidence in forensic investigations. Distinguished from other blowflies, Aldrichina grahami has some unique biological characteristics and is a species of forensic importance. Its development rate, pattern, and life cycle can provide valuable information for the estimation of the minimum postmortem interval. FINDINGS Herein we provide a chromosome-level genome assembly of A. grahami that was generated by Pacific BioSciences sequencing platform and chromosome conformation capture (Hi-C) technology. A total of 50.15 Gb clean reads of the A. grahami genome were generated. FALCON and Wtdbg were used to construct the genome of A. grahami, resulting in an assembly of 600 Mb and 1,604 contigs with an N50 size of 1.93 Mb. We predicted 12,823 protein-coding genes, 99.8% of which was functionally annotated on the basis of the de novo genome (SRA: PRJNA513084) and transcriptome (SRA: SRX5207346) of A. grahami. According to the co-analysis with 11 other insect species, clustering and phylogenetic reconstruction of gene families were performed. Using Hi-C sequencing, a chromosome-level assembly of 6 chromosomes was generated with scaffold N50 of 104.7 Mb. Of these scaffolds, 96.4% were anchored to the total A. grahami genome contig bases. CONCLUSIONS The present study provides a robust genome reference for A. grahami that supplements vital genetic information for nonhuman forensic genomics and facilitates the future research of A. grahami and other necrophagous blowfly species used in forensic medicine.
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Affiliation(s)
- Fanming Meng
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
| | - Zhuoying Liu
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
| | - Han Han
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
| | | | - Yangshuai Jiang
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
| | - Mingfei Zhu
- Nextomics Biosciences, Wuhan, Hubei Pro, China
| | - Yang Wang
- Nextomics Biosciences, Wuhan, Hubei Pro, China
| | - Zongyi Sun
- Nextomics Biosciences, Wuhan, Hubei Pro, China
| | - Chao Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences
| | - Yadong Guo
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
| | - Jifeng Cai
- School of Basic Medicine, Central South University, Changsha, Hunan Pro, China
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Ding X, Mei W, Lin Q, Wang H, Wang J, Peng S, Li H, Zhu J, Li W, Wang P, Chen H, Dong W, Guo D, Cai C, Huang S, Cui P, Dai H. Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. Gigascience 2020; 9:giaa013. [PMID: 32118265 PMCID: PMC7050300 DOI: 10.1093/gigascience/giaa013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/01/2019] [Accepted: 02/03/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUD Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. FINDINGS We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18-84.37 million years ago. CONCLUSIONS Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.
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Affiliation(s)
- Xupo Ding
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wenli Mei
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Qiang Lin
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Rd. Pengfei No. 7, Shenzhen 518120, China
| | - Hao Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Jun Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Shiqing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Huiliang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Jiahong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wei Li
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Pei Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Huiqin Chen
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wenhua Dong
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Caihong Cai
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Shengzhuo Huang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Peng Cui
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Rd. Pengfei No. 7, Shenzhen 518120, China
| | - Haofu Dai
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
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Wang Q, Dan N, Zhang X, Lin S, Bao M, Fu X. Identification, Characterization and Functional Analysis of C-Class Genes Associated with Double Flower Trait in Carnation ( Dianthus caryphyllus L.). PLANTS 2020; 9:plants9010087. [PMID: 31936710 PMCID: PMC7020439 DOI: 10.3390/plants9010087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/19/2019] [Accepted: 01/06/2020] [Indexed: 11/23/2022]
Abstract
Flowers with more petals are of more ornamental value. It is well known that AGAMOUS (AG) is the core member of the C-class gene which plays an essential role in double flower formation and identification of stamens and carpels in Arabidopsisthaliana. We searched C-class genes in the genome of the carnation, and found two AG orthologs (DcaAGa, DcaAGb). Phylogenetic analysis showed that the two genes were closely related to the euAG subclade. Then we searched the genomes of other Caryophyllales plants (Beta vulgaris, Spinacia oleracea, Chenopodium quinoa) for C-class genes, and found that their C-class genes all belonged to the euAG subclade. Semi-quantitative PCR (sq-PCR) analysis indicated that the expression of DcaAG genes in the single flower phenotype was higher than that in the double flower phenotype. Quantitative real-time RT-PCR (qRT-PCR) analysis showed that the expressions of DcaAG genes in the flower bud were significantly different from those in the root, stem, and leaf between the single and double flower phenotype carnations, and that DcaAG genes were specifically expressed in the stamen and carpel of carnation. Moreover, the expression of other floral organ identity genes (AP1 and AP2, PI and AP3, SEP1 and SEP3 corresponding to the A-, B-, and E-class of genes, respectively) showed no significant difference in all floral organs between the single and double flower phenotype carnations, suggesting that C-class (DcaAG) genes might play an important role in the double flower phenotype in carnation. Petal loss or decrease, precocious flowering, silique shortening, and seed sterility were observed in 35S::DcaAGa and 35S::DcaAGb transgenic Arabidopsis plants. All these results show that DcaAG genes might affect the petal number negatively and have a specific function in stamen and carpel development in carnation.
