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Li T, Bian J, Tang M, Shangguan H, Zeng Y, Luo R, Sun H, Ke Q, Nie X, Li Y, Cui L. BGFD: an integrated multi-omics database of barley gene families. BMC PLANT BIOLOGY 2022; 22:454. [PMID: 36131236 PMCID: PMC9490965 DOI: 10.1186/s12870-022-03846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history. RESULTS We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com ). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable. CONCLUSIONS BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Minqiang Tang
- College of Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Hongbin Shangguan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Huifan Sun
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Qinglin Ke
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
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Sui J, Jia W, Xin Y, Zhang Y. Transcriptomics-Based Identification of Genes Related to Tapetum Degradation and Microspore Development in Lily. Genes (Basel) 2022; 13:genes13020366. [PMID: 35205410 PMCID: PMC8872214 DOI: 10.3390/genes13020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 12/04/2022] Open
Abstract
Lily is a popular and economically ornamental crop around the world. However, its high production of pollen grains causes serious problems to consumers, including allergies and staining of clothes. During anther development, the tapetum is a crucial step for pollen formation and microspore release. Therefore, it is important to understand the mechanism of tapetum degradation and microspore development in lily where free pollen contamination occurs. Here, we used the cut lily cultivar ‘Siberia’ to characterize the process of tapetum degradation through the use of cytology and transcriptomic methods. The cytological observation indicated that, as the lily buds developed from 4 cm (Lo 4 cm) to 8 cm (Lo 8 cm), the tapetum completed the degradation process and the microspores matured. Furthermore, by comparing the transcriptome profiling among three developmental stages (Lo 4 cm, Lo 6 cm and Lo 8 cm), we identified 27 differentially expressed genes. These 27 genes were classed into 4 groups by function, namely, cell division and expansion, cell-wall morphogenesis, transcription factors, LRR-RLK (leucine-rich repeat receptor-like kinases), plant hormone biosynthesis and transduction. Quantitative real-time PCR was performed as validation of the transcriptome data. These selected genes are candidate genes for the tapetum degradation and microspore development of lily and our work provides a theoretical basis for breeding new lily cultivars without pollen.
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Affiliation(s)
- Juanjuan Sui
- Department of Biology, Biology and Food Engineering College, Fuyang Normal University, Fuyang 236037, China;
| | - Wenjie Jia
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.J.); (Y.X.)
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Yin Xin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China; (W.J.); (Y.X.)
| | - Yuanyuan Zhang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Correspondence:
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Liu X, Wu Z, Feng J, Yuan G, He L, Zhang D, Teng N. A Novel R2R3-MYB Gene LoMYB33 From Lily Is Specifically Expressed in Anthers and Plays a Role in Pollen Development. FRONTIERS IN PLANT SCIENCE 2021; 12:730007. [PMID: 34630475 PMCID: PMC8495421 DOI: 10.3389/fpls.2021.730007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Lily (Lilium spp.) is an important commercial flower crop, but its market popularity and applications are adversely affected by severe pollen pollution. Many studies have examined pollen development in model plants, but few studies have been conducted on flower crops such as lily. GAMYBs are a class of R2R3-MYB transcription factors and play important roles in plant development and biotic resistance; their functions vary in different pathways, and many of them are involved in anther development. However, their function and regulatory role in lily remain unclear. Here, the GAMYB homolog LoMYB33 was isolated and identified from lily. The open reading frame of LoMYB33 was 1620 bp and encoded a protein with 539 amino acids localized in the nucleus and cytoplasm. Protein sequence alignment showed that LoMYB33 contained a conserved R2R3 domain and three BOX motifs (BOX1, BOX2, and BOX3), which were unique to the GAMYB family. LoMYB33 had transcriptional activation activity, and its transactivation domain was located within 90 amino acids of the C-terminal. LoMYB33 was highly expressed during the late stages of anther development, especially in pollen. Analysis of the promoter activity of LoMYB33 in transgenic Arabidopsis revealed that the LoMYB33 promoter was highly activated in the pollen of stage 12 to 13 flowers. Overexpression of LoMYB33 in Arabidopsis significantly retarded growth; the excess accumulation of LoMYB33 also negatively affected normal anther development, which generated fewer pollen grains and resulted in partial male sterility in transgenic plants. Silencing of LoMYB33 in lily also greatly decreased the amount of pollen. Overall, our results suggested that LoMYB33 might play an important role in the anther development and pollen formation of lily.
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Affiliation(s)
- Xinyue Liu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jingxian Feng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guozhen Yuan
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ling He
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Dehua Zhang
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nianjun Teng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Guo W, Zhan X, Jiang F, Xi Y. Analysis of allergen components and identification of bioactivity of HSP70 in pollen of Populus deltoides. Proteome Sci 2021; 19:10. [PMID: 34479544 PMCID: PMC8417992 DOI: 10.1186/s12953-021-00178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Allergies caused by pollen from Populus deltoides are common, but the allergic components are still unclear. Methods The total proteins in pollen of P. deltoides were analyzed by proteomics, and the potential allergens were identified via the WHO/IUIS database and the allergenOnline database retrieval. One target protein was screened by bioinformatics and expressed in Escherichia coli. The biological activity of the expressed product was verified by animal experiments. Results The total of 3929 proteins in pollen of P. deltoides were identified, and 46 potential allergens belonging to 10 protein families were recognized by database retrieval. B9N9W6 protein of Hsp70 family was screened by bioinformatics analysis and expressed successfully. ELISA showed that B9N9W6 can stimulate the immune system to produce specific IgE and promote the generation of IL-4. Flow cytometry showed that B9N9W6 can significantly stimulate the proliferation of CD4+ T cells and promote the polarization of Th2 cells. The pathological sections of mice lung tissues indicated that alveolar destruction was more severe in the B9N9W6 group than that of extract group, and there were more inflammatory cells infiltration, mucus exudation and bleeding. Conclusion B9N9W6 is an important antigenic substance in the pollen of P. deltoides. Due to the conserved structure of Hsp70 family, more attention should be paid to the possibility of sensitization when Hsp70 from any pathogenic species is administered. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00178-8.
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Affiliation(s)
- Wei Guo
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.,Department of Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, 241002, China
| | - Xiaodong Zhan
- Department of Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, 241002, China
| | - Feng Jiang
- Department of Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, 241002, China
| | - Yilong Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
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