Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses
Abstract
:1. Introduction
2. Results
2.1. Identification and Analysis of the BBX Gene Family
2.2. Conserved Motif Analysis of the BBX Gene Family
2.3. Phylogenetic Analysis of the BBX Gene Family
2.4. Structural Information Analysis of the BBX Gene Family
2.5. GO Analysis of the BBX Gene Family
2.6. Potential Phosphorylation Sites and Glycosylation Analysis of the BBX Gene Family
2.7. Protein–Protein Interaction Networks
2.8. Inducible Expression Analysis of the BBX Gene in Bambusa pervariabilis × Dendrocalamopsis grandis under Abiotic Stress
2.9. Induced Expression Analysis of the BBX Gene in Bambusa pervariabilis × Dendrocalamopsis grandis under Disease Infestation
2.10. Comparison of Amino Acid Sequences of BBX Proteins of Different Species
3. Discussion
4. Materials and Methods
4.1. Test Materials
4.2. BBX Gene Family Identification and Analysis
4.3. Analysis of the Basic Physicochemical Properties and Conserved Motifs of the BBX Gene Family
4.4. Phylogenetic Relationship Analysis of the BBX Gene Family
4.5. Structural Information Analysis of the BBX Gene Family
4.6. GO Analysis of the BBX Gene Family
4.7. Potential Phosphorylation Sites and Glycosylation Analysis of BBX Gene Family
4.8. BDBBX Protein Interaction Network Prediction and Functional Annotation
4.9. Treatment of Biotic and Abiotic Stress Conditions
disease rating)/(total plants × most serious disease rating)] × 100
4.10. Quantitative PCR Analysis
4.11. Comparison of Amino Acid Sequences of BBX Genes from Different Species
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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Transcriptome ID | Gene | Protein Length (AA) | Molecular Weight (Da) | Theoretical pI | Instability Index | Aliphatic Index | Grand Average of Hydropathicity (GRAVY) | Signal Peptide | Subcellular Localization |
---|---|---|---|---|---|---|---|---|---|
PH01000042G1610 | BDBBX1 | 127 | 13,945.96 | 10.26 | 70.44 | 60.08 | −0.521 | NO | Nucleus |
PH01000149G0140 | BDBBX2 | 227 | 24,305.66 | 4.82 | 59.77 | 80.84 | −0.013 | NO | Nucleus |
PH01000192G1360 | BDBBX3 | 210 | 22,874.85 | 11.57 | 63.94 | 90.29 | −0.337 | NO | Nucleus |
PH01000303G0990 | BDBBX4 | 309 | 32,565.29 | 6.41 | 55.53 | 58.25 | −0.518 | NO | Chloroplast.Nucleus |
PH01000450G1030 | BDBBX5 | 102 | 10,539.61 | 8.66 | 74.10 | 51.08 | −0.52 | NO | Chloroplast. Cytoplasm |
PH01000481G0620 | BDBBX6 | 383 | 41,494.94 | 7.59 | 41.16 | 67.44 | −0.295 | NO | Cell membrane.Nucleus |
PH01000616G0330 | BDBBX7 | 83 | 8412.52 | 6.25 | 56.72 | 71.93 | −0.014 | NO | Nucleus |
PH01000917G0300 | BDBBX8 | 160 | 16,681.41 | 10.50 | 73.87 | 62.62 | −0.358 | NO | Nucleus |
PH01001451G0380 | BDBBX9 | 143 | 14,723.24 | 4.69 | 61.26 | 67.69 | −0.113 | NO | Nucleus |
PH01001725G0310 | BDBBX10 | 270 | 28,776.28 | 7.48 | 50.37 | 73.89 | −0.087 | NO | Nucleus |
PH01001870G0430 | BDBBX11 | 239 | 26,213.84 | 11.48 | 63.61 | 86.65 | −0.431 | NO | Nucleus |
PH01002961G0180 | BDBBX12 | 90 | 10,098.74 | 9.23 | 56.06 | 58.78 | −0.371 | NO | Nucleus |
PH01003421G0140 | BDBBX13 | 198 | 21,263.84 | 5.30 | 52.63 | 64.70 | −0.366 | NO | Nucleus |
Phyllostachys_edulis_newGene_30773 | BDBBX14 | 241 | 26,221.19 | 7.86 | 41.89 | 81.08 | −0.126 | NO | Nucleus |
