Comparative Analysis of the aquaporin Gene Family in 12 Fish Species
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Identification of Putative Aqp Proteins in 12 Fish
2.2. Estimates of Aqp Gene Gain and Loss
2.3. Phylogeny, Gene Organization, and Conserved Motif Analysis of the Aqp Gene Family
2.4. Recombination Events and Detecting of the Aqp Genes
2.5. Site-Specific Selection Assessment and Testing
2.6. Microarray-Based Expression Analysis of the Zebrafish Aqp Genes under Biotic Stresses
2.7. Materials, Organophosphorus Pesticide Exposure, and RNA Sequencing and Analysis
3. Results and Discussion
3.1. Identification and Gene Gain and Loss Events of the Aqp Family Genes in the Twelve Fishes
3.2. Phylogenetic Analysis, Gene orGanization, and Motifs Distribution
3.3. Detection of Intragenic Recombination Events in the Aqp Genes
3.4. Selective Pressure at Amino Acid Sites of the Aqp Members
3.5. Expression Profiles of the Zebrafish Aqp Genes under Some Biotic Stresses
3.6. Expression Profiles of the Aqp Genes under Organophosphorus Pesticide Stress based on Transcriptome Data
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Agre, P.; Preston, G.M.; Smith, B.L.; Jung, J.S.; Raina, S.; Moon, C.; Guggino, W.B.; Nielsen, S. Aquaporin CHIP: The archetypal molecular water channel. Am. J. Physiol. 1993, 265, F463–F476. [Google Scholar] [CrossRef] [PubMed]
- Heymann, J.B.; Engel, A. Aquaporins: Phylogeny, Structure, and Physiology of Water Channels. News Physiol. Sci. 1999, 14, 187–193. [Google Scholar] [CrossRef]
- Ikeda, M.; Andoo, A.; Shimono, M.; Takamatsu, N.; Taki, A.; Muta, K.; Matsushita, W.; Uechi, T.; Matsuzaki, T.; Kenmochi, N.; et al. The NPC motif of aquaporin-11, unlike the NPA motif of known aquaporins, is essential for full expression of molecular function. J. Biol. Chem. 2011, 286, 3342–3350. [Google Scholar] [CrossRef]
- Takata, K.; Matsuzaki, T.; Tajika, Y. Aquaporins: Water channel proteins of the cell membrane. Prog. Histochem. Cytochem. 2004, 39, 1–83. [Google Scholar] [CrossRef]
- Murata, K.; Mitsuoka, K.; Hirai, T.; Walz, T.; Agre, P.; Heymann, J.B.; Engel, A.; Fujiyoshi, Y. Structural determinants of water permeation through aquaporin-1. Nature 2000, 407, 599–605. [Google Scholar] [CrossRef] [PubMed]
- Sui, H.; Han, B.G.; Lee, J.K.; Walian, P.; Jap, B.K. Structural basis of water-specific transport through the AQP1 water channel. Nature 2001, 414, 872–878. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Madsen, S.S.; Engelund, M.B.; Cutler, C.P. Water transport and functional dynamics of aquaporins in osmoregulatory organs of fishes. Biol. Bull. 2015, 229, 70–92. [Google Scholar] [CrossRef] [PubMed]
- Neely, J.D.; Christensen, B.M.; Nielsen, S.; Agre, P. Heterotetrameric composition of aquaporin-4 water channels. Biochemistry 1999, 38, 11156–11163. [Google Scholar] [CrossRef] [PubMed]
- Törnroth-Horsefield, S.; Wang, Y.; Hedfalk, K.; Johanson, U.; Karlsson, M.; Tajkhorshid, E.; Neutze, R.; Kjellbom, P. Structural mechanism of plant aquaporin gating. Nature 2006, 439, 688–694. [Google Scholar] [CrossRef]
- Beitz, E.; Liu, K.; Ikeda, M.; Guggino, W.B.; Agre, P.; Yasui, M. Determinants of AQP6 trafficking to intracellular sites versus the plasma membrane in transfected mammalian cells. Biol. Cell 2006, 98, 101–109. [Google Scholar] [CrossRef] [Green Version]
