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Wang Q, Wang Y, Zhang F, Han C, Wang Y, Ren M, Qi K, Xie Z, Zhang S, Tao S, Shiratake K. Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2024; 24:444. [PMID: 38778247 PMCID: PMC11112822 DOI: 10.1186/s12870-024-05138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls. RESULTS In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets. CONCLUSIONS This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.
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Affiliation(s)
- Qi Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Yueyang Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fanhang Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengyang Han
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanling Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mei Ren
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shutian Tao
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Katsuhiro Shiratake
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
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Zhang D, Zhao X, Huang Y, Zhang MM, He X, Yin W, Lan S, Liu ZJ, Ma L. Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1372580. [PMID: 38736444 PMCID: PMC11082295 DOI: 10.3389/fpls.2024.1372580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/11/2024] [Indexed: 05/14/2024]
Abstract
The Homeodomain-Leucine Zipper (HD-ZIP) transcription factors play a pivotal role in governing various aspects of plant growth, development, and responses to abiotic stress. Despite the well-established importance of HD-ZIPs in many plants, their functions in Acoraceae, the basal lineage of monocots, remain largely unexplored. Using recently published whole-genome data, we identified 137 putative HD-ZIPs in two Acoraceae species, Acorus gramineus and Acorus calamus. These HD-ZIP genes were further classified into four subfamilies (I, II, III, IV) based on phylogenetic and conserved motif analyses, showcasing notable variations in exon-intron patterns among different subfamilies. Two microRNAs, miR165/166, were found to specifically target HD-ZIP III genes with highly conserved binding sites. Most cis-acting elements identified in the promoter regions of Acoraceae HD-ZIPs are involved in modulating light and phytohormone responsiveness. Furthermore, our study revealed an independent duplication event in Ac. calamus and a one-to-multiple correspondence between HD-ZIP genes of Ac. calamus and Ac. gramineus. Expression profiles obtained from qRT-PCR demonstrated that HD-ZIP I genes are strongly induced by salinity stress, while HD-ZIP II members have contrasting stress responses in two species. HD-ZIP III and IV genes show greater sensitivity in stress-bearing roots. Taken together, these findings contribute valuable insights into the roles of HD-ZIP genes in stress adaptation and plant resilience in basal monocots, illuminating their multifaceted roles in plant growth, development, and response to abiotic stress.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meng-Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- School of Pharmacy, Fujian Health Vocational and Technical College, Fuzhou, China
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Yang F, Zhang L, Zhang X, Guan J, Wang B, Wu X, Song M, Wei A, Liu Z, Huo D. Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2024; 24:249. [PMID: 38580941 PMCID: PMC10998406 DOI: 10.1186/s12870-024-04926-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) belongs to Polygonaceae family and has attracted increasing attention owing to its high nutritional value. UDP-glycosyltransferases (UGTs) glycosylate a variety of plant secondary metabolites to control many metabolic processes during plant growth and development. However, there have been no systematic reports of UGT superfamily in F. tataricum. RESULTS We identified 173 FtUGTs in F. tataricum based on their conserved UDPGT domain. Phylogenetic analysis of FtUGTs with 73 Arabidopsis UGTs clustered them into 21 families. FtUGTs from the same family usually had similar gene structure and motif compositions. Most of FtUGTs did not contain introns or had only one intron. Tandem repeats contributed more to FtUGTs amplification than segmental duplications. Expression analysis indicates that FtUGTs are widely expressed in various tissues and likely play important roles in plant growth and development. The gene expression analysis response to different abiotic stresses showed that some FtUGTs were involved in response to drought and cadmium stress. Our study provides useful information on the UGTs in F. tataricum, and will facilitate their further study to better understand their function. CONCLUSIONS Our results provide a theoretical basis for further exploration of the functional characteristics of FtUGTs and for understanding the growth, development, and metabolic model in F. tataricum.
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Affiliation(s)
- Fan Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Lei Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Xiao Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Jingru Guan
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Bo Wang
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoying Wu
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Minli Song
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Aili Wei
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Dongao Huo
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China.
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Wang Y, Wang H, Yu C, Yan X, Chu J, Jiang B, Zhu J. Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis. BMC Genomics 2024; 25:182. [PMID: 38360569 PMCID: PMC10870566 DOI: 10.1186/s12864-024-10067-x] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported. RESULTS A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis. CONCLUSIONS In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.
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Affiliation(s)
- Yujiao Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Hongjuan Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Chun Yu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Xiaoming Yan
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Jiasong Chu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Benli Jiang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
| | - Jiabao Zhu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
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Yu H, Wu X, Liang J, Han Z, Xiao Y, Du H, Liu Y, Guo J, Peng F. Genome-wide identification of nucleotide-binding domain leucine-rich repeat (NLR) genes and their association with green peach aphid (Myzus persicae) resistance in peach. BMC PLANT BIOLOGY 2023; 23:513. [PMID: 37880593 PMCID: PMC10598982 DOI: 10.1186/s12870-023-04474-7] [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: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023]
Abstract
Resistance genes (R genes) are a class of genes that are immune to a wide range of diseases and pests. In planta, NLR genes are essential components of the innate immune system. Currently, genes belonging to NLR family have been found in a number of plant species, but little is known in peach. Here, 286 NLR genes were identified on peach genome by using their homologous genes in Arabidopsis thaliana as queries. These 286 NLR genes contained at least one NBS domain and LRR domain. Phylogenetic and N-terminal domain analysis showed that these NLRs could be separated into four subfamilies (I-IV) and their promoters contained many cis-elements in response to defense and phytohormones. In addition, transcriptome analysis showed that 22 NLR genes were up-regulated after infected by Green Peach Aphid (GPA), and showed different expression patterns. This study clarified the NLR gene family and their potential functions in aphid resistance process. The candidate NLR genes might be useful in illustrating the mechanism of aphid resistance in peach.
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Affiliation(s)
- Haixiang Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xuelian Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiahui Liang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ziying Han
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yuansong Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hao Du
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong, 276000, China
| | - Jian Guo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.
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Wang Z, Wu X, Zhang B, Xiao Y, Guo J, Liu J, Chen Q, Peng F. Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach. BMC PLANT BIOLOGY 2023; 23:122. [PMID: 36864374 PMCID: PMC9979464 DOI: 10.1186/s12870-023-04061-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. Although some functions of HD-Zip transcription factor have been reported in several plants, it has not been comprehensively studied in peach, especially during adventitious root formation of peach cuttings. RESULTS In this study, 23 HD-Zip genes distributed on 6 chromosomes were identified from the peach (Prunus persica) genome, and named PpHDZ01-23 according to their positions on the chromosomes. These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. Spatio-temporal expression pattern showed that these genes were expressed in many tissues with different levels, and they had distinct expression pattern during adventitious root formation and development. CONCLUSION Our results showed the roles of PpHDZs on root formation, which is helpful to better understand the classification and function of peach HD-Zip genes.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Xuelian Wu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Binbin Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jian Guo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jin Liu
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China
| | - Qiuju Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China.
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
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