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For: Cai K, Zhao Q, Zhang J, Yuan H, Li H, Han L, Li X, Li K, Jiang T, Zhao X. Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/IAA and ARF Gene Families in Populus simonii. Plants (Basel) 2023;12:3566. [PMID: 37896029 PMCID: PMC10610179 DOI: 10.3390/plants12203566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]

For:	Cai K, Zhao Q, Zhang J, Yuan H, Li H, Han L, Li X, Li K, Jiang T, Zhao X. Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/IAA and ARF Gene Families in Populus simonii. Plants (Basel) 2023;12:3566. [PMID: 37896029 PMCID: PMC10610179 DOI: 10.3390/plants12203566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]

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Cited by Other Article(s)

Jing X, Zou Q, Yang H. Genome-Wide Identification and Characterization of the Aux/IAA Gene Family in Strawberry Species. PLANTS (BASEL, SWITZERLAND) 2024;13:2940. [PMID: 39458886 PMCID: PMC11511250 DOI: 10.3390/plants13202940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024]

Huang X, Shad MA, Shu Y, Nong S, Li X, Wu S, Yang J, Rao MJ, Aslam MZ, Huang X, Huang D, Wang L. Genome-Wide Analysis of the Auxin/Indoleacetic Acid (Aux/IAA) Gene Family in Autopolyploid Sugarcane (Saccharum spontaneum). Int J Mol Sci 2024;25:7473. [PMID: 39000581 PMCID: PMC11242263 DOI: 10.3390/ijms25137473] [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: 06/05/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open

Affiliation(s)

Xiaojin Huang State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Munsif Ali Shad State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Yazhou Shu State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Sikun Nong State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
Xianlong Li State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
Songguo Wu State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
Juan Yang National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Muhammad Junaid Rao State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Muhammad Zeshan Aslam State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China
Xiaoti Huang State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
Dige Huang State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
Lingqiang Wang State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources, Guangxi University, Nanning 530004, China (M.J.R.); (M.Z.A.) Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China National Experimental Plant Science Education Demonstration Center, College of Agriculture, Guangxi University, Nanning 530004, China

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Imani Asl E, Soorni A, Mehrabi R. Genome-wide characterization, functional analysis, and expression profiling of the Aux/IAA gene family in spinach. BMC Genomics 2024;25:567. [PMID: 38840073 PMCID: PMC11155116 DOI: 10.1186/s12864-024-10467-z] [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: 01/14/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open

Abstract

BACKGROUND

The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach.

RESULTS

A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point.

CONCLUSIONS

These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways.

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Cai K, Xie X, Han L, Chen J, Zhang J, Yuan H, Shen J, Ren Y, Zhao X. Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response. FRONTIERS IN PLANT SCIENCE 2024;15:1412175. [PMID: 38779074 PMCID: PMC11109421 DOI: 10.3389/fpls.2024.1412175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]

Abstract

Background

Populus simonii, a notable native tree species in northern China, demonstrates impressive resistance to stress, broad adaptability, and exceptional hybridization potential. DOF family is a class of specific transcription factors that only exist in plants, widely participating in plant growth and development, and also playing an important role in abiotic stress response. To date, there have been no reported studies on the DOF gene family in P. simonii, and the expression levels of this gene family in different tissues of poplar, as well as its expression patterns under cold, heat, and other stress conditions, remain unclear.

Methods

In this study, DOF gene family were identified from the P. simonii genome, and various bioinformatics data on the DOF gene family, gene structure, gene distribution, promoters and regulatory networks were analyzed. Quantitative real time PCR technology was used to verify the expression patterns of the DOF gene family in different poplar tissues.

Results

This research initially pinpointed 41 PSDOF genes in P. simonii genome. The chromosomal localization results revealed that the PSDOF genes is unevenly distributed among 19 chromosomes, with the highest number of genes located on chromosomes 4, 5, and 11. A phylogenetic tree was constructed based on the homology between Arabidopsis thaliana and P. simonii, dividing the 41 PSDOF genes into seven subgroups. The expression patterns of PSDOF genes indicated that specific genes are consistently upregulated in various tissues and under different stress conditions, suggesting their pivotal involvement in both plant development and response to stress. Notably, PSDOF35 and PSDOF28 serve as pivotal hubs in the interaction network, playing a unique role in coordinating with other genes within the family.

Conclusion

The analysis enhances our comprehension of the functions of the DOF gene family in tissue development and stress responses within P. simonii. These findings provide a foundation for future exploration into the biological roles of DOF gene family.

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Peng Y, Zhao K, Zheng R, Chen J, Zhu X, Xie K, Huang R, Zhan S, Su Q, Shen M, Niu M, Chen X, Peng D, Ahmad S, Liu ZJ, Zhou Y. A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome. Int J Mol Sci 2024;25:806. [PMID: 38255880 PMCID: PMC10815038 DOI: 10.3390/ijms25020806] [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: 12/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open

Affiliation(s)

Yukun Peng Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Kai Zhao College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
Ruiyue Zheng Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Jiemin Chen Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Xuanyi Zhu Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Kai Xie Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Ruiliu Huang Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Suying Zhan Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Qiuli Su Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Mingli Shen College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
Muqi Niu Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Xiuming Chen Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Donghui Peng Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Sagheer Ahmad Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Zhong-Jian Liu Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
Yuzhen Zhou Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)

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