- Finn, R.N.; Cerdà, J. Evolution and functional diversity of aquaporins. Biol. Bull. 2015, 229, 6–23. [Google Scholar] [CrossRef]
- Ishibashi, K.; Morishita, Y.; Tanaka, Y. The Evolutionary Aspects of Aquaporin Family. Adv. Exp. Med. Biol. 2017, 969, 35–50. [Google Scholar] [PubMed]
- Jung, S.Y.; Kim, S.S.; Kim, Y.I.; Kim, S.H.; Yeo, S.G. A Review: Expression of Aquaporins in Otitis Media. Int. J. Mol. Sci. 2017, 18, 2164. [Google Scholar] [CrossRef]
- Cerdà, J.; Finn, R.N. Piscine aquaporins: An overview of recent advances. J. Exp. Zool. A Ecol. Genet. Physiol. 2010, 313, 623–650. [Google Scholar] [CrossRef] [PubMed]
- Froger, A.; Clemens, D.; Kalman, K.; Németh-Cahalan, K.L.; Schilling, T.F.; Hall, J.E. Two distinct aquaporin 0s required for development and transparency of the zebrafish lens. Invest. Ophthalmol. Vis. Sci. 2010, 51, 6582–6592. [Google Scholar] [CrossRef] [PubMed]
- Koun, S.; Kim, J.D.; Rhee, M.; Kim, M.J.; Huh, T.L. Spatiotemporal expression pattern of the zebrafish aquaporin 8 family during early developmental stages. Gene Expr. Patterns 2016, 21, 1–6. [Google Scholar] [CrossRef]
- Moeller, H.B.; Olesen, E.T.; Fenton, R.A. Regulation of the water channel aquaporin-2 by posttranslational modification. Am. J. Physiol. Renal Physiol. 2011, 300, F1062–1073. [Google Scholar] [CrossRef] [PubMed]
- Chauvigné, F.; Boj, M.; Finn, R.N.; Cerdà, J. Mitochondrial aquaporin-8-mediated hydrogen peroxide transport is essential for teleost spermatozoon motility. Sci. Rep. 2015, 5, 7789. [Google Scholar] [CrossRef] [Green Version]
- Fushimi, K.; Sasaki, S.; Marumo, F. Phosphorylation of serine 256 is required for cAMP-dependent regulatory exocytosis of the aquaporin-2 water channel. J. Biol. Chem. 1997, 272, 14800–14804. [Google Scholar] [CrossRef]
- Leitch, V.; Agre, P.; King, L.S. Altered ubiquitination and stability of aquaporin-1 in hypertonic stress. Proc. Natl. Acad. Sci. USA 2001, 98, 2894–2898. [Google Scholar] [CrossRef] [Green Version]
- Catalán, V.; Gómez-Ambrosi, J.; Pastor, C.; Rotellar, F.; Silva, C.; Rodríguez, A.; Gil, M.J.; Cienfuegos, J.A.; Salvador, J.; Vendrell, J.; Frühbeck, G. Influence of morbid obesity and insulin resistance on gene expression levels of AQP7 in visceral adipose tissue and AQP9 in liver. Obes. Surg. 2008, 18, 695–701. [Google Scholar] [CrossRef]
- Umenishi, F.; Schrier, R.W. Hypertonicity-induced aquaporin-1 (AQP1) expression is mediated by the activation of MAPK pathways and hypertonicity-responsive element in the AQP1 gene. J. Biol. Chem. 2003, 278, 15765–15770. [Google Scholar] [CrossRef]
- Choi, H.J.; Jung, H.J.; Kwon, T.H. Extracellular pH affects phosphorylation and intracellular trafficking of AQP2 in inner medullary collecting duct cells. Am. J. Physiol. Renal Physiol. 2015, 308, F737–F748. [Google Scholar] [CrossRef]
- Brunet, F.G.; Roest Crollius, H.; Paris, M.; Aury, J.M.; Gibert, P.; Jaillon, O.; Laudet, V.; Robinson-Rechavi, M. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol. Biol. Evol. 2006, 23, 1808–1816. [Google Scholar] [CrossRef]
- Hughes, T.; Liberles, D.A. Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. J. Mol. Evol. 2008, 67, 343–357. [Google Scholar] [CrossRef]
