Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives
Abstract
:1. Introduction
2. Results
2.1. Identification and Characteristic of ACTINs in the Sweet Potato and Its Two Diploid Relatives
2.2. Phylogenetic Relationships of ACTINs in the Sweet Potato and Its Two Diploid Relatives
2.3. Analysis of Conserved Motifs and Exon-Intron Structure of ACTINs in the Sweet Potato and Its Two Diploid Relatives
2.4. Analysis of cis-Elements in the Promoter of IbACTINs in the Sweet Potato
2.5. Protein Interaction Network of ACTINs in the Sweet Potato
2.6. Expression Analysis of ACTINs in the Sweet Potato and Its Two Diploid Relatives
2.6.1. Analysis of Expression in Various Tissues
2.6.2. Analysis of Expression in Different Developmental Stages
2.6.3. Analysis of the Expression of Hormone Response
2.6.4. Analysis of Expression under Abiotic Stresses
3. Discussion
3.1. Evolution of the ACTIN Gene Family in the Sweet Potato and Its Two Diploid Relatives
3.2. Stable Expression of ACTIN in the Sweet Potato and Its Two Diploid Relatives
3.3. Differences in the Functions of ACTINs in Growth and Development between the Sweet Potato and Its Two Diploid Relatives
3.4. Different Functions of ACTINs in Hormone Crosstalk in the Sweet Potato and Its Two Diploid Relatives
3.5. Different Functions of ACTINs in Abiotic Stress Responses in the Sweet Potato and Its Two Diploid Relatives
4. Materials and Methods
4.1. Identification of ACTINs
4.2. Chromosomal Distribution of ACTINs
4.3. Protein Properties Prediction of ACTINs
4.4. Phylogenetic Analysis of ACTINs
4.5. Domain Identification and Conserved Motifs Analysis of ACTINs
4.6. Exon-Intron Structures and Promoter Analysis of ACTINs
4.7. Protein Interaction Network of ACTINs
4.8. Transcriptome 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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Number | Gene ID | Gene Name | PI | Molecular Weight (kDa) | CDS Length (bp) | Phosphorylation Site | Protein Size (aa) | Aliphatic Index | Instability Index | GRAVY | Subcellular Locations | Arabidopsis Homologs | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ser | Thr | Tyr | ||||||||||||
1 | g40378 | IbACTIN1 | 5.17 | 36.83 | 1008 | 14 | 12 | 9 | 330 | 73.27 | 36.01 | −0.268 | Cytoplasm | ACTIN1 |
2 | g5780 | IbACTIN2.1 | 5.05 | 48.02 | 1329 | 24 | 12 | 7 | 435 | 84.97 | 39.93 | −0.289 | Nucleus | ACTIN2 |
3 | g52926 | IbACTIN2.2 | 6.98 | 58.59 | 1599 | 29 | 10 | 8 | 524 | 81.49 | 51.07 | −0.355 | Nucleus | ACTIN2 |
4 | g4902 | IbACTIN5.1 | 5.31 | 41.73 | 1152 | 17 | 6 | 8 | 377 | 84.08 | 35.25 | −0.202 | Cytoskeleton | ACTIN5 |
5 | g40273 | IbACTIN5.2 | 5.31 | 41.70 | 1152 | 16 | 7 | 8 | 377 | 84.62 | 34.16 | −0.186 | Cytoskeleton | ACTIN5 |
6 | g9979 | IbACTIN5.3 | 5.42 | 42.32 | 1167 | 17 | 10 | 7 | 382 | 84.27 | 33.16 | −0.157 | Cytoskeleton | ACTIN5 |
7 | g18180 | IbACTIN5.4 | 7.87 | 12.45 | 345 | 2 | 2 | 1 | 113 | 106.02 | 36.03 | 0.15 | Cytoplasm | ACTIN5 |
8 | g24983 | IbACTIN5.5 | 5.31 | 41.73 | 1152 | 15 | 8 | 8 | 377 | 84.08 | 34.71 | −0.206 | Cytoskeleton | ACTIN5 |
