Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum
Abstract
:1. Introduction
2. Results and Discussion
2.1. RNA-Seq Libraries
2.2. Gene Ontology Enrichment Analyses
2.3. Comparative Analysis of DEGs at Different Time Points
2.4. DEG Categories
2.5. Validation of RNA-Seq with qRT-PCR
3. Materials and Methods
3.1. Plant Materials
3.2. Plant Treatments
3.3. RNA Sample Preparation and Illumina Sequencing
3.4. Transcriptome Assembly and Analysis
3.5. Validation of RNA-Seq with qRT-PCR
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Time (h) | Treatment | Replicate 1 | Replicate 2 | Replicate 3 | |||
---|---|---|---|---|---|---|---|
Reads | Alignment | Reads | Alignment | Reads | Alignment | ||
1 | Control | 59843094 | 98.5% | 58101312 | 98.2% | 59686650 | 98.0% |
2 | Control | 64916262 | 98.5% | 74641320 | 98.0% | 67418496 | 98.0% |
6 | Control | 64740740 | 98.6% | 68759474 | 98.0% | 71426244 | 97.8% |
12 | Control | 48624754 | 98.4% | 43314674 | 98.3% | 37368582 | 98.4% |
24 | Control | 64365702 | 98.6% | 68469240 | 98.2% | 68572898 | 97.9% |
1 | Wound | 62072772 | 98.6% | 62531754 | 98.0% | 52132476 | 98.1% |
2 | Wound | 69339124 | 98.3% | 83197276 | 97.9% | 57943888 | 98.2% |
6 | Wound | 62301400 | 98.5% | 61347708 | 98.0% | 61003562 | 98.1% |
12 | Wound | 55820584 | 98.2% | 47114420 | 98.2% | 60013782 | 98.3% |
24 | Wound | 66900286 | 98.4% | 72082570 | 98.0% | 59419184 | 98.1% |
UP | DOWN | ||||
---|---|---|---|---|---|
Total DEGs (All) | 9413 | 7704 | |||
Unannotated Sequences | 1959 | 1956 | |||
DEGs | DEGs | ||||
Keyword Search | UP () * | DOWN () * | Keyword Search | UP () * | DOWN () * |
Kinase | 637 (280) | 348 (143) | Cytochrome | 173 (89) | 131 (52) |
Receptor kinase | 281 (66) | 112 (26) | Cytochrome P450 | 133 (69) | 68 (33) |
Mitogen-activated protein kinase/MAPK | 18 (4) | 6 (1) | Dehydrogenase | 259 (121) | 211 (79) |
Phosphatase | 169 (70) | 76 (34) | Calcium/calmodulin | 130 (40) | 54 (24) |
Receptor | 431 (229) | 236 (113) | Auxin | 76 (33) | 45 (12) |
LRR receptor | 46 (23) | 15 (5) | Cytokinin | 20 (9) | 2 (0) |
Systemin/brassinosteroid receptor | 16 (3) | 3 (1) | Salicylate/salicylic | 22 (10) | 4 (1) |
Transcription | 382 (194) | 218 (81) | Ethylene | 78 (31) | 31 (13) |
Transcription factor | 273 (122) | 122 (41) | Abscisic acid | 18 (4) | 6 (0) |
WRKY | 19 (14) | 9 (6) | Gibberellin | 20 (12) | 8 (3) |
BZIP | 27 (9) | 8 (3) | Lipoxygenase | 24 (13) | 12 (3) |
Heat shock/chaperone | 63 (29) | 183 (38) | Jasmonate/jasmonic | 24 (12) | 9 (3) |
Protease/proteinase/peptidase | 264 (112) | 204 (73) | Lipase | 84 (29) | 46 (13) |
Protease/proteinase/peptidase Inhibitor | 25 (7) | 8 (0) | Phospholipase | 34 (8) | 17 (4) |
Ubiquitin | 124 (42) | 79 (29) | Proline | 74 (31) | 50 (15) |
Chloroplast/chloroplastic | 657 (154) | 384 (80) | Glycine betaine/proline transporter | 5 (2) | 1 (1) |
Photosystem | 62 (10) | 15 (8) | Phenylalanine ammonia-lyase | 15 (8) | 1 (1) |
Chlorophyll | 44 (13) | 27 (9) | Glucanase | 60 (27) | 18 (7) |
Phytochrome | 27 (10) | 7 (3) | Ferric reductase | 8 (0) | 9 (0) |
Sucrose | 54 (21) | 25 (5) | Expansin | 9 (4) | 16 (4) |
Glucose | 111 (47) | 94 (19) | Xyloglucan endotransglycosylase | 19 (6) | 2 (1) |
Glucan | 106 (50) | 49 (17) | Cellulose synthase | 19 (3) | 19 (2) |
Glucosyltransferase | 107 (46) | 43 (16) | ATP | 433 (158) | 377 (117) |
