1
|
Zhang H, Yu Y, Wang S, Yang J, Ai X, Zhang N, Zhao X, Liu X, Zhong C, Yu H. Genome-wide characterization of phospholipase D family genes in allotetraploid peanut and its diploid progenitors revealed their crucial roles in growth and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1102200. [PMID: 36743478 PMCID: PMC9895952 DOI: 10.3389/fpls.2023.1102200] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses such as cold, drought and salinity are the key environmental factors that limit the yield and quality of oil crop peanut. Phospholipase Ds (PLDs) are crucial hydrolyzing enzymes involved in lipid mediated signaling and have valuable functions in plant growth, development and stress tolerance. Here, 22, 22 and 46 PLD genes were identified in Arachis duranensis, Arachis ipaensis and Arachis hypogaea, respectively, and divided into α, β, γ, δ, ε, ζ and φ isoforms. Phylogenetic relationships, structural domains and molecular evolution proved the conservation of PLDs between allotetraploid peanut and its diploid progenitors. Almost each A. hypogaea PLD except for AhPLDα6B had a corresponding homolog in A. duranensis and A. ipaensis genomes. The expansion of Arachis PLD gene families were mainly attributed to segmental and tandem duplications under strong purifying selection. Functionally, the most proteins interacting with AhPLDs were crucial components of lipid metabolic pathways, in which ahy-miR3510, ahy-miR3513-3p and ahy-miR3516 might be hub regulators. Furthermore, plenty of cis-regulatory elements involved in plant growth and development, hormones and stress responses were identified. The tissue-specific transcription profiling revealed the broad and unique expression patterns of AhPLDs in various developmental stages. The qRT-PCR analysis indicated that most AhPLDs could be induced by specific or multiple abiotic stresses. Especially, AhPLDα3A, AhPLDα5A, AhPLDβ1A, AhPLDβ2A and AhPLDδ4A were highly up-regulated under all three abiotic stresses, whereas AhPLDα9A was neither expressed in 22 peanut tissues nor induced by any abiotic stresses. This genome-wide study provides a systematic analysis of the Arachis PLD gene families and valuable information for further functional study of candidate AhPLDs in peanut growth and abiotic stress responses.
Collapse
|
2
|
Zhao J, Pu X, Li W, Li M. Characterization and evolutionary diversification of the phospholipase D gene family in mosses. Front Genet 2022; 13:1015393. [PMID: 36313445 PMCID: PMC9607936 DOI: 10.3389/fgene.2022.1015393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Plant phospholipase D (PLD) exerts important roles in various biological processes, such as intracellular signaling and morphological development. Our knowledge about early land plant PLDs is still underdeveloped. In this study, we identified 84 PLD genes in six mosses, i.e., Physcomitrella patens, Ceratodon purpureus, Fontinalis antipyretica, Pleurozium schreberi, Sphagnum magellanicum, and Sphagnum fallax. These PLDs were classified into four clades (I–IV). We showed that PLD underwent rapid expansion in mosses. A total of six conserved domains and two core HKD motifs were detected. Structure analysis uncovered that the moss PLDs from within a clade generally exhibited similar exon-intron organization. Cis-elements prediction and expression analyses indicated that P. patens PLDs had key roles in stress responsiveness and plant development. Particularly, about half of the P. patens PLDs (e.g., PpPLD1, PpPLD2, and PpPLD5) were differentially expressed under biotic and abiotic stresses. We also determined the expression pattern of P. patens PLD genes in various tissues and at different stages of development. Although the moss, clubmoss, liverwort, and fern PLDs evolved largely under functional constraints, we found episodic positive selection in the moss PLDs, e.g., C. purpureus PLD2 and P. patens PLD11. We infer that the evolutionary force acting on the PLDs may have facilitated moss colonization of land. Our work provides valuable insights into the diversification of moss PLD genes, and can be used for future studies of their functions.
