Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Algal Culture
2.2. Toxin Analysis
2.3. Analysis of Physiological Parameters
2.4. Confocal Laser Scanning Microscope (CLSM) Analysis
2.5. Lipid Analysis
2.6. Starch Content Measurements
2.7. RNA Extraction, Sequencing, and Transcriptome Analysis
2.8. RT-qPCR
2.9. Statistical Analysis
3. Results
3.1. Physiological Responses of P. lima under Phosphate Limitation
3.2. Transcriptomic Analysis
3.3. Transcriptomic Analysis of Differential Gene Expression
3.4. RT-qPCR Validation of Differentially Expressed Genes
3.5. Lipid and Starch Accumulation under P-Limited Conditions
3.6. DSP Toxin Content in P. lima under P-Limited Conditions
4. Discussion
4.1. Carbon Metabolism and Photosynthesis under P-Limited Conditions
4.2. Phosphate Transport, Utilization, and Homeostasis
4.3. Lipid and Starch Accumulation under P-Limited Conditions
4.4. DSP Toxins Production in P. lima
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sample | Raw Reads | Clean Reads | GC Content (%) | Q20 Percentage (%) | Number of Unigenes | BLASTx Analysis Percentage (%) | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG | NR | Swiss-Prot | TrEMBL | KOG | GO | Pfam | ||||||
1P | 110,831,089 | 81,618,516 | 58.86 | 97.48 | 88,186 | 15.63 | 22.46 | 11.73 | 45.91 | 15.02 | 35.42 | 43.44 |
1/4P | 110,497,380 | 83,366,479 | 58.87 | 97.57 | 90,706 | 17.97 | 24.61 | 14.19 | 47.42 | 17.38 | 37.21 | 45.00 |
1/16P | 115,006,749 | 90,073,946 | 58.54 | 97.71 | 91,890 | 19.03 | 25.58 | 15.30 | 48.09 | 18.45 | 38.02 | 45.72 |
Average Data | 112,111,739 | 85,019,647 | 58.76 | 97.59 | 90,261 | 17.54 | 24.22 | 13.74 | 47.14 | 16.95 | 36.88 | 44.72 |
Functional Classification | Gene | Description | Unigene ID | log2 (Fold Change) (1/16P vs. 1P) |
---|---|---|---|---|
Ribosome | RP-S20e | Small subunit ribosomal protein S20e | Cluster-1527.83547 | 3.92 |
RP-S11e | Small subunit ribosomal protein S11e | Cluster-1527.1298 | 3.56 | |
RP-L34e | Large subunit ribosomal protein L34e | Cluster-1527.8476 | 3.77 | |
RP-S5e | Small subunit ribosomal protein S5e | Cluster-1527.76135 | 3.65 | |
RP-L10e | Large subunit ribosomal protein L10e | Cluster-5599.0 | 7.70 | |
Stress–shock proteins | Hsp 70 | Heat shock 70 kDa protein, mitochondrial-like | Cluster-1527.8250 | 4.34 |
Hsp 90 | Heat shock protein 90 | Cluster-1527.77292 | 5.04 | |
Hsp 83 | Heat shock protein 83 | Cluster-1527.9757 | 4.57 | |
HSPA1s | Heat shock 70 kDa protein 1/2/6/8 | Cluster-1527.86746 | 4.97 | |
Photosynthesis system | PsbA | Photosystem II P680 reaction center D1 protein | Cluster-1527.39156 | −2.94 |
PsbC | Photosystem II CP43 chlorophyll apoprotein | Cluster-1527.45732 | −3.30 | |
PsbB | Photosystem II CP47 chlorophyll apoprotein | Cluster-1527.50539 | −2.51 | |
PsaA | Photosystem I P700 chlorophyll a apoprotein A1 | Cluster-1527.41047 | −2.44 | |
PsaB | Photosystem I P700 chlorophyll a apoprotein A2 | Cluster-1527.52290 | −2.79 | |
PetB | Cytochrome b6 | Cluster-1527.15944 | −3.60 | |
PetD | Cytochrome b6-f complex subunit 4 | Cluster-1527.82828 | −3.59 | |
PetF | Ferredoxin | Cluster-1527.21762 | −8.44 | |
Carbon fixation | PpdK | Pyruvate orthophosphate dikinase | Cluster-1527.73147 | 1.25 |
RbcL | Ribulose bisphosphate carboxylase | Cluster-1527.41437 | 1.95 | |
