Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes
Abstract
:1. Introduction
2. Materials and methods
2.1. Ethics Statement
2.2. Genome-Wide Identification of Spotted Sea Bass Slc4 Genes
2.3. Phylogenetic and Syntenic Analysis
2.4. Gene Structure and Domain Analysis
2.5. Selective Pressure Analysis
2.6. Carbonate Alkalinity Exposure Experiment
2.7. Freshwater and Seawater Transition Experiments
2.8. RNA Extraction and Quantitative Real-Time PCR (qPCR) Analysis
2.9. Statistical Analysis
3. Results
3.1. Characterizations of Slc4 Gene Sequences in Spotted Sea Bass
3.2. Phylogenetic, Syntenic, and Chromosomal Distribution Analysis of slc4 Genes
3.3. Gene Structure Analysis of Spotted Sea Bass slc4 Genes
3.4. Copy Number Comparison of slc4 Genes in Selected Vertebrates
3.5. Selective Pressure Analysis
3.6. Expression Patterns of slc4 Genes in Response to Alkalinity Stress
3.7. Branchial Expression Patterns of slc4 Genes During FW and SW Acclimation
4. Discussion
4.1. Features of slc4 Genes in Spotted Sea Bass
4.2. Function Studies of slc4 Genes of Spotted Sea Bass in Response to Salinity and Alkalinity Stresses
4.2.1. Anion Exchanger Proteins (AEs)
4.2.2. Na+-Coupled Bicarbonate Transporters (NCBTs)
4.2.3. Na+-Coupled Borate Transporter (NaBC)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Classification | Gene Name | CDS Length (bp) | Predicted Protein Length (Amino Acid) | Molecular Weight (kDa) | Isoelectric Point (pI) | Accession Number of NCBI |
---|---|---|---|---|---|---|
Cl−/HCO3− exchanger | slc4a1a | 2766 | 921 | 103.29 | 5.31 | MN909728 |
slc4a1b | 2523 | 840 | 94.05 | 8.68 | MN909729 | |
slc4a2a | 3417 | 1138 | 126.82 | 5.99 | MN909730 | |
slc4a2b | 3678 | 1225 | 137.11 | 6.09 | MN909731 | |
slc4a3 | 3702 | 1234 | 139.71 | 5.85 | MN909732 | |
Na+/HCO3− cotransporter | slc4a4 | 3213 | 1070 | 120.51 | 6.23 | MN909733 |
slc4a5a | 2586 | 861 | 96.92 | 5.80 | MN909734 | |
slc4a5b | 3423 | 1140 | 129.03 | 6.63 | MN909735 | |
slc4a7a | 2799 | 932 | 103.90 | 6.82 | MN909736 | |
slc4a7b | 3015 | 1004 | 111.26 | 6.66 | MN909737 | |
slc4a8 | 3363 | 1120 | 125.37 | 6.03 | MN909738 | |
slc4a10a | 3261 | 1086 | 122.58 | 6.18 | MN909739 | |
slc4a10b | 4023 | 1340 | 149.04 | 5.83 | MN909740 | |
Na+/Borate cotransporter | slc4a11a | 2529 | 842 | 94.91 | 6.11 | MN909741 |
slc4a11b | 2316 | 771 | 86.84 | 6.73 | MN909742 |
Model | np | LnL | Models Compared | 2△LnL | df | p | Positively Selected Sites |
---|---|---|---|---|---|---|---|
Null model A—slc4a1a | 43 | −27215.89837 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a1a | 44 | −27215.89837 | |||||
Null model A—slc4a1b | 43 | −27204.09798 | MA vs. NMA | 42.52516 | 1 | 0.00000 | 138S * 141T ** 148N ** 152T ** 470V ** 471N ** |
Model A—slc4a1b | 44 | −27182.83540 | |||||
Null model A—slc4a2a | 43 | −16901.01428 | MA vs. NMA | 2.0 × 10−5 | 1 | 0.99643 | |
Model A—slc4a2a | 44 | −16901.01429 | |||||
Null model A—slc4a2b | 43 | −16900.85034 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a2b | 44 | −16900.85034 | |||||
Null model A—slc4a3 | 27 | −22702.55961 | MA vs. NMA | 2.6 × 10−4 | 1 | 0.4791 | |
Model A—slc4a3 | 28 | −22702.55948 | |||||
Null model A—slc4a4 | 43 | −27709.75538 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a4 | 44 | −27709.75538 | |||||
Null model A—slc4a5a | 45 | −22011.18613 | MA vs. NMA | 0.08432 | 1 | 0.77153 | |
Model A—slc4a5a | 46 | −22011.14397 | |||||
Null model A—slc4a5b | 45 | −22013.51479 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a5b | 46 | −22013.51479 | |||||
Null model A—slc4a7a | 39 | −3957.77188 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a7a | 40 | −3957.77188 | |||||
Null model A—slc4a7b | 39 | −3957.65280 | MA vs. NMA | 0.23816 | 1 | 0.62554 | |
Model A—slc4a7b | 40 | −3957.77188 | |||||
Null model A—slc4a8 | 27 | −7554.82350 | MA vs. NMA | 7.70544 | 1 | 0.00551 | 33L * 34S ** |
Model A—slc4a8 | 28 | −7550.97078 | |||||
Null model A—slc4a10a | 43 | −27358.78420 | MA vs. NMA | 0.28100 | 1 | 0.59605 | |
Model A—slc4a10a | 44 | −27358.64370 | |||||
Null model A—slc4a10b | 43 | −27346.85330 | MA vs. NMA | 31.10466 | 1 | 0.00000 | 200S * 214S ** 215A ** 216T ** 349R * |
Model A—slc4a10b | 44 | −27331.30097 | |||||
Null model A—slc4a11a | 35 | −6835.90728 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a11a | 36 | −6835.90728 | |||||
Null model A—slc4a11b | 35 | −6835.90728 | MA vs. NMA | 0.00000 | 1 | 1.00000 | |
Model A—slc4a11b | 36 | −6835.90728 |
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Wang, L.-Y.; Tian, Y.; Wen, H.-S.; Yu, P.; Liu, Y.; Qi, X.; Gao, Z.-C.; Zhang, K.-Q.; Li, Y. Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes. Genes 2020, 11, 1271. https://doi.org/10.3390/genes11111271
Wang L-Y, Tian Y, Wen H-S, Yu P, Liu Y, Qi X, Gao Z-C, Zhang K-Q, Li Y. Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes. Genes. 2020; 11(11):1271. https://doi.org/10.3390/genes11111271
Chicago/Turabian StyleWang, Ling-Yu, Yuan Tian, Hai-Shen Wen, Peng Yu, Yang Liu, Xin Qi, Zhi-Chao Gao, Kai-Qiang Zhang, and Yun Li. 2020. "Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes" Genes 11, no. 11: 1271. https://doi.org/10.3390/genes11111271