Collapse
Affiliation(s)
- Jinjie Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Xinyuan Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Wenfei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Meng Li
- Yunnan Academy of Tobacco Science, Kunming, Yunnan, China
- *Correspondence: Meng Li,
| |
Collapse
|
3
|
Sadat MA, Ullah MW, Hossain MS, Ahmed B, Bashar KK. Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress. J Genet Eng Biotechnol 2022; 20:28. [PMID: 35147846 PMCID: PMC8837719 DOI: 10.1186/s43141-022-00311-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/30/2022] [Indexed: 11/17/2022]
Abstract
Background Plant grows in nature facing various types of abiotic stresses for their normal growth and development. During abiotic stress, plants evolve different types of mechanisms to survive in a hostile environment. Phospholipase D (PLD) plays important role in the regulation of diverse cellular processes including stress responses in plants. Member of PLD genes are well studied in different model plants; however, their functions in the jute are not clear yet. Result In the present study, a total of 12 and 11 PLD genes were identified in the genome of C. capsularis and C. olitorius, respectively. The presence of the two conserved HKD motifs in PLD genes except for CoPLDδ-2 in jute suggests their strong lipase activity. Twenty different motifs were found in the identified PLD genes, and PLD-β1, PLD-γ1, and all members of PLD-δ1 of both jute species contained the highest number of motifs. Phylogenetic analysis showed the close evolutionary relationship among the five groups of jute PLD proteins along with the PLD proteins from Arabidopsis. Tissue-specific expression pattern of PLDα1-2, PLD-α2, PLDβ1, PLDγ1, and PLDδ1 of two jute species suggested their involvement in plant growth and development. However, the expression pattern of PLDα1-2, PLDα1-3, PLD-α4, PLDδ1, and PLDδ3 indicated their association during waterlogging stress. In addition, PLD-α2, PLDβ1, and PLDδ2 seemed to be involved in drought stress as well as salinity stress. Conclusion This genome-wide identification of jute PLD genes from C. capsularis and C. olitorius will help to further functional characterization of the PLD genes for developing stress-tolerant jute variety.
Collapse
Affiliation(s)
- Md Abu Sadat
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh.
| | - Md Wali Ullah
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Kazi Khayrul Bashar
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| |
Collapse
|
4
|
Ma C, Zhang Q, Lv J, Qiao K, Fan S, Ma Q, Zhang C. Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence. FRONTIERS IN PLANT SCIENCE 2021; 12:728025. [PMID: 34659294 PMCID: PMC8517146 DOI: 10.3389/fpls.2021.728025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Phospholipase D (PLD) and its hydrolysis product phosphatidic acid play an important role in the regulation of several cellular processes, including root growth, pollen tube elongation, and microtubule reorganization. Here, we systematically identified and analyzed the membership, characterization, and evolutionary relationship of PLDs in five species of cotton. The results of the transcriptomic analysis suggested that the evaluated PLD genes showed high expression levels in anther tissue and during the fiber initiation and elongation periods. Quantitative real-time polymerase chain reaction showed differential expression of GhPLD genes in the anthers of photoperiod sensitive male sterility mutant 5 (psm5). Previous research on multiple stable quantitative trait loci also suggests the role of PLD genes in the fiber development. Further analyses showed that GhPLD2 protein is localized to the plasma membrane. The virus-induced gene silencing of GhPLD2 in cotton seedlings repressed its expression by 40-70%, which led to a reduction in reactive oxygen species (ROS) levels, 22% anther indehiscence, and disrupted fiber initiation and elongation. Thus, we inferred that GhPLD2 may promote ROS production, which, in turn, may regulate anther dehiscence and fiber development.
