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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Chen X, Zhang J, Wang S, Cai H, Yang M, Dong Y. Genome-wide molecular evolution analysis of the GRF and GIF gene families in Plantae (Archaeplastida). BMC Genomics 2024; 25:74. [PMID: 38233778 PMCID: PMC10795294 DOI: 10.1186/s12864-024-10006-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Plant growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) interact with each other and collectively have important regulatory roles in plant growth, development, and stress responses. Therefore, it is of great significance to explore the systematic evolution of GRF and GIF gene families. However, our knowledge and understanding of the role of GRF and GIF genes during plant evolution has been fragmentary. RESULTS In this study, a large number of genomic and transcriptomic datasets of algae, mosses, ferns, gymnosperms and angiosperms were used to systematically analyze the evolution of GRF and GIF genes during the evolution of plants. The results showed that GRF gene first appeared in the charophyte Klebsormidium nitens, whereas the GIF genes originated relatively early, and these two gene families were mainly expanded by segmental duplication events after plant terrestrialization. During the process of evolution, the protein sequences and functions of GRF and GIF family genes are relatively conservative. As cooperative partner, GRF and GIF genes contain the similar types of cis-acting elements in their promoter regions, which enables them to have similar transcriptional response patterns, and both show higher levels of expression in reproductive organs and tissues and organs with strong capacity for cell division. Based on protein-protein interaction analysis and verification, we found that the GRF-GIF protein partnership began to be established in pteridophytes and is highly conserved across different terrestrial plants. CONCLUSIONS These results provide a foundation for further exploration of the molecular evolution and biological functions of GRF and GIF genes.
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Affiliation(s)
- Xinghao Chen
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Jun Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Hongyu Cai
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
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Liu Z, Zhang Y, Altaf MA, Hao Y, Zhou G, Li X, Zhu J, Ma W, Wang Z, Bao W. Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica. FRONTIERS IN PLANT SCIENCE 2022; 13:979988. [PMID: 36082298 PMCID: PMC9445626 DOI: 10.3389/fpls.2022.979988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The myeloblastosis (MYB) proteins perform key functions in mediating cadmium (Cd) tolerance of plants. Ipomoea aquatica has strong adaptability to Cd Stress, while the roles of the I. aquatica MYB gene family with respect to Cd stress are still unclear. Here, we identified a total of 183 MYB genes in the I. aquatica genome (laMYB), which were classified into 66 1R-type IaMYB, 112 2R-type IaMYB, four 3R-type IaMYB, and one 4R-type IaMYB based on the number of the MYB repeat in each gene. The analysis of phylogenetic tree indicated that most of IaMYB genes are associated with the diverse biological processes including defense, development and metabolism. Analysis of sequence features showed that the IaMYB genes within identical subfamily have the similar patterns of the motif distributions and gene structures. Analysis of gene duplication events revealed that the dispersed duplication (DSD) and whole-genome duplication (WGD) modes play vital roles in the expansion of the IaMYB gene family. Expression profiling manifests that approximately 20% of IaMYB genes had significant role in the roots of I. aquatica under Cd stress. Promoter profiling implied that the differentially expressed genes might be induced by environmental factors or inherent hormones and thereby execute their function in Cd response. Remarkably, the 2R-type IaMYB157 with abundant light-responsive element G-box and ABA-responsive element ABRE in its promoter region exhibited very strong response to Cd stress. Taken together, our findings provide an important candidate IaMYB gene for further deciphering the molecular regulatory mechanism in plant with respect to Cd stress.
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Affiliation(s)
- Zheng Liu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yuxin Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Guangzhen Zhou
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xinyu Li
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Wuqiang Ma
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Wenlong Bao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
- *Correspondence: Wenlong Bao,
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