Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of the Chitinase Genes in Tomato
2.2. Phylogeny, Gene Organization, and Conserved Motif Analysis of the Chitinase Gene Family
2.3. Chromosomal Location and Duplication Time Inference
2.4. Analyses of Synteny
2.5. Site-Specific Selection Assessment and Testing
2.6. Transcriptome-Based Expression Analysis
2.7. Plant Materials, Stress Treatments, RNA Isolation, Quantitative Real-Time PCR (qRT-PCR) Analysis, and Promoter Sequence Analysis
2.8. Network Assembly
3. Results
3.1. Identification and Phylogenetic Analysis of the Chitinase Gene Family in Tomato
3.2. Gene Organization and Conserved Motif Distribution of the Chitinases
3.3. Chromosomal Localization, Gene Duplication and Synteny Analyses
3.4. Selective Pressure Analysis among Different Amino Acid Sites
3.5. Divergent Expression Profile of Tomato Chitinase Genes in Different Tissues
3.6. Divergent Expression Profile of Tomato Chitinase Genes under Various Abiotic and Biotic Stresses
3.7. Protein–Protein Interaction Network Analysis of the Chitinases in Tomato
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene ID | Chrome Location | Length | Mw/Kda | pI | GRAVY | Domains | TargetP Localization |
---|---|---|---|---|---|---|---|
Solyc01g095250.1 | ch01:86587643..86588539 (+) | 298 | 31.91 | 4.51 | −0.022 | GH18 | S (0.995) |
Solyc01g095260.1 | ch01:86590501..86591397 (+) | 298 | 31.95 | 4.41 | −0.019 | GH18 | S (0.993) |
Solyc01g095310.1 | ch01:86626834..86627742 (+) | 302 | 32.35 | 5.34 | −0.05 | GH18 | S (0.994) |
Solyc01g097270.2 | ch01:88179851..88181214 (−) | 212 | 22.69 | 8.36 | −0.295 | GH19 | S (0.910) |
Solyc01g097280.2 | ch01:88183566..88184361 (−) | 199 | 21.49 | 8.78 | −0.37 | GH19 | S (0.959) |
Solyc02g061770.2 | ch02:33290113..33291907 (+) | 263 | 28.52 | 8.69 | −0.17 | GH19 | S (0.953) |
Solyc02g082920.2 | ch02:46550982..46552140 (+) | 253 | 27.63 | 5.93 | −0.265 | GH19 | S (0.988) |
Solyc02g082930.2 | ch02:46554240..46555813 (+) | 247 | 26.58 | 4.68 | −0.228 | GH19 | S (0.841) |
Solyc02g082960.2 | ch02:46564405..46566106 (+) | 273 | 30.14 | 9.56 | −0.194 | GH19 | S (0.887) |
Solyc03g116190.1 | ch03:65691845..65692213 (−) | 122 | 13.98 | 8.09 | −0.202 | GH19 | S (0.896) |
Solyc03g116230.2 | ch03:65723988..65725192 (−) | 295 | 30.59 | 5.38 | −0.196 | GH19 | S (0.982) |
Solyc03g116240.2 | ch03:65733982..65736687 (−) | 87 | 9.26 | 4.94 | 0.526 | GH19 | S (0.985) |
Solyc04g072000.2 | ch04:59066373..59068261 (−) | 276 | 30.01 | 4.58 | −0.294 | GH19 | S (0.994) |
Solyc05g050130.2 | ch05:60108919..60110761 (−) | 292 | 31.26 | 8.46 | 0.087 | GH18 | S (0.972) |
Solyc06g053380.2 | ch06:36128793..36130489 (−) | 289 | 31.81 | 5.37 | −0.284 | GH19 | S (0.977) |
Solyc07g005080.1 | ch07:112239..113536 (+) | 386 | 41.83 | 4.82 | −0.125 | GH18 | Other (0.554); C (0.337) |