Collapse
Affiliation(s)
- Changkai Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Qian Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jiaoyan Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Kaikai Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| |
Collapse
|
5
|
Mo S, Zhang Y, Wang X, Yang J, Sun Z, Zhang D, Chen B, Wang G, Ke H, Liu Z, Meng C, Li Z, Wu L, Zhang G, Duan H, Ma Z. Cotton GhSSI2 isoforms from the stearoyl acyl carrier protein fatty acid desaturase family regulate Verticillium wilt resistance. MOLECULAR PLANT PATHOLOGY 2021; 22:1041-1056. [PMID: 34169624 PMCID: PMC8358998 DOI: 10.1111/mpp.13093] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 05/04/2023]
Abstract
Lipids are major and essential constituents of plant cells and provide energy for various metabolic processes. However, the function of the lipid signal in defence against Verticillium dahliae, a hemibiotrophic pathogen, remains unknown. Here, we characterized 19 conserved stearoyl-ACP desaturase family proteins from upland cotton (Gossypium hirsutum). We further confirmed that GhSSI2 isoforms, including GhSSI2-A, GhSSI2-B, and GhSSI2-C located on chromosomes A10, D10, and A12, respectively, played a dominant role to the cotton 18:1 (oleic acid) pool. Suppressing the expression of GhSSI2s reduced the 18:1 level, which autoactivated the hypersensitive response (HR) and enhanced cotton Verticillium wilt and Fusarium wilt resistance. We found that low 18:1 levels induced phenylalanine ammonia-lyase-mediated salicylic acid (SA) accumulation and activated a SA-independent defence response in GhSSI2s-silenced cotton, whereas suppressing expression of GhSSI2s affected PDF1.2-dependent jasmonic acid (JA) perception but not the biosynthesis and signalling cascade of JA. Further investigation showed that structurally divergent resistance-related genes and nitric oxide (NO) signal were activated in GhSSI2s-silenced cotton. Taken together, these results indicate that SA-independent defence response, multiple resistance-related proteins, and elevated NO level play an important role in GhSSI2s-regulated Verticillium wilt resistance. These findings broaden our knowledge regarding the lipid signal in disease resistance and provide novel insights into the molecular mechanism of cotton fungal disease resistance.
Collapse
Affiliation(s)
- Shaojing Mo
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and RegulationNorth China Key Laboratory for Crop Germplasm Resources of Education MinistryHebei Agricultural UniversityBaodingChina
| |
Collapse
|
6
|
Genome-Wide Analysis and Expression Profiling of the Phospholipase D Gene Family in Solanum tuberosum. BIOLOGY 2021; 10:biology10080741. [PMID: 34439973 PMCID: PMC8389595 DOI: 10.3390/biology10080741] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/17/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022]
Abstract
Phospholipase D (PLD) is the most important phospholipid hydrolase in plants, which can hydrolyze phospholipids into phosphatidic acid (PA) and choline. When plants encounter low temperature, drought and high salt stress, phospholipase D and its products play an important role in regulating plant growth and development and coping with stress. In this study, 16 members of StPLD gene family were identified in potato genome, which were distributed in α, β, δ, and ζ subfamilies, and their expression patterns under salt, high temperature, drought, and ABA stress were detected by qRT-PCR method. Gene expression analysis showed that the expression of StPLD genes in potato was upregulated and downregulated to varying degrees under the four stresses, indicating that the PLD gene family is involved in the interaction of potato plant hormones and abiotic stress signals. Chromosome distribution showed that StPLD gene was unevenly distributed on 8 chromosomes, and only one pair of tandem repeat genes was found. All StPLD promoters contain hormone and stress-related cis-regulatory elements to respond to different stresses. Structural analysis showed that StPLD genes in the same subgroup had a similar exon-intron structure. Our study provides a valuable reference for further research of the function and structure of PLD gene.