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Affiliation(s)
- Qijian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
| | - Naizhen Dan
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
| | - Xiaoni Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (N.D.); (X.Z.); (S.L.); (M.B.)
- Key Laboratory of Urban Agriculture in Central China (pilot run), Ministry of Agriculture, Wuhan 430070, China
- Correspondence: ; Tel.: +86-159-2625-8658; Fax: +86-027-8728-2010
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Yang Y, Liu X, Cai J, Chen Y, Li B, Guo Z, Huang G. Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae. BMC Genomics 2019; 20:782. [PMID: 31660859 PMCID: PMC6819638 DOI: 10.1186/s12864-019-6095-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 09/10/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte. RESULTS In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity. CONCLUSIONS The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.
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Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Xiaobao Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Jimiao Cai
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Yipeng Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Boxun Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Zhikai Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
| | - Guixiu Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101 China
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Li W, Wan XL, Yu JY, Wang KL, Zhang J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation ( Dianthus caryophyllus). Int J Mol Sci 2019; 20:ijms20205233. [PMID: 31652538 PMCID: PMC6829504 DOI: 10.3390/ijms20205233] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 01/26/2023] Open
Abstract
Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Xue-Li Wan
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jia-Yu Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Kui-Ling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Hirakawa H, Sumitomo K, Hisamatsu T, Nagano S, Shirasawa K, Higuchi Y, Kusaba M, Koshioka M, Nakano Y, Yagi M, Yamaguchi H, Taniguchi K, Nakano M, Isobe SN. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res 2019; 26:195-203. [PMID: 30689773 PMCID: PMC6589549 DOI: 10.1093/dnares/dsy048] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.
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Affiliation(s)
| | - Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Soichiro Nagano
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.,Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Juo, Hitachi, Ibaraki, Japan
| | | | - Yohei Higuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Masaji Koshioka
- College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Kanagawa, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Kenji Taniguchi
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Michiharu Nakano
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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46
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Wu Z, Sloan DB. Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes. Heredity (Edinb) 2019; 122:647-659. [PMID: 30356223 PMCID: PMC6461862 DOI: 10.1038/s41437-018-0153-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/08/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022] Open
Abstract
Although mitochondrial genomes are typically thought of as single circular molecules, these genomes are fragmented into multiple chromosomes in many eukaryotes, raising intriguing questions about inheritance and (in)stability of mtDNA in such systems. A previous comparison of mitochondrial genomes from two different individuals of the angiosperm species Silene noctiflora found variation in the presence of entire mitochondrial chromosomes. Here, we expand on this work with a geographically diverse sampling of 25 S. noctiflora populations and the closely related species S. turkestanica and S. undulata. Using a combination of deep sequencing and PCR-based screening for the presence of 22 different mitochondrial chromosomes, we found extensive variation in the complement of chromosomes across individuals. Much of this variation could be attributed to recent chromosome loss events, suggesting that the massively expanded and fragmented mitochondrial genomes of S. noctiflora may have entered a phase of genome reduction in which they are losing entire chromosomes at a rapid rate. Sequence analysis of mitochondrial and plastid genomes revealed genealogical differences both between these organelles and within the mitochondrial genome, indicating a history of recombination. Evidence that recombination has generated novel combinations of alleles was more frequent between loci on different mitochondrial chromosomes than it was within chromosomes. Therefore, the fragmentation of mitochondrial genomes and the assortment of chromosomes during mitochondrial inheritance appears to have contributed to a history of sexual-like recombination in the mtDNA of this species.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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47
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Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 446] [Impact Index Per Article: 89.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
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48
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Li G, Tembrock LR, Wu Z, Liu F. Complete chloroplast genome of carnation (Caryophyllaceae: Dianthus caryophyllus L.). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1598789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Guoliang Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Luke R. Tembrock
- Department of Bioagricultural Sciences and Pest Management College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Fengqi Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Science, Beijing, China
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49
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Kishi-Kaboshi M, Aida R, Sasaki K. Genome engineering in ornamental plants: Current status and future prospects. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:47-52. [PMID: 29709514 DOI: 10.1016/j.plaphy.2018.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 05/21/2023]
Abstract
Ornamental plants, like roses, carnations, and chrysanthemums, are economically important and are sold all over the world. In addition, numerous cut and garden flowers add colors to homes and gardens. Various strategies of plant breeding have been employed to improve traits of many ornamental plants. These approaches span from conventional techniques, such as crossbreeding and mutation breeding, to genetically modified plants. Recently, genome editing has become available as an efficient means for modifying traits in plant species. Genome editing technology is useful for genetic analysis and is poised to become a common breeding method for ornamental plants. In this review, we summarize the benefits and limitations of conventional breeding techniques and genome editing methods and discuss their future potential to accelerate the rate breeding programs in ornamental plants.