Solyc07g005090.2 | ch07:113980..115328 (−) | 371 | 41.51 | 8.66 | −0.111 | GH18 | S (0.899) |
Solyc07g005100.2 | ch07:123941..126335 (+) | 376 | 41.85 | 9.34 | −0.271 | GH18 | S (0.951) |
Solyc07g009500.1 | ch07:4618503..4618766 (+) | 87 | 9.49 | 8.36 | −0.298 | GH19 | S (0.704) |
Solyc07g009510.1 | ch07:4622506..4622769 (+) | 87 | 9.49 | 8.36 | −0.298 | GH19 | S (0.704) |
Solyc07g009530.1 | ch07:4681799..4681990 (+) | 63 | 6.49 | 7.48 | 0.733 | GH19 | S (0.995) |
Solyc07g026990.1 | ch07:32915139..32915324 (−) | 61 | 7.43 | 7.77 | −0.387 | GH19 | Other (0.784) |
Solyc09g098540.2 | ch09:72338607..72340235 (−) | 319 | 35.56 | 7.95 | −0.205 | GH19 | S (0.964) |
Solyc10g017970.1 | ch10:6248916..6249098 (−) | 60 | 6.17 | 5.57 | 0.497 | GH19 | S (0.992) |
Solyc10g017980.1 | ch10:6273805..6273996 (+) | 63 | 6.56 | 7.48 | 0.471 | GH19 | S (0.995) |
Solyc10g055790.1 | ch10:57408394..57408612 (−) | 72 | 7.72 | 7.51 | 0.408 | GH19 | S (0.976) |
Solyc10g055800.1 | ch10:57410647..57411787 (−) | 329 | 35.41 | 8.64 | −0.423 | GH19 | S (0.838) |
Solyc10g055810.1 | ch10:57417284..57418434 (−) | 322 | 34.35 | 6.19 | −0.248 | GH19 | S (0.989) |
Solyc10g055820.1 | ch10:57435941..57437097 (−) | 322 | 34.89 | 6.36 | −0.348 | GH19 | S (0.975) |
Solyc10g068350.1 | ch10:65525076..65525336 (−) | 86 | 9.23 | 7.65 | −0.494 | GH19 | Other (0.600); C (0.419) |
Solyc10g074360.1 | ch10:57700740..57701259 (−) | 154 | 17.16 | 8.51 | −0.161 | GH19 | Other (0.677); M (0.523) |
Solyc10g074380.1 | ch10:57722610..57722870 (−) | 64 | 7.19 | 9.6 | −1.008 | GH19 | Other (0.504); C (0.363) |
Solyc10g074390.1 | ch10:57732393..57733097 (−) | 216 | 22.81 | 8.47 | −0.315 | GH19 | S (0.964) |
Solyc10g074400.1 | ch10:57738774..57739374 (−) | 173 | 18.43 | 9.11 | −0.381 | GH19 | S (0.436); M (0.435) |
Solyc10g074460.1 | ch10:57954087..57956593 (−) | 194 | 20.89 | 8.36 | −0.132 | GH19 | S (0.966) |
Solyc11g005890.1 | ch11:710226..711943 (−) | 295 | 33.33 | 5.7 | −0.052 | GH18 | S (0.876) |
Solyc11g020130.1 | ch11:10197594..10198487 (+) | 163 | 17.39 | 7.75 | −0.111 | GH19 | S (0.995) |
Solyc11g020450.1 | ch11:11116611..11117328 (−) | 206 | 22.18 | 8.17 | −0.675 | GH19 | M (0.368) |
Solyc11g020530.1 | ch11:11364445..11364994 (−) | 167 | 18.29 | 8.47 | −0.499 | GH19 | M (0.470) |
Solyc11g072750.1 | ch11:55960411..55961439 (−) | 342 | 38.89 | 6.89 | −0.139 | GH18 | M (0.597) |
Solyc11g072760.1 | ch11:55962509..55963429 (−) | 306 | 34.63 | 6.29 | −0.037 | GH18 | S (0.909) |
Solyc11g072830.1 | ch11:56024533..56025453 (+) | 306 | 33.74 | 4.79 | −0.15 | GH18 | S (0.974) |
Solyc12g098810.1 | ch12:66187159..66189951 (+) | 328 | 36.44 | 6.32 | −0.242 | GH19 | S (0.962) |
Paralogous Pairs | Ka | Ks | Ka/Ks | Data (Mya) | Duplication Style | |
---|---|---|---|---|---|---|
Solyc10g055810.1 | Solyc10g055820.1 | 0.07390 | 0.35721 | 0.20688 | 11.91 | Tandem duplication |