Phyllostachys_edulis_newGene_38997 | BDBBX15 | 269 | 29,499.68 | 6.45 | 60.16 | 82.75 | −0.099 | NO | Nucleus |
PH01000037G0060 | BDBBX16 | 194 | 20,980.48 | 9.49 | 79.35 | 55.46 | −0.699 | NO | Nucleus |
PH01000780G0510 | BDBBX17 | 332 | 36,625.69 | 11.90 | 93.79 | 41.08 | −0.932 | NO | Chloroplas. |
PH01002146G0170 | BDBBX18 | 409 | 44,318.82 | 6.43 | 63.00 | 58.58 | −0.593 | NO | Nucleus |
PH01002727G0080 | BDBBX19 | 316 | 34,063.68 | 6.08 | 37.30 | 74.56 | −0.199 | NO | Nucleus |
Phyllostachys_edulis_newGene_62371 | BDBBX20 | 298 | 32,384.84 | 6.81 | 59.12 | 74.03 | −0.345 | NO | Nucleus |
PH01003160G0610 | BDBBX21 | 256 | 27,100.62 | 4.96 | 50.25 | 76.33 | −0.155 | NO | Nucleus |
Motif | Motif Length (AA) | Motif Sequence | Function Annotation |
---|---|---|---|
1 | 34 | VVCCADEAALCARCDADVHAANKLASRHQRLPLD | zf-B_box |
2 | 50 | MGEGREARLMRYREKRKNRRFEKTIRYASRKAYAEKRPRIKGRFAKRADH | CCT |
3 | 11 | MKIQCDACEGA | UnKnown |
4 | 47 | VQEKAAFIFCVEDRALLCRDCDEPIHVPGTLSGNHQRYLATGIRVGF | zf-B_box |
5 | 8 | PRCDVCQV | UnKnown |
6 | 21 | DLDVEDDDEKLDYRFPDFDPY | UnKnown |
7 | 50 | MMELHKYWGVGGRRCGTCEASPAAVHCRTCGGAYLCTACDARPAHARAGH | zf-B_box |
8 | 50 | NVEFARFPHADSVVPNGAGVGAVVELDFTCGLGAKPSYSSYTATSLAHSV | UnKnown |
9 | 18 | TGTLPGWAVEDLLFDSPA | UnKnown |
10 | 40 | DEGCWAIWEEPQVJSLEDJIVPTTSCHGFQPLLAPPSPKV | UnKnown |
Gene ID | Phosphorylation Sites | Glycosylation Sites | |||||
---|---|---|---|---|---|---|---|
Serine | Threonine | Tyrosine | Position | Potential | Jury Agreement | N-Glyc Result | |
BDBBX1 | 9 | 5 | / | None | |||
BDBBX2 | 13 | 7 | 1 | 105 NASA | 0.5176 | (4/9) | + |
216 NGTS | 0.669 | (8/9) | + | ||||
BDBBX3 | 2 | / | 1 | None | |||
BDBBX4 | 27 | 6 | 2 | 299 NCSN | 0.5557 | (5/9) | + |
BDBBX5 | 11 | 1 | 1 | None | |||
BDBBX6 | 17 | 9 | 6 | None | |||
BDBBX7 | 4 | / | 2 | None | |||
BDBBX8 | 12 | 3 | 3 | None | |||
BDBBX9 | 16 | 5 | 1 | 70 NSSS | 0.57 | (8/9) | + |
BDBBX10 | 20 | 7 | 1 | 209 NRTR | 0.5787 | (6/9) | + |
BDBBX11 | 5 | 2 | 3 | None | |||
BDBBX12 | 5 | 1 | 1 | None | |||
BDBBX13 | 6 | 8 | / | None | |||
BDBBX14 | 14 | 9 | 2 | 234 NLTL | 0.6876 | (9/9) | ++ |
BDBBX15 | 25 | 12 | 3 | 152 NSSS | 0.611 | (8/9) | + |
BDBBX16 | 21 | 5 | 3 | None | |||
BDBBX17 | 30 | 28 | / | 200 NSSA | 0.5469 | (6/9) | + |
BDBBX18 | 29 | 8 | 1 | None | |||
BDBBX19 | 10 | 5 | 6 | None | |||
BDBBX20 | 18 | 15 | 1 | 179 NSTL | 0.6232 | (8/9) | + |
227 NSTE | 0.5468 | (6/9) | + | ||||
BDBBX21 | 10 | 6 | 3 | None |
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Liu, Y.; Wang, Y.; Liao, J.; Chen, Q.; Jin, W.; Li, S.; Zhu, T.; Li, S. Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses. Int. J. Mol. Sci. 2023, 24, 13465. https://doi.org/10.3390/ijms241713465
Liu Y, Wang Y, Liao J, Chen Q, Jin W, Li S, Zhu T, Li S. Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses. International Journal of Molecular Sciences. 2023; 24(17):13465. https://doi.org/10.3390/ijms241713465
Chicago/Turabian StyleLiu, Yi, Yaxuan Wang, Jiao Liao, Qian Chen, Wentao Jin, Shuying Li, Tianhui Zhu, and Shujiang Li. 2023. "Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses" International Journal of Molecular Sciences 24, no. 17: 13465. https://doi.org/10.3390/ijms241713465