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Ma Y, Liu H, Wang J, Zhao G, Niu K, Zhou X, Zhang R, Yao R. Genomic identification and expression profiling of DMP genes in oat (Avena sativa) elucidate their responsiveness to seed aging. BMC Genomics 2024; 25:863. [PMID: 39285326 PMCID: PMC11403964 DOI: 10.1186/s12864-024-10743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/28/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND The Domain of unknown function 679 membrane protein (DMP) family, which is unique to plants, plays a crucial role in reproductive development, stress response and aging. A comprehensive study was conducted to identify the DMP gene members of oat (Avena sativa) and to investigate their structural features and tissue-specific expression profiles. Utilizing whole genome and transcriptome data, we analyzed the physicochemical properties, gene structure, cis-acting elements, phylogenetic relationships, conserved structural (CS) domains, CS motifs and expression patterns of the AsDMP family in A. sativa. RESULTS The DMP family genes of A. sativa were distributed across 17 chromosomal scaffolds, encompassing a total of 33 members. Based on phylogenetic relationships, the AsDMP genes were classified into five distinct subfamilies. The gene structure also suggests that A. sativa may have undergone an intron loss event during its evolution. Covariance analysis indicates that genome-wide duplication and segmental duplication may be the major contributor to the expansion of the AsDMP gene family. Ka/Ks selective pressure analysis of the AsDMP gene family suggests that DMP gene pairs are generally conserved over evolutionary time. The upstream promoters of these genes contain several cis-acting elements, suggesting a potential role in abiotic stress responses and hormone induction. Transcriptome data revealed that the expression patterns of the DMP genes are involved in tissue and organ development. In this study, the AsDMP genes (AsDMP1, AsDMP19, and AsDMP22) were identified as potential regulators of seed senescence in A. sativa. These genes could serve as candidates for breeding studies focused on seed longevity and anti-aging germplasm in A. sativa. The study provides valuable insights into the regulatory mechanisms of the AsDMP gene family in the aging process of A. sativa germplasm and offers theoretical support for further function investigation into the functions of AsDMP genes and the molecular mechanisms underlying seed anti-aging. CONCLUSIONS This study identified the AsDMP genes as being involved in the aging process of A. sativa seeds, marking the first report on the potential role of DMP genes in seed aging for A. sativa.
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Affiliation(s)
- Yuan Ma
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huan Liu
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Jinglong Wang
- Tibet Grassland Science Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, China
| | - Guiqin Zhao
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Kuiju Niu
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiangrui Zhou
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ran Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Grassland Research Center, National Forestry and Grassland Administration, Beijing, 100091, China
| | - Ruirui Yao
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
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Guo X, Zhu W, Wang F, Wang H. Genome-Wide Investigation of the PLD Gene Family in Tomato: Identification, Analysis, and Expression. Genes (Basel) 2024; 15:326. [PMID: 38540385 PMCID: PMC10970076 DOI: 10.3390/genes15030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Phospholipase Ds (PLDs) are important phospholipid hydrolases in plants that play crucial roles in the regulation of plant growth, development, and stress tolerance. In this study, 14 PLD genes were identified in the tomato genome and were localized on eight chromosomes, and one tandem-duplicated gene pair was identified. According to a phylogenetic analysis, the genes were categorized into four subtypes: SlPLDα, β, and δ belonged to the C2-PLD subfamily, while SlPLDζ belonged to the PXPH-PLD subfamily. The gene structure and protein physicochemical properties were highly conserved within the same subtype. The promoter of all the SlPLD genes contained hormone-, light-, and stress-responsive cis-acting regulatory elements, but no significant correlation between the number, distribution, and type of cis-acting elements was observed among the members of the same subtype. Transcriptome data showed that the expression of the SlPLD genes was different in multiple tissues. A quantitative RT-PCR analysis revealed that the SlPLD genes responded positively to cold, salt, drought, and abscisic acid treatments, particularly to salt stress. Different expression patterns were observed for different genes under the same stress, and for the same gene under different stresses. The results provide important insights into the functions of SlPLD genes and lay a foundation for further studies of the response of SlPLD genes to abiotic stresses.
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Affiliation(s)
| | | | | | - Hui Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (X.G.)
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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] [Key Words] [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.
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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
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Wei J, Shao W, Liu X, He L, Zhao C, Yu G, Xu J. Genome-wide identification and expression analysis of phospholipase D gene in leaves of sorghum in response to abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1261-1276. [PMID: 35910446 PMCID: PMC9334518 DOI: 10.1007/s12298-022-01200-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 06/03/2023]
Abstract
Abiotic stress caused by unsuitable environmental changes brings serious impacts on the growth and development of sorghum, resulting in significant loss in yield and quality every year. Phospholipase D is one of the key enzymes that catalyze the hydrolysis of phospholipids, and participates in plants response to abiotic stresses and phytohormones, whereas as the main producers of Phosphatidic acid (PA) signal, the detailed information about Phospholipase D associated (SbPLD) family in sorghum has been rarely reported. This study was performed to identify the PLD family gene in sorghum based on the latest genome annotation and to determine the expression of PLDs under abiotic stresses by qRT-PCR analysis. In this study, 13 PLD genes were identified in sorghum genome and further divided into 7 groups according to the phylogenetic analysis. All sorghum PLD family members harbored two conserved domains (HDK1&2) with catalytic activity, and most members contained a C2 domain. In ζ subfamily, C2 domain was replaced by PX and PH domain. The exon-intron structure of SbPLD genes within the same subfamily was highly conservative. The tissue specific expression analysis revealed different expression of SbPLD genes in various developmental stages. High level expression of SbPLDα3 was observed in almost all tissues, whereas SbPLDα4 was mainly expressed in roots. Under abiotic stress conditions, SbPLD genes responded actively to NaCl, ABA, drought (PEG) and cold (4 °C) treatment at the transcriptional level. The expression of SbPLDβ1 was significantly up-regulated, while the transcription of SbPLDζ was suppressed under various stress conditions. In addition, SbPLDβ1 and SbPLDδ2 were predicted to be the target genes of sbi-miR159 and sbi-miR167, respectively. This study will help to decipher the roles of PLDs in sorghum growth and abiotic stress responses. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01200-9.