Solyc10g074400.1 | Solyc10g074460.1 | 0.07391 | 0.17341 | 0.42622 | 5.78 | Tandem duplication |
Solyc02g061770.2 | Solyc02g082960.2 | 0.18678 | 0.83819 | 0.22284 | 27.94 | Tandem duplication |
Solyc02g082920.2 | Solyc02g082930.2 | 0.17407 | 0.63165 | 0.27579 | 21.06 | Tandem duplication |
Solyc10g055790.1 | Solyc10g074380.1 | 1.35815 | 0.70977 | 1.91351 | 23.66 | Tandem duplication |
Solyc10g017970.1 | Solyc10g017980.1 | 0 | 0.01667 | 0 | 0.56 | Tandem duplication |
Solyc01g097270.2 | Solyc01g097280.2 | 0.09717 | 0.57283 | 0.16963 | 19.09 | Tandem duplication |
Solyc07g009500.1 | Solyc07g009510.1 | 0 | 0.14145 | 0 | 4.72 | Tandem duplication |
Solyc11g020450.1 | Solyc11g020530.1 | 0.05676 | 0.06623 | 0.85701 | 2.21 | Tandem duplication |
Solyc11g072750.1 | Solyc11g072760.1 | 0.07842 | 0.2463 | 0.31839 | 8.21 | Tandem duplication |
Solyc07g005080.1 | Solyc07g005090.2 | 0.46577 | 1.45233 | 0.32071 | 48.41 | Tandem duplication |
Solyc01g095250.1 | Solyc01g095260.1 | 0.01671 | 0.14434 | 0.11577 | 4.81 | Tandem duplication |
Solyc03g116190.1 | Solyc07g026990.1 | 1.30202 | 1.25040 | 1.04128 | 41.68 | Transposition |
Solyc07g009530.1 | Solyc10g068350.1 | 1.10203 | 0.77691 | 1.41848 | 25.89 | Transposition |
Solyc04g072000.2 | Solyc06g053380.2 | 0.18915 | 0.72624 | 0.26045 | 24.21 | Transposition |
Solyc09g098540.2 | Solyc12g098810.1 | 0.14047 | 0.67931 | 0.20678 | 22.64 | Transposition |
Branches | Models | Ka/Ks | Log-Likelihood | Number of PSS |
---|---|---|---|---|
GH19-A | M8 | 0.3927 | −15690.8 | 0 |
M7 | 0.3748 | −15691.3 | 0 | |
M5 | 0.4004 | −15694.2 | 22 | |
GH19-B | M8 | 0.4587 | −2023.77 | 0 |
M7 | 0.5158 | −2024.59 | 0 | |
M5 | 0.6367 | −2029.54 | 6 | |
GH19-C | M8 | 0.3059 | −9827.03 | 0 |
M7 | 0.2989 | −9829.36 | 0 | |
M5 | 0.3199 | −9831.15 | 0 | |
GH19-D | M8 | 0.2091 | −5411.06 | 0 |
M7 | 0.2046 | −5414.26 | 0 | |
M5 | 0.2182 | −5409.51 | 0 | |
GH19-E | M8 | 0.6195 | −6088.14 | 10 |
M7 | 0.4399 | −6099.04 | 0 | |
M5 | 0.5484 | −6091.2 | 13 | |
GH18-A | M8 | 0.5305 | −15342.2 | 47 |
M7 | 0.4669 | −15380.5 | 0 | |
M5 | 0.5576 | −15367.2 | 57 | |
GH18-B | M8 | 0.3478 | −5749.57 | 0 |
M7 | 0.3589 | −5751.15 | 0 | |
M5 | 0.3503 | −5749.08 | 0 | |
GH18-C | M8 | 0.3696 | −20704.8 | 16 |
M7 | 0.3409 | −20745.7 | 0 | |
M5 | 0.3923 | −20736.3 | 33 |
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Cao, J.; Tan, X. Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum). Plants 2019, 8, 52. https://doi.org/10.3390/plants8030052
Cao J, Tan X. Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum). Plants. 2019; 8(3):52. https://doi.org/10.3390/plants8030052
Chicago/Turabian StyleCao, Jun, and Xiaona Tan. 2019. "Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum)" Plants 8, no. 3: 52. https://doi.org/10.3390/plants8030052