- Tingaud-Sequeira, A.; Calusinska, M.; Finn, R.N.; Chauvigné, F.; Lozano, J.; Cerdà, J. The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals. BMC Evol. Biol. 2010, 10, 38. [Google Scholar] [CrossRef]
- Finn, R.N.; Chauvigné, F.; Hlidberg, J.B.; Cutler, C.P.; Cerdà, J. The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation. PLoS ONE 2014, 9, e113686. [Google Scholar] [CrossRef]
- Dong, C.; Chen, L.; Feng, J.; Xu, J.; Mahboob, S.; Al-Ghanim, K.; Li, X.; Xu, P. Genome Wide Identification, Phylogeny, and Expression of Aquaporin Genes in Common Carp (Cyprinus carpio). PLoS ONE 2016, 11, e0166160. [Google Scholar] [CrossRef]
- Sémon, M.; Wolfe, K.H. Consequences of genome duplication. Curr. Opin. Genet. Dev. 2007, 17, 505–512. [Google Scholar] [CrossRef]
- Morinaga, T.; Nakakoshi, M.; Hirao, A.; Imai, M.; Ishibashi, K. Mouse aquaporin 10 gene (AQP10) is a pseudogene. Biochem. Biophys. Res. Commun. 2002, 294, 630–644. [Google Scholar] [CrossRef]
- Tanaka, Y.; Morishita, Y.; Ishibashi, K. Aquaporin10 is a pseudogene in cattle and their relatives. Biochem. Biophys. Rep. 2015, 1, 16–21. [Google Scholar] [CrossRef] [Green Version]
- Kwong, T.C. Organophosphate pesticides: Biochemistry and clinical toxicology. Ther. Drug Monit. 2002, 24, 144–149. [Google Scholar] [CrossRef]
- Fulton, M.H.; Key, P.B. Acetylcholinesterase inhibition in estuarine fish and invertebrates as an indicator of organophosphorus insecticide exposure and effects. Environ. Toxicol. Chem. 2001, 20, 37–45. [Google Scholar] [CrossRef]
- Yeh, S.P.; Sung, T.G.; Chang, C.C.; Chen, W.; Kuo, C.M. Effects of an organophosphorus insecticide, trichlorfon, on hematological parameters of the giant freshwater prawn, Macrobrachium rosenbergii (de Man). Aquaculture 2005, 243, 383–392. [Google Scholar] [CrossRef]
- Yang, Y.; Bazhin, A.V.; Werner, J.; Karakhanova, S. Reactive oxygen species in the immune system. Int. Rev. Immunol. 2013, 32, 249–270. [Google Scholar] [CrossRef]
- Wendelaar Bonga, S.; Lock, R. Toxicants and osmoregulation in fish. Neth. J. Zool. 1991, 42, 2–3. [Google Scholar]
- Katuli, K.K.; Amiri, B.M.; Massarsky, A.; Yelghi, S.; Ghasemzadeh, J. Impact of a short-term diazinon exposure on the osmoregulation potentiality of Caspian roach (Rutilus rutilus) fingerlings. Chemosphere 2014, 108, 396–404. [Google Scholar] [CrossRef]
- Yamamoto, N.; Yoneda, K.; Asai, K.; Sobue, K.; Tada, T.; Fujita, Y.; Katsuya, H.; Fujita, M.; Aihara, N.; Mase, M.; Yamada, K.; Miura, Y.; Kato, T. Alterations in the expression of the AQP family in cultured rat astrocytes during hypoxia and reoxygenation. Brain Res. Mol. Brain Res. 2001, 90, 26–38. [Google Scholar] [CrossRef]
- Herrero, J.; Muffato, M.; Beal, K.; Fitzgerald, S.; Gordon, L.; Pignatelli, M.; Vilella, A.J.; Searle, S.M.; Amode, R.; Brent, S.; Spooner, W.; Kulesha, E.; Yates, A.; Flicek, P. Ensembl comparative genomics resources. Database 2016, 2016, bav096. [Google Scholar] [CrossRef]
- Marchler-Bauer, A.; Derbyshire, M.K.; Gonzales, N.R.; Lu, S.; Chitsaz, F.; Geer, L.Y.; Geer, R.C.; He, J.; Gwadz, M.; Hurwitz, D.I. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 2015, 43, D222–D226. [Google Scholar] [CrossRef]
- Punta, M.; Coggill, P.C.; Eberhardt, R.Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J.; et al. The Pfam protein families database. Nucleic Acids Res. 2012, 40, D290–D301. [Google Scholar] [CrossRef]
