Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Chromosomal Location of OsGLR Genes
2.2. Structural Characteristics and Phylogenetic Analysis of OsGLR Genes
2.3. Prediction of Transmembrane Helices and Signal Peptide of the OsGLR Genes
2.4. Three-Dimensional (3D) Structure and Conserved Motifs of OsGLR Genes
2.5. Cis-Acting Regulatory Elements, Functional Interaction Network and Chromatin Accessibility of OsGLR Genes
2.6. Population Variation, Gene-Coding Sequence Haplotype (gcHap) and KAKS of OsGLR Genes
2.7. Expression Difference of OsGLR Genes under Different Hormone Treatments
2.8. Semi-Quantitative PCR Analysis of OsGLR Genes under Low-Temperature Stress
3. Results
3.1. Genome-Wide Identification and Characterization of the OsGLR Genes in Rice
3.2. Transmembrane (TM) Helices and Signal Peptides of OsGLR Genes
3.3. Three-Dimensional (3D) Structure of OsGLR Genes
3.4. Cis-Acting Regulatory Elements and Functional Interaction Network of the OsGLR Genes
3.5. Chromatin Accessibility of OsGLR Genes
3.6. Evolutionary, Population Variation and Gene-Coding Sequence Haplotype (gcHap) Analysis of the GLR Genes in Rice
3.7. Expression Analysis of OsGLR Genes under Multiple Abiotic Stress and Hormone Treatments
3.8. Semi-Quantitative PCR Analysis of OsGLR Genes under Low-Temperature Stress
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene id | Gene Name | The Upstream Primer (5’-3’) | Downstream Primers (5’-3’) |
---|---|---|---|
Os09t0431100 | OsGLR9.7 | GATGGTTGCTGATGGGGCATTC | CTTCAGGAACACCCACGTCC |
Os09t0429000 | OsGLR9.3 | ATAACAGCTTCTGGGTATGCGAT | ATGGCTGCATCATATACCCCTAG |
Os06t0680500 | OsGLR6.12 | CTAAACACAATCGACGAGTACGC | AATCTCTCTGGAATGCGAATCCC |
Os04t0585200 | OsGLR4.1 | ACCGTCAATTTGTATCAGTTGATAG | ATAAGCTCCGAATAGCTTGGATTC |
Os06t0188700 | OsGLR6.4 | TCGTGGTGGACATGACGAGC | CTTGATAAGGTCTTCGGCGGC |
Os07t0103100 | OsGLR7.1 | ATCATCCAAGGTCTGCAGGTGAT | AGGAAGTAAGGGTATTGGGAGGA |
Os02t0787600 | OsGLR2.2 | TGTTCGACGAGGTCATGAAGATT | CATCTGCCTTCTGTGACGACA |
Os09t0428300 | OsGLR9.1 | AGAAAGGCAGAGGAATTCCATGT | CCAGCAAATCAAGAACTGCAGAT |
Os03t0234200 | OsUBQ | AAGAAGCTGAAGCATCCAGC | CCAGGACAAGATGATCTGCC |
Subfamily | RAP ID | Gene Name | No. of Amino Acids | Molecular Weight (Da) | Isoelectric Point (PI) | Aliphatic Index | Start (bp) | End (bp) | Location |
---|---|---|---|---|---|---|---|---|---|
I | Os02g0787600 | OsGLR2.2 | 988 | 107,252.1 | 6.4 | 83.94 | 33,469,138 | 33,475,994 | P(9/14),Ch(3/14) |
I | Os06g0155000 | OsGLR6.1 | 217 | 22,390.23 | 6.29 | 76.54 | 2,836,446 | 2,837,851 | Ch(11/14),N(3/14) |
I | Os06g0188400 | OsGLR6.2 | 481 | 52,305.65 | 8.34 | 91.73 | 4,459,007 | 4,463,882 | Cy(7/14),Ch(3/14) |
I | Os09g0431100 | OsGLR9.7 | 955 | 100,789.9 | 6.18 | 86.15 | 15,752,949 | 15,762,817 | P(7/14),V(3/14) |
II | Os09g0428300 | OsGLR9.1 | 872 | 96,824.56 | 7.99 | 96.9 | 15,564,675 | 15,569,470 | P(12/14) |
II | Os09g0428600 | OsGLR9.2 | 541 | 60,230.77 | 6.15 | 88.84 | 15,574,058 | 15,580,334 | E(5/14), Ch(3/14), V(3/14) |
II | Os09g0429000 | OsGLR9.3 | 933 | 104,346.78 | 5.96 | 92.18 | 15,588,269 | 15,594,378 | P(13/14) |
