Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Sequence Analysis of the CmaGSTs
2.2. Phylogenetic Analysis
2.3. Chromosome Localization and Gene Duplication Analysis
2.4. Microsynteny of the GST Gene Family
2.5. Plant Materials, Growth, and Treatments
2.6. RNA Extraction and cDNA Synthesis
2.7. Qualitative and Quantitative PCR Expression Analyses
2.8. Statistical Analysis
3. Results
3.1. Identification of GST Genes in C. maxima
3.2. Phylogenetic Analysis
3.3. Chromosomal Locations and Gene Duplications of the CmaGSTs
3.4. Structural and Motif Analyses of the CmaGSTs
3.5. Microsynteny Relationships and Analysis of CmaGST Protein Interactions
3.6. Expression Profiles of CmaGST Genes in Various Organs
3.7. Expression Profiling of the CmaGST Genes during Cold Treatment
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sl. No. | Gene Name | Accession No. | Chromosome | Start Location | End Location | Strand | pI | MW(kDa) | AA | Localization |
---|---|---|---|---|---|---|---|---|---|---|
01 | CmaGSTU1 | CmaCh13G011300 | 13 | 8381645 | 8382352 | + | 5.74 | 27.04 | 235 | Cytoplasm |
02 | CmaGSTU2 | CmaCh11G002990 | 11 | 1483599 | 1484338 | + | 5.17 | 25.08 | 219 | Cytoplasm |
03 | CmaGSTU3 | CmaCh14G019610 | 14 | 13801828 | 13805918 | + | 6.31 | 44.50 | 387 | Cytoplasm |
04 | CmaGSTU4 | CmaCh06G011550 | 06 | 7777316 | 7778827 | − | 5.93 | 26.16 | 227 | Cytoplasm |
05 | CmaGSTU5 | CmaCh00G006890 | 00 | 47643604 | 47645087 | − | 6.98 | 27.96 | 242 | Cytoplasm |
06 | CmaGSTU6 | CmaCh06G012770 | 06 | 8499592 | 8500393 | − | 6.02 | 26.29 | 226 | Cytoplasm |
07 | CmaGSTU7 | CmaCh14G018620 | 14 | 13214607 | 13217686 | − | 5.98 | 41.95 | 370 | Cytoplasm |
08 | CmaGSTU8 | CmaCh06G012780 | 06 | 8501349 | 8502406 | + | 6.62 | 25.61 | 222 | Cytoplasm |
09 | CmaGSTU9 | CmaCh14G018610 | 14 | 13213235 | 13214322 | − | 5.28 | 25.41 | 222 | Cytoplasm |
10 | CmaGSTU10 | CmaCh03G003840 | 03 | 4366133 | 4366923 | + | 5.94 | 24.72 | 217 | Cytoplasm |
11 | CmaGSTU11 | CmaCh07G010310 | 07 | 5378533 | 5380070 | − | 6.20 | 25.66 | 220 | Cytoplasm |
12 | CmaGSTU12 | CmaCh16G004650 | 16 | 2333498 | 2334374 | + | 6.14 | 24.95 | 219 | Cytoplasm |
13 | CmaGSTU13 | CmaCh04G006390 | 04 | 3269916 | 3271375 | − | 8.63 | 33.08 | 288 | Cytoplasm |
14 | CmaGSTU14 | CmaCh16G004640 | 16 | 2326120 | 2328293 | + | 7.66 | 23.19 | 202 | Cytoplasm |
15 | CmaGSTU15 | CmaCh04G006400 | 04 | 3271577 | 3272321 | − | 5.27 | 24.41 | 212 | Cytoplasm |
16 | CmaGSTU16 | CmaCh04G006410 | 04 | 3273122 | 3286431 | − | 9.02 | 91.29 | 810 | Nucleus |
17 | CmaGSTU17 | CmaCh04G022700 | 04 | 15857294 | 15858045 | − | 5.58 | 25.47 | 224 | Cytoplasm |
18 | CmaGSTU18 | CmaCh04G006380 | 04 | 3268691 | 3269778 | − | 5.65 | 25.65 | 224 | Cytoplasm |
19 | CmaGSTF1 | CmaCh08G004090 | 08 | 2344840 | 2346569 | + | 6.38 | 24.14 | 217 | Cytoplasm |
20 | CmaGSTF2 | CmaCh08G004100 | 08 | 2346863 | 2348162 | − | 5.75 | 24.12 | 214 | Cytoplasm |
21 | CmaGSTF3 | CmaCh12G003850 | 12 | 1988809 | 1990016 | − | 5.51 | 25.09 | 220 | Cytoplasm |
22 | CmaEF1G1 | CmaCh16G007670. | 16 | 4206363 | 4213994 | + | 5.54 | 61.96 | 547 | Cytoplasm |
23 | CmaEF1G2 | CmaCh04G008920 | 04 | 4645271 | 4652681 | + | 5.65 | 60.31 | 531 | Cytoplasm |
24 | CmaEF1G3 | CmaCh06G008870 | 06 | 5603706 | 5606718 | − | 6.01 | 47.14 | 415 | Cytoplasm |