- Wilkins, M.R.; Gasteiger, E.; Bairoch, A.; Sanchez, J.C.; Williams, K.L.; Appel, R.D.; Hochstrasser, D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 1999, 112, 531–552. [Google Scholar]
- Yu, C.S.; Lin, C.J.; Hwang, J.K. Predicting subcellular localization of proteins fro Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004, 13, 1402–1406. [Google Scholar] [CrossRef]
- Omasits, U.; Ahrens, C.H.; Müller, S.; Wollscheid, B. Protter: Interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics 2014, 30, 884–886. [Google Scholar] [CrossRef]
- Chen, K.; Durand, D.; Farach-Colton, M. NOTUNG: A program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 2000, 7, 429–447. [Google Scholar] [CrossRef]
- Edgar, R.C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 2004, 5, 113. [Google Scholar] [CrossRef]
- Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 2013, 30, 2725–2729. [Google Scholar] [CrossRef]
- Bailey, T.L.; Williams, N.; Misleh, C.; Li, W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34, W369–373. [Google Scholar] [CrossRef]
- Martin, D.P.; Lemey, P.; Lott, M.; Moulton, V.; Posada, D.; Lefeuvre, P. RDP3: A flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26, 2462–2463. [Google Scholar] [CrossRef]
- Martin, D.; Rybicki, E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16, 562–563. [Google Scholar] [CrossRef] [Green Version]
- Padidam, M.; Sawyer, S.; Fauquet, C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265, 218–225. [Google Scholar] [CrossRef]
- Posada, D.; Crandall, K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 2001, 98, 13757–13762. [Google Scholar] [CrossRef]
- Stern, A.; Doron-Faigenboim, A.; Erez, E.; Martz, E.; Bacharach, E.; Pupko, T. Selecton 2007: Advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res. 2007, 35, W506–W511. [Google Scholar] [CrossRef]
- Kelley, L.A.; Mezulis, S.; Yates, C.M.; Wass, M.N.; Sternberg, M.J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 2015, 10, 845–858. [Google Scholar] [CrossRef] [Green Version]
- Capriotti, E.; Fariselli, P.; Casadio, R. I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 2005, 33, W306–W310. [Google Scholar] [CrossRef]
- Feng, H.; Zhang, Y.B.; Zhang, Q.M.; Li, Z.; Zhang, Q.Y.; Gui, J.F. Zebrafish IRF1 regulates IFN antiviral response through binding to IFNϕ1 and IFNϕ3 promoters downstream of MyD88 signaling. J. Immunol. 2015, 194, 1225–1238. [Google Scholar] [CrossRef]
- Benard, E.L.; Rougeot, J.; Racz, P.I.; Spaink, H.P.; Meijer, A.H. Transcriptomic Approaches in the Zebrafish Model for Tuberculosis-Insights Into Host- and Pathogen-specific Determinants of the Innate Immune Response. Adv. Genet. 2016, 95, 217–251. [Google Scholar]
- Sturn, A.; Quackenbush, J.; Trajanoski, Z. Genesis: Cluster analysis of microarray data. Bioinformatics 2002, 18, 207–208. [Google Scholar] [CrossRef]
- Cao, J.; Tan, X. Comparative and evolutionary analysis of the 14-3-3 family genes in eleven fishes. Gene 2018, 662, 76–82. [Google Scholar] [CrossRef]
- Cao, J.; Tan, X. Comparative analysis of the tetraspanin gene family in six teleost fishes. Fish Shellfish Immunol. 2018, 82, 432–441. [Google Scholar] [CrossRef]
- Mendeley Data. Available online: https://data.mendeley.com/datasets/fch4sczvx7/1 (accessed on 8 May 2019).