Collapse
|
7
|
Roshan NM, Ashouri M, Sadeghi SM. Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea ( Camellia sinensis). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1219-1232. [PMID: 34177145 PMCID: PMC8212259 DOI: 10.1007/s12298-021-01007-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 05/16/2023]
Abstract
UNLABELLED Phospholipase D (PLD) (EC 3.1.4.4) plays important roles in plants growth, development, and response to environmental stresses. Tea plant (Camellia sinensis) is the most important non-alcoholic beverage in the world with health benefits, but tea production decreases in response to environmental stresses such as cold and drought. Therefore, a genome-wide analysis of the C. sinensis PLD gene family (CsPLDs) was carried out. In the current study, identification, evolutionary relationship, duplication, selection pressure, gene structure, promoter analysis, transcript-targeted miRNA, and simple sequence repeat markers prediction, RNA-seq data analysis, and three-dimensional structure of the CsPLDs have been investigated using bioinformatics tools. 15 PLDs were identified from the tea genome which belongs to five groups, including CsPLDα, CsPLDβ, CsPLDδ, CsPLDε, and CsPLDζ. Both segmental and tandem duplications have occurred in the CsPLD gene family. Ka/Ks ratio for the most duplicated pair genes was less than 1 which implies negative selection to conserve their function during the tea evolution. 68 cis-elements have been found in CsPLDs indicating the contribution of these genes in response to environmental stresses. Likewise, 72 SSR loci and 96 miRNA molecules in 14 and 15 CsPLDs have been detected. According to RNA-seq data, the highest expression in all tissues under various abiotic stresses was related to CsPLDα1. Besides, a three-dimensional structure of the CsPLDα1 was evaluated to better understand its biological activity. This research provides comprehensive information that could be useful in future studies to develop stress-tolerant tea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01007-0.
Collapse
Affiliation(s)
| | - Majid Ashouri
- Department of Agronomy and Plant Breeding, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Seyyed Mostafa Sadeghi
- Department of Agronomy and Plant Breeding, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| |
Collapse
|
8
|
Tian B, Sun M, Jayawardana K, Wu D, Chen G. Characterization of a PLDζ2 Homology Gene from Developing Castor Bean Endosperm. Lipids 2020; 55:537-548. [PMID: 32115716 DOI: 10.1002/lipd.12231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Castor oil contains approximately 90% ricinoleic acid (RA) which is stored mainly in the form of tri-ricinoleic acid containing triacylglycerols (TAG). Ricinoleate is synthesized from oleate (18:1n-9) esterified to the sn-2 position of phosphatidylcholine (PtdCho) catalyzed by oleoyl-12-hydroxylase. PtdCho-derived diacylglycerol (DAG) is an important substrate pool for TAG synthesis, and the interconversion between PtdCho and DAG has been shown to play a critical role in channeling hydroxy fatty acids (HFA) to TAG. Although phospholipase D (PLD) has been reported to catalyze the hydrolysis of PtdCho to produce phosphatidic acid which can then be converted to DAG, its potential functions in the channeling of RA from PtdCho to DAG and the assembly of RA on TAG is largely unknown. In the present study, 11 PLD genes were identified from the Castor Bean Genome Database. Gene expression analysis indicated that RcPLD9 is expressed at relatively high levels in developing seeds compared to other plant tissues. Sequence and phylogenetic analyses revealed that RcPLD9 is a homolog of Arabidopsis PLDζ2. Overexpression of RcPLD9 in the Arabidopsis CL7 line producing C18-HFA resulted in RA content reductions in the polar lipid fraction (mainly PtdCho) and mono-HFA-TAG, but increased RA content in di-HFA-TAG. Since part of RA in di-HFA-TAG is derived from HFA-DAG, the results indicated that RcPLD9 facilitates the channeling of RA from PtdCho to DAG for its assembly on TAG in developing seeds.
Collapse
Affiliation(s)
- Bo Tian
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Meijuan Sun
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Kethmi Jayawardana
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Ding Wu
- Jingdezhen University, Jingdezhen, 333000, China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| |
Collapse
|
9
|
Lu S, Fadlalla T, Tang S, Li L, Ali U, Li Q, Guo L. Genome-Wide Analysis of Phospholipase D Gene Family and Profiling of Phospholipids under Abiotic Stresses in Brassica napus. PLANT & CELL PHYSIOLOGY 2019; 60:1556-1566. [PMID: 31073607 DOI: 10.1093/pcp/pcz071] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/06/2019] [Indexed: 05/28/2023]
Abstract
Oil crop Brassica napus is subjected to environmental stresses such as drought, cold and salt. Phospholipase Ds (PLDs) have vital roles in regulation of plant growth, development and stress tolerance. In this study, 32 BnaPLD genes were identified and classified into six subgroups depending on the conserved protein structures. High similarity in gene and protein structures exists between BnaPLDs and AtPLDs. Gene expression analysis showed that BnaPLDα1s and BnaPLDδs had higher expression than other PLDs. BnaPLDα1 and BnaPLDδ were significantly induced by abiotic stresses including dehydration, NaCl, abscisic acid (ABA) and 4�C. Lipidomic analysis showed that the content of main membrane phospholipids decreased gradually under stresses, except phosphatidylglycerol increased under the treatment of ABA and phosphatidylethanolamine increased under 4�C. Correspondingly, their product of phosphatidic acid increased often with a transient peak at 8 h. The plant height of mutants of PLDα1 was significantly reduced. Agronomic traits such as yield, seed number, silique number and branches were significantly impaired in PLDα1 mutants. These results indicate that there is a large family of PLD genes in B. napus, especially BnaPLDα1s and BnaPLDδs may play important roles in membrane lipids remodeling and maintaining of the growth and stress tolerance of B. napus.