25 | CmaGSTT1 | CmaCh16G005900 | 16 | 3054792 | 3058033 | − | 9.38 | 27.09 | 238 | Cytoplasm |
26 | CmaGSTT2 | CmaCh04G007350 | 00 | 47643604 | 47645087 | + | 9.34 | 26.96 | 238 | Cytoplasm |
27 | CmaGSTZ1 | CmaCh02G006430 | 02 | 3895323 | 3899120 | + | 5.85 | 24.89 | 222 | Cytoplasm |
28 | CmaGSTZ2 | CmaCh02G006410 | 02 | 3887013 | 3892301 | + | 5.17 | 24.99 | 223 | Cytoplasm |
29 | CmaGSTZ3 | CmaCh06G011350 | 06 | 7652425 | 7656514 | + | 5.20 | 25.63 | 228 | Cytoplasm |
30 | CmaGSTL1 | CmaCh06G003420 | 06 | 1588222 | 1591488 | − | 5.25 | 29.35 | 257 | Cytoplasm |
31 | CmaGHR1 | CmaCh18G005590 | 18 | 3671672 | 3674403 | − | 7.62 | 40.83 | 355 | Chloroplast |
32 | CmaGHR2 | CmaCh19G001140 | 19 | 681203 | 684746 | + | 8.79 | 45.58 | 415 | Cytoplasm |
Duplicated Gene Pairs | Ks | Ka | Ka/Ks | Duplication Type | Type of Selection | Divergence Time (Mya) | ||
---|---|---|---|---|---|---|---|---|
CmaGSTU3 | vs. | CmaGSTU4 | 0.215 | 0.127 | 0.593 | Segmental | Purifying | 7.18 |
CmaGSTU4 | vs. | CmaGSTU5 | 0.139 | 0.056 | 0.405 | Segmental | Purifying | 4.66 |
CmaGSTU12 | vs. | CmaGSTU14 | 0.038 | 0.017 | 0.452 | Tandem | Purifying | 1.30 |
CmaGSTU12 | vs. | CmaGSTU13 | 0.412 | 0.142 | 0.346 | Segmental | Purifying | 13.75 |
CmaGSTU12 | vs. | CmaGSTU15 | 0.455 | 0.137 | 0.302 | Segmental | Purifying | 15.19 |
CmaGSTU12 | vs. | CmaGSTU16 | 0.533 | 0.229 | 0.430 | Segmental | Purifying | 17.78 |
CmaGSTU13 | vs. | CmaGSTU14 | 0.387 | 0.142 | 0.367 | Segmental | Purifying | 12.91 |
CmaGSTU13 | vs. | CmaGSTU15 | 0.405 | 0.172 | 0.424 | Tandem | Purifying | 13.52 |
CmaGSTU13 | vs. | CmaGSTU16 | 0.309 | 0.242 | 0.784 | Tandem | Purifying | 10.32 |
CmaGSTU14 | vs. | CmaGSTU15 | 0.398 | 0.151 | 0.379 | Segmental | Purifying | 13.27 |
CmaGSTU15 | vs. | CmaGSTU16 | 0.308 | 0.226 | 0.735 | Tandem | Purifying | 10.28 |
CmaGSTZ1 | vs. | CmaGSTZ2 | 0.382 | 0.220 | 0.575 | Tandem | Purifying | 12.76 |
CmaEF1G1 | vs. | CmaEF1G2 | 0.080 | 0.119 | 1.483 | Segmental | Positive | 2.68 |
CmaEF1G1 | vs. | CmaEF1G3 | 0.536 | 0.293 | 0.547 | Segmental | Purifying | 17.89 |
CmaEF1G2 | vs. | CmaEF1G3 | 0.566 | 0.279 | 0.493 | Segmental | Purifying | 18.87 |
CmaGSTT1 | vs. | CmaGSTT2 | 0.201 | 0.130 | 0.646 | Segmental | Purifying | 6.72 |
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Abdul Kayum, M.; Nath, U.K.; Park, J.-I.; Biswas, M.K.; Choi, E.K.; Song, J.-Y.; Kim, H.-T.; Nou, I.-S. Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance. Genes 2018, 9, 84. https://doi.org/10.3390/genes9020084
Abdul Kayum M, Nath UK, Park J-I, Biswas MK, Choi EK, Song J-Y, Kim H-T, Nou I-S. Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance. Genes. 2018; 9(2):84. https://doi.org/10.3390/genes9020084
Chicago/Turabian StyleAbdul Kayum, Md., Ujjal Kumar Nath, Jong-In Park, Manosh Kumar Biswas, Eung Kyoo Choi, Jae-Young Song, Hoy-Taek Kim, and Ill-Sup Nou. 2018. "Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance" Genes 9, no. 2: 84. https://doi.org/10.3390/genes9020084
APA StyleAbdul Kayum, M., Nath, U. K., Park, J.-I., Biswas, M. K., Choi, E. K., Song, J.-Y., Kim, H.-T., & Nou, I.-S. (2018). Genome-Wide Identification, Characterization, and Expression Profiling of Glutathione S-Transferase (GST) Family in Pumpkin Reveals Likely Role in Cold-Stress Tolerance. Genes, 9(2), 84. https://doi.org/10.3390/genes9020084