- Hamdi, M.; Sanchez, M.A.; Beene, L.C.; Liu, Q.; Landfear, S.M.; Rosen, B.P.; Liu, Z. Arsenic transport by zebrafish aquaglyceroporins. BMC Mol. Biol. 2009, 10, 104. [Google Scholar] [CrossRef]
- Castillo-Davis, C.I.; Mekhedov, S.L.; Hartl, D.L.; Koonin, E.V.; Kondrashov, F.A. Selection for short introns in highly expressed genes. Nat. Genet. 2002, 31, 415–418. [Google Scholar] [CrossRef] [Green Version]
- Le Hir, H.; Nott, A.; Moore, M.J. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 2003, 28, 215–220. [Google Scholar] [CrossRef]
- Roy, S.W.; Gilbert, W. The evolution of spliceosomal introns: Patterns, puzzles and progress. Nat. Rev. Genet. 2006, 7, 211–221. [Google Scholar]
- Gomes, D.; Agasse, A.; Thiébaud, P.; Delrot, S.; Gerós, H.; Chaumont, F. Aquaporins are multifunctional water and solute transporters highly divergent in living organisms. Biochim. Biophys. Acta 2009, 1788, 1213–1228. [Google Scholar] [CrossRef] [Green Version]
- de Silva, E.; Kelley, L.A.; Stumpf, M.P. The extent and importance of intragenic recombination. Hum. Genomics 2004, 1, 410–420. [Google Scholar] [CrossRef]
- Wicker, T.; Yahiaoui, N.; Keller, B. Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes. Plant J. 2007, 51, 631–641. [Google Scholar] [CrossRef] [Green Version]
- Posada, D. Evaluation of methods for detecting recombination from DNA sequences: Empirical data. Mol. Biol. Evol. 2002, 19, 708–717. [Google Scholar] [CrossRef]
- Reizer, J.; Reizer, A., Jr.; Saier, M.H. The MIP family of integral membrane channel proteins: Sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins. Cri. Rev. Biochem. Mol. Biol. 1993, 28, 235–257. [Google Scholar] [CrossRef]
- Hurst, L.D. The Ka/Ks ratio: Diagnosing the form of sequence evolution. Trends Genet. 2002, 18, 486. [Google Scholar] [CrossRef]
- Duarte, J.M.; Cui, L.; Wall, P.K.; Zhang, Q.; Zhang, X.; Leebens-Mack, J.; Ma, H.; Altman, N.; dePamphilis, C.W. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol. 2006, 23, 469–478. [Google Scholar] [CrossRef]
- Finn, R.N.; Cerdà, J. Aquaporin evolution in fishes. Front. Physiol. 2011, 2, 44. [Google Scholar] [CrossRef]
- Ahne, W.; Bjorklund, H.V.; Essbauer, S.; Fijan, N.; Kurath, G.; Winton, J.R. Spring viremia of carp (SVC). Dis. Aquat. Organ. 2002, 52, 261–272. [Google Scholar] [CrossRef]
- Ashraf, U.; Lu, Y.; Lin, L.; Yuan, J.; Wang, M.; Liu, X. Spring viraemia of carp virus: Recent advances. J. Gen. Virol. 2016, 97, 1037–1051. [Google Scholar] [CrossRef]
- Chan, K.; Knaak, T.; Satkamp, L.; Humbert, O.; Falkow, S.; Ramakrishnan, L. Complex pattern of Mycobacterium marinum gene expression during long-term granulomatous infection. Proc. Natl. Acad. Sci. USA 2002, 99, 3920–3925. [Google Scholar] [CrossRef]
- Wu, T.S.; Chiu, C.H.; Yang, C.H.; Leu, H.S.; Huang, C.T.; Chen, Y.C.; Wu, T.L.; Chang, P.Y.; Su, L.H.; Kuo, A.J.; Chia, J.H.; Lu, C.C.; Lai, H.C. Fish tank granuloma caused by Mycobacterium marinum. PLoS ONE 2012, 7, e41296. [Google Scholar] [CrossRef]
- Gonen, T.; Walz, T. The structure of aquaporins. Q. Rev. Biophys. 2006, 39, 361–396. [Google Scholar] [CrossRef]
- Saadoun, S.; Papadopoulos, M.C.; Hara-Chikuma, M.; Verkman, A.S. Impairment of angiogenesis and cell migration by targeted aquaporin-1 gene disruption. Nature 2005, 434, 786–792. [Google Scholar] [CrossRef]