Collapse
Affiliation(s)
- Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- These authors contributed equally to this work
| | - Tarig Fadlalla
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- These authors contributed equally to this work
| | - Shan Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Usman Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
10
|
Li J, Wang X. Phospholipase D and phosphatidic acid in plant immunity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:45-50. [PMID: 30709492 DOI: 10.1016/j.plantsci.2018.05.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 05/20/2023]
Abstract
Phospholipase D (PLD) hydrolyzes membrane phospholipids to generate phosphatidic acid (PA). Both PLD and its lipid product PA are involved in various physiological processes, including plant response to pathogens. The PLD family is comprised of multiple members in higher plants, and PLDs have been reported to play positive and/or negative roles in plant immunity, depending on the types of pathogens and specific PLDs involved. Individual PLDs have distinguishable biochemical properties, such as Ca2+ and phosphatidylinositide requirements. In addition, PLDs and PA are found to interact with various proteins in hormone and stress signaling. The different biochemical and regulatory properties of PLDs and PA shed light on the mechanisms for the functional diversity of PLDs in plant defense signaling and response.
Collapse
Affiliation(s)
- Jianwu Li
- Henan Agricultural University, Henan, 450002, China; Department of Biology, University of Missouri, St. Louis, MO 63121, United States; Donald Danforth Plant Science Center, St. Louis, MO 63132, United States.
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121, United States; Donald Danforth Plant Science Center, St. Louis, MO 63132, United States.
| |
Collapse
|
11
|
Liu Z, Qanmber G, Lu L, Qin W, Liu J, Li J, Ma S, Yang Z, Yang Z. Genome-wide analysis of BES1 genes in Gossypium revealed their evolutionary conserved roles in brassinosteroid signaling. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1566-1582. [PMID: 30607883 DOI: 10.1007/s11427-018-9412-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/23/2018] [Indexed: 01/11/2023]
Abstract
Brassinosteroids (BRs), which are essential phytohormones for plant growth and development, are important for cotton fiber development. Additionally, BES1 transcription factors are critical for BR signal transduction. However, cotton BES1 family genes have not been comprehensively characterized. In this study, we identified 11 BES1 genes in G. arboreum, 11 in G. raimondii, 16 in G. barbadense, and 22 in G. hirsutum. The BES1 sequences were significantly conserved in the Arabidopsis thaliana, rice, and upland cotton genomes. A total of 94 BES1 genes from 10 different plant species were divided into three clades according to the neighbor-joining and minimum-evolution methods. Moreover, the exon/intron patterns and motif distributions were highly conserved among the A. thaliana and cotton BES1 genes. The collinearity among the orthologs from the At and Dt subgenomes was estimated. Segmental duplications in the At and Dt subgenomes were primarily responsible for the expansion of the cotton BES1 gene family. Of the GhBES1 genes, GhBES1.4_At/Dt exhibited BL-induced expression and was predominantly expressed in fibers. Furthermore, Col-0/mGhBES1.4_At plants produced curled leaves with long and bent petioles. These transgenic plants also exhibited decreased hypocotyl sensitivity to brassinazole and constitutive BR induced/repressed gene expression patterns. The constitutive BR responses of the plants overexpressing mGhBES1.4_At were similar to those of the bes1-D mutant.
