Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L.
Abstract
:1. Introduction
2. Results
2.1. Identification of GbARF Proteins
2.2. Phylogenetic Analysis
2.3. Domain, Motif Identification, and Gene Structure Analysis
2.4. Analysis of cis-Elements in the Promoter of GbARFs
2.5. Protein Tertiary Structure and Interaction Network Analysis
2.6. Chromosomal Location and Collinearity Analysis
2.7. GO Annotation of GbARF Family
2.8. GbARF Family Transcriptional Profiles
2.9. Quantitative Real-Time PCR(qRT-PCR) Verification of Tissue-Specific Expression
2.10. GbARF6a, GbARF10b, and GbARF10a Cloning and Expression Profiles of GbARFs in Flower Development
2.11. Expression of GbARFs in Response to Exogenous Salicylic Acid (SA)
3. Discussion
4. Materials and Methods
4.1. Identification and Sequence Analysis of GbARFs
4.2. Phylogenesis, Protein Conserved Domain, Motif and Gene Structure Analysis
4.3. Protein Tertiary Structure, Cis-Acting Element and Interaction Network Analysis
4.4. Chromosomal Location and Synteny Analysis
4.5. GO Annotation Analysis
4.6. Transcription Analysis of GbARF Family Genes
4.7. GbARF6a, GbARF10b, and GbARF10a Cloning
4.8. qRT-PCR Expression of GbARFs
4.9. Plant Materials and Exogenous SA Treatments
4.10. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | ORF | AA | MW (Da) | pI | GRAVY | Subcellular Localization |
---|---|---|---|---|---|---|---|
GbARF3 | evm.model.chr1.3000 | 2922 | 973 | 108,130.40 | 5.46 | −0.458 | Nuclear |
GbARF1 | evm.model.chr3.2036 | 3009 | 1002 | 110,896.65 | 6.63 | −0.530 | Nuclear |
GbARF2a | evm.model.chr4.677 | 3834 | 1277 | 141,221.98 | 6.5 | −0.335 | Plasma membrane |
GbARF2b | evm.model.chr5.1456 | 2982 | 993 | 109,968.78 | 6.62 | −0.516 | Chloroplast |
GbARF6a | evm.model.chr5.1462 | 860 | 285 | 33,086.80 | 8.89 | −0.242 | Extracellular |
GbARF10b | evm.model.chr5.854 | 2250 | 749 | 82,844.92 | 6.64 | −0.476 | Nuclear |
GbARF19a | evm.model.chr6.93 | 3384 | 1127 | 126,560.12 | 6.06 | −0.516 | Nuclear |
GbARF2c | evm.model.chr7.1996 | 2640 | 879 | 97,850.61 | 5.59 | −0.615 | Nuclear |
GbARF19b | evm.model.chr8.1790 | 3222 | 1073 | 121,038.59 | 6.36 | −0.692 | Nuclear |
GbARF10c | evm.model.chr8.618 | 2352 | 783 | 86,475.31 | 7.60 | −0.447 | Nuclear |
GbARF4a | evm.model.chr10.1507 | 2649 | 882 | 97,626.73 | 5.83 | −0.469 | Nuclear |
GbARF10a | evm.model.chr10.178 | 2412 | 803 | 88,729.16 | 6.44 | −0.512 | Nuclear |
GbARF6b | evm.model.chr10.810 | 2790 | 929 | 103,431.84 | 6.13 | −0.506 | Nuclear |
GbARF8 | evm.model.chr11.851 | 3345 | 1114 | 123,501.21 | 7.34 | −0.482 | Nuclear |
GbARF4b | evm.model.chr11.970 | 1290 | 429 | 48,215.21 | 8.70 | −0.209 | Chloroplast |
Gene 1 | Gene 2 | Ka | Ks | Ka/Ks(ω) | Selection | Duplication Mode |
---|---|---|---|---|---|---|
GbARF3 | GbARF1 | 3.18237 | 2.30424 | 1.38109 | Positive | Segmental |
GbARF1 | GbARF2a | 0.28025 | 0.89312 | 0.31379 | Purifying | Segmental |
GbARF2a | GbARF2c | 0.18970 | 0.86208 | 0.22005 | Purifying | Segmental |
GbARF2a | GbARF19b | 0.93854 | 1.34106 | 0.69985 | Purifying | Segmental |
GbARF10b | GbARF10a | 0.14941 | 0.96258 | 0.15522 | Purifying | Segmental |
GbARF2c | GbARF19b | 0.72979 | 0.89579 | 0.81469 | Purifying | Segmental |
GbARF3 | GbARF10c | 0.84295 | 1.16164 | 0.72566 | Purifying | Segmental |
Project Number | Sample Type | Library | Platform | Reference |
---|---|---|---|---|
PRJNA289172 | Ovulate strobilus | Paired end | Illumina HiSeq 2500 | [52] |
PRJNA289172 | Staminate strobilus | Paired end | Illumina HiSeq 2500 | [52] |
PRJNA289172 | Female and male buds | Paired end | Illumina HiSeq 2500 | [52] |
PRJNA373812 | Roots | Paired end | Illumina HiSeq 4000 | [53] |
PRJNA473396 | Stems | Paired end | Illumina HiSeq 4000 | [54] |
PRJNA488475 | Cambium | Paired end | Illumina HiSeq 2000 | [55] |
PRJNA473396 | Immature leave | Paired end | Illumina HiSeq 4000 | [54] |
PRJNA517218 | Mature leave | Paired end | HiSeq X Ten | [56] |
PRJNA578374 | Turning stage and yellow leave | Paired end | Illumina HiSeq 4000 | [57] |
PRJNA473396 | Immature and mature fruits | Paired end | Illumina HiSeq 4000 | [54] |
PRJNA292849 | Kernel1–5 | Paired end | Illumina HiSeq 2000 | [58] |
PRJNA553587 | Treatment of MEJ | Paired end | HiSeq X Ten | [59] |
PRJNA598887 | Treatment of SA | Paired end | HiSeq X Ten | [59] |
PRJNA595103 | Treatment of UV-B | Paired end | Illumina HiSeq 4000 | [60] |
PRJNA604486 | Treatment of PEG-6000 | Paired end | Illumina NovaSeq 6000 | [61] |
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Guo, F.; Xiong, W.; Guo, J.; Wang, G. Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. Int. J. Mol. Sci. 2022, 23, 6754. https://doi.org/10.3390/ijms23126754
Guo F, Xiong W, Guo J, Wang G. Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. International Journal of Molecular Sciences. 2022; 23(12):6754. https://doi.org/10.3390/ijms23126754
Chicago/Turabian StyleGuo, Fangyun, Wulai Xiong, Jing Guo, and Guibin Wang. 2022. "Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L." International Journal of Molecular Sciences 23, no. 12: 6754. https://doi.org/10.3390/ijms23126754