- Saadoun, S.; Papadopoulos, M.C.; Watanabe, H.; Yan, D.; Manley, G.T.; Verkman, A.S. Involvement of aquaporin-4 in astroglial cell migration and glial scar formation. J. Cell Sci. 2005, 118, 5691–5698. [Google Scholar] [CrossRef] [Green Version]
- Da, T.; Verkman, A.S. Aquaporin-4 gene disruption in mice protects against impaired retinal function and cell death after ischemia. Invest. Ophthalmol. Vis. Sci. 2004, 45, 4477–4483. [Google Scholar] [CrossRef]
- Díaz-Resendiz, K.J.; Toledo-Ibarra, G.A.; Girón-Pérez, M.I. Modulation of immune response by organophosphorus pesticides: Fishes as a potential model in immunotoxicology. J. Immunol. Res. 2015, 2015, 213836. [Google Scholar] [CrossRef]
Species | Recombination Methods | Genes undergone Recombination Events | ||
---|---|---|---|---|
RDP | GENECONV | MaxChi | ||
A. mexicanus | 1 | 1 | 4 | Ame_aqp3a; Ame_aqp7; Ame_aqp8a1; Ame_aqp8a2; Ame_aqp10b; Ame_mipa |
D. rerio | 1 | 2 | 5 | Dre_aqp3a; Dre_aqp3 |
G. aculeatus | 3 | 0 | 4 | Gac_aqp4; Gac_aqp8a1; Gac_aqp9b; Gac_aqp10a |
G. morhua | 1 | 0 | 2 | Gmo_aqp1a; Gmo_aqp10b |
L. chalumnae | 2 | 0 | 3 | Lch_aqp3; Lch_aqp4; Lch_aqp4l; Lch_aqp7; Lch_aqp9; Lch_mipb; Lch_mipc |
L. oculatus | 2 | 0 | 1 | Loc_aqp3b; Loc_aqp9b; Loc_aqp10b; Loc_mipb |
O. latipes | 1 | 0 | 5 | Ola_aqp4; Ola_aqp9b; Ola_10b; Ola_mipa |
O. niloticus | 1 | 0 | 2 | Oni_aqp4; Oni_aqp8a1; Oni_aqp9a |
P. formosa | 4 | 0 | 4 | Pfo_aqp1; Pfo_aqp9l; Pfo_aqp9b; Pfo_aqp10; Pfo_aqp10a; Pfo_mipb |
T. nigroviridis | 4 | 1 | 6 | Tni_aqp3a; Tni_aqp4; Tni_aqp7; Tni_aqp9b |
T. rubripes | 3 | 0 | 5 | Tru_aqp1a1; Tru_aqp3a; Tru_aqp7; Tru_aqp9 |
X. maculatus | 2 | 0 | 6 | Xma_aqp1a; Xma_aqp3a; Xma_aqp7; Xma_aqp8a; Xma_aqp9b; Xma_10a2 |
Gene Branches | Selection Models | Ka/Ks | Log-Likehood | Numbers of PSS * |
---|---|---|---|---|
Group I | M8(beta+w ≥ 1) | 0.2236 | −29,922.3 | 0 |
M8a(beta+w = 1) | 0.2222 | −29,924.8 | 0 | |
M7(beta) | 0.2069 | −29,913.2 | 0 | |
M5(gamma) | 0.2279 | −29,941 | 0 | |
Group II | M8(beta+w ≥ 1) | 0.2219 | −5268.97 | 0 |
M8a(beta+w = 1) | 0.2185 | −5267.87 | 0 | |
M7(beta) | 0.2165 | −5265.73 | 0 | |
M5(gamma) | 0.2403 | −5279.27 | 0 | |
Group III | M8(beta+w ≥ 1) | 0.2628 | −11,574.5 | 7 |
M8a(beta+w = 1) | 0.2567 | −11,572.8 | 0 | |
M7(beta) | 0.2521 | −11,580.1 | 0 | |
M5(gamma) | 0.2719 | −11,582.4 | 0 | |
Group IV | M8(beta+w ≥ 1) | 0.2141 | −37,259.4 | 5 |
M8a(beta+w = 1) | 0.2096 | −37,265.2 | 0 | |
M7(beta) | 0.2004 | −37,281.1 | 0 | |
M5(gamma) | 0.2120 | −37,277.5 | 0 |
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Cao, J.; Shi, F. Comparative Analysis of the aquaporin Gene Family in 12 Fish Species. Animals 2019, 9, 233. https://doi.org/10.3390/ani9050233
Cao J, Shi F. Comparative Analysis of the aquaporin Gene Family in 12 Fish Species. Animals. 2019; 9(5):233. https://doi.org/10.3390/ani9050233
Chicago/Turabian StyleCao, Jun, and Feng Shi. 2019. "Comparative Analysis of the aquaporin Gene Family in 12 Fish Species" Animals 9, no. 5: 233. https://doi.org/10.3390/ani9050233
APA StyleCao, J., & Shi, F. (2019). Comparative Analysis of the aquaporin Gene Family in 12 Fish Species. Animals, 9(5), 233. https://doi.org/10.3390/ani9050233