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Affiliation(s)
- Jinpeng Wei
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
- Ministry of Agriculture and Rural Affairs Agro-Products and Processed Products Quality Supervision, Inspection and Testing Center, Daqing, 163319 China
- National Coarse Cereal Engineering Research Center, Daqing, 163319 China
| | - Wenjing Shao
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Xinyu Liu
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Lin He
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Changjiang Zhao
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Gaobo Yu
- College of Horticulture and Landscape, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Jingyu Xu
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Engineering Technology Research Center for Crop Straw Utilization, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
- National Coarse Cereal Engineering Research Center, Daqing, 163319 China
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Zhang Y, Yao J, Yin K, Liu Z, Zhang Y, Deng C, Liu J, Zhang Y, Hou S, Zhang H, Yu D, Zhao N, Zhao R, Chen S. Populus euphratica Phospholipase Dδ Increases Salt Tolerance by Regulating K +/Na + and ROS Homeostasis in Arabidopsis. Int J Mol Sci 2022; 23:ijms23094911. [PMID: 35563299 PMCID: PMC9105705 DOI: 10.3390/ijms23094911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Phospholipase Dα (PLDα), which produces signaling molecules phosphatidic acid (PA), has been shown to play a critical role in plants adapting to salt environments. However, it is unclear whether phospholipase Dδ (PLDδ) can mediate the salt response in higher plants. PePLDδ was isolated from salt-resistant Populus euphratica and transferred to Arabidopsis thaliana to testify the salt tolerance of transgenic plants. The NaCl treatment (130 mM) reduced the root growth and whole-plant fresh weight of wild-type (WT) A. thaliana, vector controls (VC) and PePLDδ-overexpressed lines, although a less pronounced effect was observed in transgenic plants. Under salt treatment, PePLDδ-transgenic Arabidopsis exhibited lower electrolyte leakage, malondialdehyde content and H2O2 levels than WT and VC, resulting from the activated antioxidant enzymes and upregulated transcripts of genes encoding superoxide dismutase, ascorbic acid peroxidase and peroxidase. In addition, PePLDδ-overexpressed plants increased the transcription of genes encoding the plasma membrane Na+/H+ antiporter (AtSOS1) and H+-ATPase (AtAHA2), which enabled transgenic plants to proceed with Na+ extrusion and reduce K+ loss under salinity. The capacity to regulate reactive oxygen species (ROS) and K+/Na+ homeostasis was associated with the abundance of specific PA species in plants overexpressing PePLDδ. PePLDδ-transgenic plants retained a typically higher abundance of PA species, 34:2 (16:0–18:2), 34:3 (16:0–18:3), 36:4 (18:2–18:2), 36:5 (18:2–18:3) and 36:6 (18:3–18:3), under control and saline conditions. It is noteworthy that PA species 34:2 (16:0–18:2), 34:3 (16:0–18:3), 36:4 (18:2–18:2) and 36:5 (18:2–18:3) markedly increased in response to NaCl in transgenic plants. In conclusion, we suppose that PePLDδ-derived PA enhanced the salinity tolerance by regulating ROS and K+/Na+ homeostasis in Arabidopsis.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China;
| | - Kexin Yin
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Zhe Liu
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Yanli Zhang
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Chen Deng
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Jian Liu
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Yinan Zhang
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
- Forestry Institute of New Technology, Chinese Academy of Forestry, Beijing 100091, China
| | - Siyuan Hou
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Huilong Zhang
- Research Center of Saline and Alkali Land of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China;
| | - Dade Yu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing 100700, China;
| | - Nan Zhao
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Rui Zhao
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
| | - Shaoliang Chen
- Key Laboratory of Forest and Flower Genetics and Breeding of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (K.Y.); (Z.L.); (Y.Z.); (C.D.); (J.L.); (Y.Z.); (S.H.); (N.Z.); (R.Z.)
- Correspondence: ; Tel.: +86-10-6233-8129
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Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress. Curr Issues Mol Biol 2021; 43:1632-1651. [PMID: 34698114 PMCID: PMC8929030 DOI: 10.3390/cimb43030116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family is the largest family of the receptor-like protein kinases (RLKs) superfamily in higher plants, which is involved in regulating the plant growth and development, stress responses, signal transduction and so on. However, no comprehensive analyses of LRR-RLKs have been reported in sugarcane. Here, we performed a comprehensive analysis of the LRR-RLK gene family in sugarcane ancestor species Saccharum spontaneum. A total of 437 LRR-RLK genes were identified and categorized into 14 groups based on a maximum likelihood phylogenetic tree. The chromosome location showed an uneven distribution on all 32 chromosomes in sugarcane. Subsequently, the exon-intron organization structure and conserved motif arrangement were relatively conserved among the same groups or subgroups and between Arabidopsis and S. spontaneum genomes. Furthermore, the promoter sequences analyses showed that sugarcane LRR-RLK genes (SsLRR-RLKs) were strongly regulated by various environmental stimuli, phytohormonal factors and transcription factors (TFs). Eventually, the expression profiles of SsLRR-RLK genes at different stresses were analyzed based on RNA-seq data, suggesting their potential roles in the regulation of sugarcane responses to diverse abiotic and biotic stress. Overall, the findings provide insight into the potential functional roles and lay the foundation for further functional study.
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