Collapse
Affiliation(s)
- Zhao Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shuya Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoen Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China.
| |
Collapse
|
12
|
Chen ZW, Cao JF, Zhang XF, Shangguan XX, Mao YB, Wang LJ, Chen XY. Cotton genome: challenge into the polyploidy. Sci Bull (Beijing) 2017; 62:1622-1623. [PMID: 36659376 DOI: 10.1016/j.scib.2017.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Zhi-Wen Chen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jun-Feng Cao
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiu-Fang Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiao-Xia Shangguan
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Ying-Bo Mao
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai 201602, China.
| |
Collapse
|
13
|
Wu Z, Yang Y, Huang G, Lin J, Xia Y, Zhu Y. Cotton functional genomics reveals global insight into genome evolution and fiber development. J Genet Genomics 2017; 44:511-518. [PMID: 29169921 DOI: 10.1016/j.jgg.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/22/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.
Collapse
Affiliation(s)
- Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Lin
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuying Xia
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
14
|
Han EH, Petrella DP, Blakeslee JJ. 'Bending' models of halotropism: incorporating protein phosphatase 2A, ABCB transporters, and auxin metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3071-3089. [PMID: 28899081 DOI: 10.1093/jxb/erx127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Salt stress causes worldwide reductions in agricultural yields, a problem that is exacerbated by the depletion of global freshwater reserves and the use of contaminated or recycled water (i.e. effluent water). Additionally, salt stress can occur as cultivated areas are subjected to frequent rounds of irrigation followed by periods of moderate to severe evapotranspiration, which can result in the heterogeneous aggregation of salts in agricultural soils. Our understanding of the later stages of salt stress and the mechanisms by which salt is transported out of cells and roots has greatly improved over the last decade. The precise mechanisms by which plant roots perceive salt stress and translate this perception into adaptive, directional growth away from increased salt concentrations (i.e. halotropism), however, are not well understood. Here, we provide a review of the current knowledge surrounding the early responses to salt stress and the initiation of halotropism, including lipid signaling, protein phosphorylation cascades, and changes in auxin metabolism and/or transport. Current models of halotropism have focused on the role of PIN2- and PIN1-mediated auxin efflux in initiating and controlling halotropism. Recent studies, however, suggest that additional factors such as ABCB transporters, protein phosphatase 2A activity, and auxin metabolism should be included in the model of halotropic growth.
Collapse
Affiliation(s)
- Eun Hyang Han
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
| | - Dominic P Petrella
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Science, OARDC Metabolite Analysis Cluster (OMAC), The Ohio State University/OARDC, Wooster, OH, USA
| |
Collapse
|
15
|
Zhang B, Wang Y, Liu JY. Genome-wide identification and characterization of phospholipase C gene family in cotton (Gossypium spp.). SCIENCE CHINA-LIFE SCIENCES 2017; 61:88-99. [PMID: 28547583 DOI: 10.1007/s11427-017-9053-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/01/2017] [Indexed: 01/05/2023]
Abstract
Phospholipase C (PLC) are important regulatory enzymes involved in several lipid and Ca2+-dependent signaling pathways. Previous studies have elucidated the versatile roles of PLC genes in growth, development and stress responses of many plants, however, the systematic analyses of PLC genes in the important fiber-producing plant, cotton, are still deficient. In this study, through genome-wide survey, we identified twelve phosphatidylinositol-specific PLC (PI-PLC) and nine non-specific PLC (NPC) genes in the allotetraploid upland cotton Gossypium hirsutum and nine PI-PLC and six NPC genes in two diploid cotton G. arboretum and G.raimondii, respectively. The PI-PLC and NPC genes of G. hirsutum showed close phylogenetic relationship with their homologous genes in the diploid cottons and Arabidopsis. Segmental and tandem duplication contributed greatly to the formation of the gene family. Expression profiling indicated that few of the PLC genes are constitutely expressed, whereas most of the PLC genes are preferentially expressed in specific tissues and abiotic stress conditions. Promoter analyses further implied that the expression of these PLC genes might be regulated by MYB transcription factors and different phytohormones. These results not only suggest an important role of phospholipase C members in cotton plant development and abiotic stress response but also provide good candidate targets for future molecular breeding of superior cotton cultivars.
