1
|
Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [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: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
Collapse
Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| |
Collapse
|
2
|
Wang Z, Fu W, Zhang X, Liusui Y, Saimi G, Zhao H, Zhang J, Guo Y. Identification of the Gossypium hirsutum SDG Gene Family and Functional Study of GhSDG59 in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1257. [PMID: 38732472 PMCID: PMC11085088 DOI: 10.3390/plants13091257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
SET-domain group histone methyltransferases (SDGs) are known to play crucial roles in plant responses to abiotic stress. However, their specific function in cotton's response to drought stress has not been well understood. This study conducted a comprehensive analysis of the SDG gene family in Gossypium hirsutum, identifying a total of 82 SDG genes. An evolutionary analysis revealed that the SDG gene family can be divided into eight subgroups. The expression analysis shows that some GhSDG genes are preferentially expressed in specific tissues, indicating their involvement in cotton growth and development. The transcription level of some GhSDG genes is induced by PEG, with GhSDG59 showing significant upregulation upon polyethylene glycol (PEG) treatment. Quantitative polymerase chain reaction (qPCR) analysis showed that the accumulation of transcripts of the GhSDG59 gene was significantly upregulated under drought stress. Further functional studies using virus-induced gene silencing (VIGS) revealed that silencing GhSDG59 reduced cotton tolerance to drought stress. Under drought conditions, the proline content, superoxide dismutase (SOD) and peroxidase (POD) enzyme activities in the GhSDG59-silenced plants were significantly lower than in the control plants, while the malondialdehyde (MDA) content was significantly higher. Transcriptome sequencing showed that silencing the GhSDG59 gene led to significant changes in the expression levels of 1156 genes. The KEGG enrichment analysis revealed that these differentially expressed genes (DEGs) were mainly enriched in the carbon metabolism and the starch and sucrose metabolism pathways. The functional annotation analysis identified known drought-responsive genes, such as ERF, CIPK, and WRKY, among these DEGs. This indicates that GhSDG59 is involved in the drought-stress response in cotton by affecting the expression of genes related to the carbon metabolism and the starch and sucrose metabolism pathways, as well as known drought-responsive genes. This analysis provides valuable information for the functional genomic study of SDGs and highlights potential beneficial genes for genetic improvement and breeding in cotton.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jingbo Zhang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, XinjiangNormal University, Urumqi 830017, China; (Z.W.); (W.F.); (X.Z.); (Y.L.); (G.S.); (H.Z.)
| | - Yanjun Guo
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, XinjiangNormal University, Urumqi 830017, China; (Z.W.); (W.F.); (X.Z.); (Y.L.); (G.S.); (H.Z.)
| |
Collapse
|
3
|
Yue C, Cao H, Zhang S, Shen G, Wu Z, Yuan L, Luo L, Zeng L. Multilayer omics landscape analyses reveal the regulatory responses of tea plants to drought stress. Int J Biol Macromol 2023; 253:126582. [PMID: 37652332 DOI: 10.1016/j.ijbiomac.2023.126582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/12/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
Adverse environments, especially drought conditions, deeply influence plant development and growth in all aspects, and the yield and quality of tea plants are largely dependent on favorable growth conditions. Although tea plant responses to drought stress (DS) have been studied, a comprehensive multilayer epigenetic, transcriptomic, and proteomic investigation of how tea responds to DS is lacking. In this study, we generated DNA methylome, transcriptome, proteome, and phosphoproteome data to explore multiple regulatory landscapes in the tea plant response to DS. An integrated multiomics analysis revealed the response of tea plants to DS at multiple regulatory levels. Furthermore, a set of DS-responsive genes involved in photosynthesis, transmembrane transportation, phytohormone metabolism and signaling, secondary metabolite pathways, transcription factors, protein kinases, posttranslational and epigenetic modification, and other key stress-responsive genes were identified for further functional investigation. These results reveal the multilayer regulatory landscape of the tea plant response to DS and provide insight into the mechanisms of these DS responses.
Collapse
Affiliation(s)
- Chuan Yue
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China.
| | - Hongli Cao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Shaorong Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Gaojian Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Zhijun Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Lianyu Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Liyong Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Liang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China.
| |
Collapse
|
4
|
Zhang ZW, Fu YF, Yang XY, Yuan M, Zheng XJ, Luo XF, Zhang MY, Xie LB, Shu K, Reinbothe S, Reinbothe C, Wu F, Feng LY, Du JB, Wang CQ, Gao XS, Chen YE, Zhang YY, Li Y, Tao Q, Lan T, Tang XY, Zeng J, Chen GD, Yuan S. Singlet oxygen induces cell wall thickening and stomatal density reducing by transcriptome reprogramming. J Biol Chem 2023; 299:105481. [PMID: 38041932 PMCID: PMC10731243 DOI: 10.1016/j.jbc.2023.105481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Singlet oxygen (1O2) has a very short half-life of 10-5 s; however, it is a strong oxidant that causes growth arrest and necrotic lesions on plants. Its signaling pathway remains largely unknown. The Arabidopsis flu (fluorescent) mutant accumulates a high level of 1O2 and shows drastic changes in nuclear gene expression. Only two plastid proteins, EX1 (executer 1) and EX2 (executer 2), have been identified in the singlet oxygen signaling. Here, we found that the transcription factor abscisic acid insensitive 4 (ABI4) binds the promoters of genes responsive to 1O2-signals. Inactivation of the ABI4 protein in the flu/abi4 double mutant was sufficient to compromise the changes of almost all 1O2-responsive-genes and rescued the lethal phenotype of flu grown under light/dark cycles, similar to the flu/ex1/ex2 triple mutant. In addition to cell death, we reported for the first time that 1O2 also induces cell wall thickening and stomatal development defect. Contrastingly, no apparent growth arrest was observed for the flu mutant under normal light/dim light cycles, but the cell wall thickening (doubled) and stomatal density reduction (by two-thirds) still occurred. These results offer a new idea for breeding stress tolerant plants.
Collapse
Affiliation(s)
- Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Xin-Yue Yang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Ming Yuan
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Xiao-Jian Zheng
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Xiao-Feng Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Meng-Yao Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Lin-Bei Xie
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Steffen Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes and Biologie Environnementale et Systémique (BEeSy), Université Grenoble Alpes, Grenoble, France
| | - Christiane Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes and Biologie Environnementale et Systémique (BEeSy), Université Grenoble Alpes, Grenoble, France
| | - Fan Wu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Ling-Yang Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jun-Bo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chang-Quan Wang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Xue-Song Gao
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Yang-Er Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yan-Yan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Yang Li
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Ting Lan
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Xiao-Yan Tang
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China
| | - Guang-Deng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China.
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Investigation and Monitoring, Protection and Utilization for Cultivated Land Resources, Ministry of Natural Resources, Chengdu, China.
| |
Collapse
|