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Affiliation(s)
- Mitsuko Kishi-Kaboshi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan
| | - Ryutaro Aida
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan
| | - Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan.
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50
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Miyahara T, Sugishita N, Ishida-Dei M, Okamoto E, Kouno T, Cano EA, Sasaki N, Watanabe A, Tasaki K, Nishihara M, Ozeki Y. Carnation I locus contains two chalcone isomerase genes involved in orange flower coloration. BREEDING SCIENCE 2018; 68:481-487. [PMID: 30369823 PMCID: PMC6198906 DOI: 10.1270/jsbbs.18029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/19/2018] [Indexed: 05/21/2023]
Abstract
Carnations carrying a recessive I gene show accumulation of the yellow pigment chalcononaringenin 2'-glucoside (Ch2'G) in their flowers, whereas those with a dominant I gene do accumulation the red pigment, anthocyanin. Although this metabolic alternative at the I gene could explain yellow and red flower phenotypes, it does not explain the development of orange flower phenotypes which result from the simultaneous accumulation of both Ch2'G and anthocyanin. The carnation whole genome sequencing project recently revealed that two chalcone isomerase genes are present, one that is consistent with the I gene (Dca60979) and another (Dca60978) that had not been characterized. Here, we demonstrate that Dca60979 shows a high level of gene expression and strong enzyme activity in plants with a red flower phenotype; however, functional Dca60979 transcripts are not detected in plants with an orange flower phenotype because of a dTdic1 insertion event. Dca60978 was expressed at a low level and showed a low level of enzyme activity in plants, which could catalyze a part of chalcone to naringenin to advance anthocyanin synthesis but the other part remained to be catalyzed chalcone to Ch2'G by chalcone 2'-glucosyltransferase, resulting in accumulation of anthocyanin and Ch2'G simultaneously to give orange color.
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Affiliation(s)
- Taira Miyahara
- Department of Biotechnology, Tokyo University of Agriculture and Technology,
Koganei, Tokyo 184-8588,
Japan
| | - Natsu Sugishita
- Department of Biotechnology, Tokyo University of Agriculture and Technology,
Koganei, Tokyo 184-8588,
Japan
| | - Madoka Ishida-Dei
- Department of Biotechnology, Tokyo University of Agriculture and Technology,
Koganei, Tokyo 184-8588,
Japan
| | - Emi Okamoto
- Department of Biotechnology, Tokyo University of Agriculture and Technology,
Koganei, Tokyo 184-8588,
Japan
| | - Takanobu Kouno
- Japan Agribio Company Limited,
110-5 Itayamachi, Naka-ku, Hamamatsu, Shizuoka 430-0928,
Japan
| | - Emilio A. Cano
- Barberet & Blanc,
Camino Viejo 205, 30890, Puerto Lumbreras-Murcia,
Spain
| | - Nobuhiro Sasaki
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Aiko Watanabe
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Keisuke Tasaki
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Masahiro Nishihara
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Yoshihiro Ozeki
- Department of Biotechnology, Tokyo University of Agriculture and Technology,
Koganei, Tokyo 184-8588,
Japan
- Corresponding author (e-mail: )
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