9 | g43021 | IbACTIN5.6 | 5.47 | 40.56 | 1110 | 17 | 8 | 8 | 363 | 86.25 | 34.98 | −0.211 | Cytoplasm | ACTIN5 |
10 | g3675 | IbACTIN5.7 | 5.07 | 38.73 | 1065 | 16 | 5 | 7 | 349 | 82.12 | 34.98 | −0.143 | Cytoskeleton | ACTIN5 |
11 | g24981 | IbACTIN5.8 | 5.31 | 41.76 | 1152 | 17 | 8 | 8 | 377 | 83.55 | 35.22 | −0.22 | Cytoskeleton | ACTIN5 |
12 | g52274 | IbACTIN6 | 9.33 | 39.10 | 1053 | 26 | 8 | 6 | 345 | 79.88 | 55.76 | −0.266 | Chloroplast | ACTIN6 |
13 | g51848 | IbACTIN7 | 9.78 | 24.93 | 693 | 29 | 5 | 3 | 227 | 78.19 | 69.01 | −0.406 | Chloroplast | ACTIN7 |
14 | g25621 | IbACTIN9 | 5.38 | 41.68 | 1149 | 14 | 9 | 8 | 376 | 85.88 | 36.46 | −0.178 | Cytoskeleton | ACTIN9 |
15 | g2351 | IbACTIN10.1 | 5.68 | 73.78 | 1965 | 32 | 10 | 9 | 644 | 68.32 | 53.54 | −0.738 | Cytoplasm | ACTIN10 |
16 | g2496 | IbACTIN10.2 | 5.78 | 82.66 | 2196 | 35 | 11 | 9 | 720 | 68.83 | 54.01 | −0.749 | Cytoplasm | ACTIN10 |
17 | g64096 | IbACTIN12.1 | 6.11 | 57.53 | 1551 | 20 | 14 | 7 | 508 | 81.48 | 46.25 | −0.305 | Cytoplasm | ACTIN12 |
18 | g48567 | IbACTIN12.2 | 8.54 | 33.65 | 915 | 11 | 9 | 5 | 300 | 83.47 | 43.54 | −0.202 | Chloroplast | ACTIN12 |
19 | g18621 | IbACTIN12.3 | 9.05 | 28.13 | 771 | 18 | 10 | 4 | 252 | 80.91 | 53 | −0.208 | Nucleus | ACTIN12 |
20 | g26691 | IbACTIN13 | 6.43 | 57.52 | 1584 | 31 | 21 | 3 | 519 | 91.81 | 42.68 | −0.125 | Cytoplasm | ACTIN13 |
21 | g58376 | IbACTIN15 | 5.54 | 38.77 | 1065 | 16 | 8 | 7 | 349 | 86.1 | 36.11 | −0.193 | Cytoskeleton | ACTIN15 |
22 | g42892 | IbACTIN16.1 | 4.71 | 27.97 | 783 | 7 | 6 | 2 | 256 | 96.41 | 45.39 | −0.026 | Cytoplasm | ACTIN16 |
23 | g63730 | IbACTIN16.2 | 4.79 | 40.02 | 1116 | 11 | 10 | 5 | 365 | 91.37 | 45.53 | −0.081 | Cytoplasm | ACTIN16 |
24 | g46627 | IbACTIN17.1 | 5.1 | 41.61 | 1152 | 19 | 6 | 8 | 377 | 86.13 | 31.71 | −0.154 | Cytoskeleton | ACTIN17 |
25 | g60046 | IbACTIN17.2 | 5.31 | 41.74 | 1152 | 17 | 8 | 8 | 377 | 85.86 | 33.06 | −0.162 | Cytoskeleton | ACTIN17 |
26 | g27691 | IbACTIN17.3 | 5.42 | 36.18 | 996 | 15 | 4 | 5 | 326 | 89.45 | 42.1 | −0.085 | Cytoplasm | ACTIN17 |
27 | g723 | IbACTIN17.4 | 5.57 | 46.15 | 1275 | 19 | 12 | 7 | 418 | 92.8 | 40.29 | −0.057 | Cytoplasm | ACTIN17 |
28 | g13139 | IbACTIN18 | 5.86 | 62.01 | 1674 | 28 | 18 | 10 | 548 | 85.05 | 53.27 | −0.389 | Chloroplast | ACTIN18 |
29 | g61314 | IbACTIN19 | 7.89 | 55.85 | 1533 | 36 | 17 | 10 | 502 | 83.92 | 43.11 | 0.001 | Chloroplast | ACTIN19 |
30 | g20278 | IbACTIN20 | 5.37 | 41.79 | 1152 | 15 | 11 | 8 | 377 | 84.62 | 35.09 | −0.19 | Cytoskeleton | ACTIN20 |
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Xia, S.; Zhang, H.; He, S. Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives. Int. J. Mol. Sci. 2023, 24, 10930. https://doi.org/10.3390/ijms241310930
Xia S, Zhang H, He S. Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives. International Journal of Molecular Sciences. 2023; 24(13):10930. https://doi.org/10.3390/ijms241310930
Chicago/Turabian StyleXia, Shuanghong, Huan Zhang, and Shaozhen He. 2023. "Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives" International Journal of Molecular Sciences 24, no. 13: 10930. https://doi.org/10.3390/ijms241310930