GAPA | Glyceraldehyde-3-phosphate dehydrogenase | Cluster-1527.43164 | 2.54 | |
TPI | Triosephosphate isomerase | Cluster-1527.53219 | 1.05 | |
Phagosome | RAB5A | Ras-related protein Rab-5A | Cluster-1527.16544 | 5.36 |
CALR | Calreticulin | Cluster-5481.0 | 4.07 | |
RAB7A | Ras-related protein Rab-7A | Cluster-1527.86789 | 4.29 | |
SEC61A | Protein transport protein SEC61 subunit alpha | Cluster-5772.0 | 3.57 | |
RAC1 | Ras-related C3 botulinum toxin substrate 1 | Cluster-1527.76712 | 3.78 | |
Endocytosis | ARF1/2 | ADP-ribosylation factor 1/2 | Cluster-1527.8157 | 4.11 |
SMAP | Stromal membrane-associated protein | Cluster-1527.1659 | 4.74 | |
HSPA1s | Heat shock 70 kDa protein 1/2/6/8 | Cluster-1527.86746 | 4.97 | |
RAB11A | Ras-related protein Rab-11A | Cluster-6525.0 | 4.52 | |
CHMP4A/B | Charged multivesicular body protein 4A/B | Cluster-9796.0 | 4.04 | |
CHMP3 | Charged multivesicular body protein 3 | Cluster-6541.0 | 4.52 | |
Glycolysis, oxidative phosphorylation | PK | Pyruvate kinase | Cluster-1527.60580 | 0.91 |
PD | Pyruvate dehydrogenase | Cluster-1527.62164 | 1.46 | |
PGK | Phosphoglycerate kinase | Cluster-1527.83027 | 4.04 | |
COX5B | Cytochrome c oxidase subunit 5b | Cluster-1527.419 | 4.42 | |
SDHA | Succinate dehydrogenase (ubiquinone) Flavoprotein subunit | Cluster-1527.79011 | 4.92 | |
ATP5B | F-type H+-transporting ATPase subunit beta | Cluster-1527.10945 | 4.34 | |
ABC transporters | ABCA3 | ATP-binding cassette, subfamily A (ABC1), member 3 | Cluster-1527.71271 | 1.35 |
ABCB1 | ATP-binding cassette, subfamily B (MDR/TAP), member 1 | Cluster-1527.63439 | 1.81 | |
ABCC1 | ATP-binding cassette, subfamily C (CFTR/MRP), member 1 | Cluster-1527.10718 | 1.64 | |
phosphate transporters | MPT | Mitochondrial phosphate transporter | Cluster-1527.80953 | 3.72 |
TPT | Triose-phosphate transporter family | Cluster-1527.55083 | 1.41 | |
Fatty acid biosynthesis | ACACA | Acetyl-CoA carboxylase/biotin carboxylase 1 | Cluster-1527.38700 | 2.00 |
MCAT | Malonyl coenzyme A-acyl carrier protein transacylase | Cluster-1527.31766 | 1.16 | |
FadD | Long-chain acyl-CoA synthetase | Cluster-4976.0 | 3.70 | |
Ubiquitin-mediated proteolysis | UB | Ubiquitin family protein | Cluster-1527.11208 | 4.41 |
UBE2D | Ubiquitin-conjugating enzyme E2 D | Cluster-1527.86049 | 4.35 | |
UBE2N | Ubiquitin-conjugating enzyme E2 N | Cluster-1527.9310 | 4.67 |
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Wan, X.; Yao, G.; Wang, K.; Liu, Y.; Wang, F.; Jiang, H. Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation. Microorganisms 2023, 11, 2216. https://doi.org/10.3390/microorganisms11092216
Wan X, Yao G, Wang K, Liu Y, Wang F, Jiang H. Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation. Microorganisms. 2023; 11(9):2216. https://doi.org/10.3390/microorganisms11092216
Chicago/Turabian StyleWan, Xiukun, Ge Yao, Kang Wang, Yanli Liu, Fuli Wang, and Hui Jiang. 2023. "Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation" Microorganisms 11, no. 9: 2216. https://doi.org/10.3390/microorganisms11092216
APA StyleWan, X., Yao, G., Wang, K., Liu, Y., Wang, F., & Jiang, H. (2023). Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation. Microorganisms, 11(9), 2216. https://doi.org/10.3390/microorganisms11092216