Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean
Abstract
1. Introduction
2. Results
2.1. Identification of the GmRER Gene Family
2.2. Architectural Diversity of GmRERs in Gene Structures and Conserved Motifs
2.3. RNA Secondary Structure and Protein Structure Prediction of GmRERs
2.4. Modular Functionality of GmRER Paralogs via Subcellular Specialization and Lineage-Specific PPI Networks
2.5. Spatiotemporal Expression Dynamics Define Functional Classes of GmRERs
2.6. Cis-Regulatory Modules Conveyed Roles of GmRERs in Stress and Development
2.7. Expression Patterns of GmRERs in Six Northern Spring Soybean Landraces
3. Discussion
3.1. Evolutionary Conservation and Functional Dynamics in the GmRER Family
3.2. Structural Diversification Coupled with Regulatory Plasticity in GmRERs
3.3. Functional Implications of GmRERs in Leaf Lipid Metabolism
4. Materials and Methods
4.1. Growth Conditions
4.2. Genome-Wide Identification of GmRER Genes
4.3. Molecular Evolution Analysis and Chromosomal Locations
4.4. Gene Structure and Conserved Motif Annotation
4.5. Cis-Element Profiling and Promoter Analysis
4.6. Protein Interaction Network Construction
4.7. Expression Profiling and Data Visualization
4.8. RNA Extraction and Sequencing
4.9. RNA-seq Data Processing, Mapping, and Differential Expression Analysis
4.10. RNA Secondary Structure and Protein Similarity Assessment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ABA | Abscisic acid |
ABRE | Abscisic acid-responsive element |
CDS | Coding sequence |
CRISPR | Clustered Regularly Interspaced Short Palindromic Repeats |
ERE | Ethylene-responsive element |
FPKM | Fragments Per Kilobase of transcript per Million mapped reads |
GO | Gene Ontology |
MYB | MYeloBlastosis transcription factor family |
PPI | Protein–protein interaction |
RER | RETICULATA-RELATED |
RMSD | Root-mean-square deviation |
UTR | Untranslated region |
WGD | Whole-genome duplication |
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Gene | Arabidopsis Gene ID | Name | Type of Duplicattion | Location (Mb) | Protein Length (aa) | Protein pI | ProteinMW (Kda) | Subcellular Localization |
---|---|---|---|---|---|---|---|---|
RE | AT2G37860 | GmREa | WGD | 16.276–16.281 | 444 | 4.813 | 47.64 | Chloroplast |
GmREb | WGD | 45.830–45.836 | 446 | 5.688 | 47.94 | Chloroplast | ||
RER1 | AT5G22790 | GmRER1a | WGD | 35.553–35.558 | 385 | 7.5 | 41.37 | Chloroplast |
GmRER1b | WGD | 40.846–40.851 | 387 | 8.021 | 41.53 | Chloroplast | ||
RER3 | AT3G08640 | GmRER3a | WGD | 38.020–38.022 | 321 | 10.196 | 34.04 | Chloroplast |
GmRER3b | WGD | 49.235–49.238 | 350 | 8.476 | 36.94 | Chloroplast | ||
GmRER3c | WGD | 50.736–50.739 | 348 | 9.149 | 36.92 | Chloroplast | ||
RER4 | AT5G12470 | GmRER4a | WGD | 1.403–1.408 | 365 | 8.461 | 38.8 | Chloroplast |
GmRER4b | WGD | 7.082–7.087 | 369 | 9.474 | 39.38 | Chloroplast | ||
GmRER4c | Dispersed | 12.077–12.090 | 432 | 9.722 | 46.96 | Chloroplast | ||
GmRER4d | WGD | 0.697–0.702 | 373 | 8.944 | 39.82 | Chloroplast | ||
GmRER4e | WGD | 45.552–45.556 | 377 | 9.156 | 40.16 | Chloroplast | ||
RER5 | AT2G40400 | GmRER5 | WGD | 1.682–1.690 | 748 | 8.777 | 82.64 | Plasma membrane |
RER6 | AT3G56140 | GmRER6 | WGD | 37.799–37.807 | 749 | 8.44 | 82.63 | Plasma membrane |
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Dong, Q.; Niu, L.; Gong, X.; Xing, Q.; Liang, J.; Lang, J.; Wang, T.; Yang, X. Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean. Plants 2025, 14, 1516. https://doi.org/10.3390/plants14101516
Dong Q, Niu L, Gong X, Xing Q, Liang J, Lang J, Wang T, Yang X. Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean. Plants. 2025; 14(10):1516. https://doi.org/10.3390/plants14101516
Chicago/Turabian StyleDong, Qianli, Lu Niu, Xiyu Gong, Qianlong Xing, Jie Liang, Jun Lang, Tianya Wang, and Xiangdong Yang. 2025. "Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean" Plants 14, no. 10: 1516. https://doi.org/10.3390/plants14101516
APA StyleDong, Q., Niu, L., Gong, X., Xing, Q., Liang, J., Lang, J., Wang, T., & Yang, X. (2025). Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean. Plants, 14(10), 1516. https://doi.org/10.3390/plants14101516