Monosaccharide transporter | 16 (9) | 2 (0) | ATPase | 116 (49) | 95 (31) |
Amino acid | 95 (43) | 45 (15) | GTP | 57 (18) | 72 (16) |
Amino acid transporter | 70 (29) | 39 (13) | GTPase | 21 (10) | 38 (10) |
Membrane | 379 (150) | 285 (117) | Dehydrin | 5 (2) | 0 |
Channel | 64 (23) | 31 (14) | Thioredoxin | 27 (5) | 14 (3) |
ABC transporter | 154 (68) | 108 (62) | Thaumatin | 11 (9) | 6 (1) |
Transport | 613 (253) | 344 (150) | Inhibitor | 80 (34) | 39 (7) |
Transferase | 641 (322) | 557 (202) | Disease | 97 (44) | 41 (20) |
Esterase | 130 (63) | 89 (31) | Pathogen | 44 (18) | 22 (7) |
Invertase | 40 (15) | 21 (4) | Chitinase | 30 (21) | 11 (3) |
Synthase | 404 (192) | 315 (126) | Avr9 | 40 (21) | 7 (2) |
Synthetase | 153 (88) | 144 (74) | Avr9 Cf-9 | 34 (19) | 6 (2) |
Reductase | 272 (119) | 225 (84) | Allene oxidase | 6 (3) | 0 |
Oxidase | 238 (100) | 133 (42) | Allene cyclase | 1 (0) | 1 (1) |
Oxygenase | 181 (89) | 71 (31) | 12-Oxophytodienoic | ||
Peroxidase | 57 (26) | 32 (7) | acid reducase | 8 (4) | 1 (0) |
Hydrolase | 319 (141) | 152 (69) | ACC oxidase | 29 (17) | 5 (1) |
Total UP DEG | 1 Hour | 2 Hour | 6 Hour | 12 Hour | 24 Hour |
1382 | 3484 | 4067 | 3418 | 2421 | |
DEG Designation | All UP () * | All UP () * | All UP () * | All UP () * | All UP () * |
Kinase | 140 (81) | 321 (135) | 272 (90) | 177 (26) | 125 (40) |
Phosphatase | 34 (22) | 82 (39) | 83 (31) | 52 (11) | 57 (20) |
Calcium/calmodulin | 46 (16) | 89 (22) | 34 (11) | 20 (2) | 18 (9) |
Transcription factor | 67 (39) | 151 (72) | 125 (46) | 68 (11) | 63 (13) |
Transcription | 85 (52) | 187 (94) | 175 (67) | 93 (19) | 95 (31) |
Synthase | 74 (39) | 158 (86) | 212 (86) | 105 (29) | 122 (47) |
Oxidase | 34 (21) | 99 (39) | 116 (49) | 74 (19) | 75 (31) |
Reductase | 34 (23) | 89 (48) | 144 (53) | 60 (11) | 105 (28) |
Peroxidase | 8 (7) | 22 (9) | 33 (16) | 24 (12) | 15 (6) |
Dehydrogenase | 42 (25) | 106 (56) | 149 (62) | 66 (7) | 81 (20) |
Transport | 112 (66) | 280 (138) | 294 (98) | 214 (38) | 189 (60) |
ABC transporter | 21 (9) | 80 (35) | 43 (20) | 41 (5) | 35 (14) |
Monosaccharide transporter | 5 (2) | 10 (10) | 13 (8) | 10 (6) | 4 (1) |
Chloroplast | 75 (49) | 141 (73) | 421 (72) | 154 (11) | 307 (32) |
Photosystem | 2 (1) | 2 (1) | 55 (6) | 4 (2) | 35 (1) |
Disease | 22 (5) | 49 (28) | 35 (11) | 34 (8) | 28 (6) |
Pathogen | 11 (4) | 31 (15) | 20 (3) | 21 (9) | 13 (4) |
Chitinase | 6 (4) | 22 (18) | 20 (12) | 13 (8) | 4 (1) |
Glucanase | 17 (11) | 38 (20) | 32 (11) | 30 (14) | 13 (7) |
Allene oxide synthase | 5 (2) | 5 (3) | 3 (1) | 1 (0) | 0 |
ACC oxidase | 5 (2) | 9 (6) | 12 (6) | 8 (3) | 13 (8) |
Thioredoxin | 3 (2) | 5 (4) | 17 (5) | 7 (0) | 11 (1) |
Xyloglucan endotransglycoslase | 1 (0) | 10 (3) | 11 (5) | 7 (2) | 5 (3) |
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Dombrowski, J.E.; Kronmiller, B.A.; Hollenbeck, V.; Martin, R.C. Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. Plants 2020, 9, 780. https://doi.org/10.3390/plants9060780
Dombrowski JE, Kronmiller BA, Hollenbeck V, Martin RC. Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. Plants. 2020; 9(6):780. https://doi.org/10.3390/plants9060780
Chicago/Turabian StyleDombrowski, James E., Brent A. Kronmiller, Vicky Hollenbeck, and Ruth C. Martin. 2020. "Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum" Plants 9, no. 6: 780. https://doi.org/10.3390/plants9060780