Collapse
Affiliation(s)
- Bing Zhang
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanmei Wang
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jin-Yuan Liu
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
16
|
Tang K, Liu JY. Molecular characterization of GhPLDα1 and its relationship with secondary cell wall thickening in cotton fibers. Acta Biochim Biophys Sin (Shanghai) 2017; 49:33-43. [PMID: 27864277 DOI: 10.1093/abbs/gmw113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
Phospholipase D (PLD) hydrolyzes phospholipids to generate a free polar head group (e.g., choline) and a second messenger phosphatidic acid and plays diverse roles in plant growth and development, including seed germination, leaf senescence, root hair growth, and hypocotyl elongation. However, the function of PLD in cotton remains largely unexplored. Here, the comprehensive molecular characterization of GhPLDα1 was explored with its role in upland cotton (Gossypium hirsutum) fiber development. The GhPLDα1 gene was cloned successfully, and a sequence alignment showed that GhPLDα1 contains one C2 domain and two HKD (HxKxxxxD) domains. Quantitative reverse transcriptase-polymerase chain reaction measured the expression of GhPLDα1 in various cotton tissues with the highest level in fibers at 20 days post anthesis (d.p.a.). Fluorescent microscopy and immunoblotting in tobacco epidermis showed the GhPLDα1 distribution in both cell membranes and the cytoplasm. An activity assay indicated changes in PLDα enzyme activity in developing fiber cells with a peak level at 20 d.p.a., coinciding with the onset of cellulose accumulation and the increased H2O2 content during fiber development. Furthermore, the inhibition of PLDα activity obviously decreased the cellulose and H2O2 contents of in vitro-cultured cotton fibers. These results provide important evidence explaining the relationship of GhPLDα1 with secondary cell wall thickening in cotton fibers in that GhPLDα1 may correlate with the increased H2O2 content at the onset of secondary cell wall thickening, ultimately promoting cellulose biosynthesis.
Collapse
Affiliation(s)
- Kai Tang
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Yuan Liu
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
17
|
Bourtsala A, Farmaki T, Galanopoulou D. Phospholipases Dα and δ are involved in local and systemic wound responses of cotton ( G. hirsutum). Biochem Biophys Rep 2016; 9:133-139. [PMID: 28955998 PMCID: PMC5614590 DOI: 10.1016/j.bbrep.2016.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/29/2022] Open
Abstract
Phospholipases D (PLDs) catabolize structural phospholipids to produce phosphatidic acid (PtdOH), a lipid playing central role in signalling pathways in animal, yeast and plant cells. In animal cells two PLD genes have been studied while in model plant Arabidopsis twelve genes exist, classified in six classes (α-ζ). This underlines the role of these enzymes in plant responses to environmental stresses. However, information concerning the PLD involvement in the widely cultivated and economically important cotton plant responses is very limited. The aim of this report was to study the activity of conventional cotton PLD and its participation in plant responses to mechanical wounding, which resembles both biotic and abiotic stresses. PLDα activity was identified and further characterized by transphosphatidylation reaction. Upon wounding, cotton leaf responses consist of an acute in vitro increase of PLDα activity in both wounded and systemic tissue. However, determination of the in vivo PtdOH levels under the same wounding conditions revealed a rapid PtdOH formation only in wounded leaves and a late response of a PtdOH increase in both tissues. Εxpression analysis of PLDα and PLDδ isoforms showed mRNA accumulation of both isoforms in the wounded tissue, but only PLDδ exerts a high and sustainable expression in systemic leaves, indicating that this isoform is mainly responsible for the systemic wound-induced PtdOH production. Therefore, our data suggest that PLDα and PLDδ isoforms are involved in different steps in cotton wound signalling. PLDα activity and PtdOH levels rapidly increase in wounded cotton leaves. PLDα is also activated rapidly in systemic tissue. Doubling of PtdOH levels occurs as a late response in both wounded and systemic tissue. PLDδ (but not PLDα) exerts a high and sustainable expression in systemic leaves. PLDα and PLDδ are involved in different steps in cotton wound signalling.