II | Os09g0429200 | OsGLR9.4 | 948 | 105,520.29 | 6.33 | 90.88 | 15,599,149 | 15,606,593 | P(8/14),ER(3/14) |
II | Os09g0429400 | OsGLR9.5 | 934 | 104,377.7 | 5.97 | 91.75 | 15,610,715 | 15,616,401 | P(11/14) |
II | Os09g0429500 | OsGLR9.6 | 946 | 105,792.31 | 5.94 | 92.32 | 15,620,335 | 15,625,678 | P(13/14) |
II | Os09g0431200 | OsGLR9.8 | 950 | 106,149.72 | 5.41 | 90.39 | 15,765,945 | 15,770,717 | P(13/14) |
III | Os06g0188600 | OsGLR6.3 | 670 | 74,295.45 | 5.87 | 80.9 | 4,472,352 | 4,476,661 | P(8/14) |
III | Os06g0188700 | OsGLR6.4 | 702 | 76,300.5 | 9.52 | 81.15 | 4,481,240 | 4,487,783 | P(10/14) |
III | Os06g0188800 | OsGLR6.5 | 197 | 21,457.38 | 8.45 | 84.67 | 4,489,588 | 4,493,909 | Ch(10/14) |
III | Os06g0189100 | OsGLR6.6 | 397 | 43,568.45 | 6.08 | 82.92 | 4,500,766 | 4,502,665 | P(6/14),V(4/14),ER(3/14) |
III | Os06g0190000 | OsGLR6.7 | 365 | 39,821.64 | 4.88 | 79.01 | 4,556,487 | 4,558,077 | E(4/14),V(3/14) |
III | Os06g0190500 | OsGLR6.8 | 531 | 59,380.02 | 9.1 | 89.76 | 4,571,098 | 4,574,904 | P(8/14),M(3/14) |
III | Os06g0190700 | OsGLR6.9 | 542 | 59,762.91 | 8.73 | 82.2 | 4,587,987 | 4,591,068 | P(8/14) |
III | Os06g0190800 | OsGLR6.10 | 820 | 91,791.68 | 8.41 | 92.21 | 4,593,916 | 4,597,945 | P(9/14), V(3/14) |
IV | Os02g0117500 | OsGLR2.1 | 944 | 105,303.79 | 5.67 | 94.29 | 918,797 | 923,968 | P(13/14) |
IV | Os04g0585200 | OsGLR4.1 | 540 | 59,717.23 | 6.36 | 95.67 | 29,565,754 | 29,570,387 | P(10/14) |
IV | Os06g0246600 | OsGLR6.11 | 147 | 15,686.37 | 4.05 | 90.27 | 7,607,108 | 7,607,939 | Ch(4/14),E(5/14),M(3/14) |
IV | Os06g0680500 | OsGLR6.12 | 890 | 98,881.67 | 5.34 | 90.39 | 28,345,366 | 28,350,758 | P(11/14) |
IV | Os07g0103100 | OsGLR7.1 | 956 | 104,440.94 | 6.22 | 92.01 | 191,053 | 196,429 | P(10/14),ER(3/14) |
IV | Os07g0522600 | OsGLR7.2 | 637 | 69,593.23 | 5.35 | 93.05 | 20,221,077 | 20,225,924 | P(5/14),ER(4/14),V(3/14) |
IV | Os09g0485700 | OsGLR9.9 | 95 | 10,497.73 | 4.54 | 83.16 | 18,740,826 | 18,741,187 | P(10/14),Cy(3/14) |
Seq_1 | Seq_2 | Ka | Ks | Ka_Ks | Mya |
---|---|---|---|---|---|
OsGLR6.8 | OsGLR6.9 | 0.17 | 0.32 | 0.53 | 24.53 |
OsGLR9.5 | OsGLR9.3 | 0.06 | 0.27 | 0.22 | 20.93 |
OsGLR9.5 | OsGLR9.6 | 0.07 | 0.28 | 0.25 | 21.61 |
OsGLR9.6 | OsGLR9.3 | 0.06 | 0.27 | 0.22 | 21.07 |
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Shi, Y.; Zeng, W.; Xu, M.; Li, H.; Zhang, F.; Chen, Z.; Anicet, G.; Huang, S.; Huang, Y.; Wang, X.; et al. Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis. Curr. Issues Mol. Biol. 2022, 44, 6404-6427. https://doi.org/10.3390/cimb44120437
Shi Y, Zeng W, Xu M, Li H, Zhang F, Chen Z, Anicet G, Huang S, Huang Y, Wang X, et al. Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis. Current Issues in Molecular Biology. 2022; 44(12):6404-6427. https://doi.org/10.3390/cimb44120437
Chicago/Turabian StyleShi, Yingyao, Wei Zeng, Minhui Xu, Hua Li, Fanlin Zhang, Zulong Chen, Gatera Anicet, Shiji Huang, Yuheng Huang, Xiyu Wang, and et al. 2022. "Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis" Current Issues in Molecular Biology 44, no. 12: 6404-6427. https://doi.org/10.3390/cimb44120437