Collapse
Affiliation(s)
- Angeliki Bourtsala
- National and Kapodistrian University of Athens, Department of Chemistry, Panepistimiopolis, 15771 Athens, Greece
| | - Theodora Farmaki
- Institute of Applied Biosciences, Centre for Research and Technology, 57001 Thessaloniki, Greece
| | - Dia Galanopoulou
- National and Kapodistrian University of Athens, Department of Chemistry, Panepistimiopolis, 15771 Athens, Greece
| |
Collapse
|
18
|
Tang K, Dong CJ, Liu JY. Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors. PLoS One 2016; 11:e0156281. [PMID: 27213891 PMCID: PMC4877076 DOI: 10.1371/journal.pone.0156281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/11/2016] [Indexed: 01/19/2023] Open
Abstract
In this study, 40 phospholipase D (PLD) genes were identified from allotetraploid cotton Gossypium hirsutum, and 20 PLD genes were examined in diploid cotton Gossypium raimondii. Combining with 19 previously identified Gossypium arboreum PLD genes, a comparative analysis was performed among the PLD gene families among allotetraploid and two diploid cottons. Based on the orthologous relationships, we found that almost each G. hirsutum PLD had a corresponding homolog in the G. arboreum and G. raimondii genomes, except for GhPLDβ3A, whose homolog GaPLDβ3 may have been lost during the evolution of G. arboreum after the interspecific hybridization. Phylogenetic analysis showed that all of the cotton PLDs were unevenly classified into six numbered subgroups: α, β/γ, δ, ε, ζ and φ. An N-terminal C2 domain was found in the α, β/γ, δ and ε subgroups, while phox homology (PX) and pleckstrin homology (PH) domains were identified in the ζ subgroup. The subgroup φ possessed a single peptide instead of a functional domain. In each phylogenetic subgroup, the PLDs showed high conservation in gene structure and amino acid sequences in functional domains. The expansion of GhPLD and GrPLD gene families were mainly attributed to segmental duplication and partly attributed to tandem duplication. Furthermore, purifying selection played a critical role in the evolution of PLD genes in cotton. Quantitative RT-PCR documented that allotetraploid cotton PLD genes were broadly expressed and each had a unique spatial and developmental expression pattern, indicating their functional diversification in cotton growth and development. Further analysis of cis-regulatory elements elucidated transcriptional regulations and potential functions. Our comparative analysis provided valuable information for understanding the putative functions of the PLD genes in cotton fiber.
Collapse
Affiliation(s)
- Kai Tang
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chun-Juan Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin-Yuan Liu
- Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
| |
Collapse
|
19
|
Zhu Y. The post-genomics era of cotton. SCIENCE CHINA-LIFE SCIENCES 2016; 59:109-11. [PMID: 26803303 DOI: 10.1007/s11427-016-5017-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 09/12/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Yuxian Zhu
- Institute for Advanced Studies and College of Life Science, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
20
|
Wang Y, Ding Y, Liu JY. Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1722. [PMID: 27909445 PMCID: PMC5112280 DOI: 10.3389/fpls.2016.01722] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 11/02/2016] [Indexed: 05/03/2023]
Abstract
Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families. Furthermore, RLM-5' RACE (RNA ligase-mediated rapid amplification of 5'-cDNA ends) experiments identified the targets of eight important miRNAs, and the expression levels of these target genes were confirmed to be negatively correlated with the expression patterns of their corresponding miRNAs. We propose a potential functional network mediated through these eight miRNAs to illustrate their important functions in fiber elongation. Our study provides novel insights into the dynamic profiles of these miRNAs and a basis for investigating the regulatory mechanisms involved in the elongation of cotton fibers.
Collapse
|