RNA-seq analysis reveals divergent adaptive response to hyper- and hypo-salinity in cobia, Rachycentron canadum

Alfieri RR, Petronini PG (2007) Hyperosmotic stress response: comparison with other cellular stresses. Pflugers Arch - Eur J Physiol 454(2):173–185

Alina SR, Gráinne K, Martin C, Ruskin HJ (2012) RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering. PLoS One 7(12):e50986

Ana C, Stefan GT, Juan Miguel GG, Javier T, Manuel T, Montserrat R (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676

Arnold CR, Kaiser JB, Holt GJ (2010) Spawning of cobia Rachycentron canadum in captivity. J World Aquacult Soc 33(2):205–208

Bayly IAE Salinity tolerance and osmotic behavior of animals in athalassic saline and marine hypersaline waters. Annu Rev Ecol Syst

Calvanese L, Pellegrini-Calace M, Oliva R (2013) In silico study of human aquaporin AQP11 and AQP12 channels. Protein Sci 22(4):455–466

Campbell EM, Ball A, Hoppler S, Bowman AS (2008) Invertebrate aquaporins: a review. J Comp Physiol B 178(8):935–955

Chong-Robles J, Charmantier G, Boulo V, Lizárraga-Valdéz J, Enríquez-Paredes LM, Giffard-Mena I (2014) Osmoregulation pattern and salinity tolerance of the white shrimp Litopenaeus vannamei (Boone, 1931) during post-embryonic development. Aquaculture 422-423(4):261–267

Chou RL, Su MS, Chen HY (2001) Optimal dietary protein and lipid levels for juvenile cobia (Rachycentron canadum). Aquaculture 193(1):81–89

Coady MJ, Wallendorff B, Gagnon DG, Lapointe JY (2002) Identification of a novel Na+/myo-inositol cotransporter. J Biol Chem 277(38):35219–35224

Denson MR, Stuart KR, Smith TIJ, Weirlch CR, Segars A (2003) Effects of salinity on growth, survival, and selected hematological parameters of juvenile cobia Rachycentron canadum. J World Aquacult Soc 34(4):496–504

Doi AS, Barbieri E (2012) Acute toxicity of ammonia on juvenile cobia (Rachycentron canadum, Linnaeus, 1766) according to the salinity. Aquac Int 20(2):373–382

Du F, Wu Y, Zhang L, Li XW, Zhao XY, Wang WH, Gao ZS, Xia YP (2014) De novo assembled transcriptome analysis and SSR marker development of a mixture of six tissues from Lilium oriental hybrid ‘Sorbonne’. Plant Mol Biol Report 33(2):281–293

Duncan RE, Eszter SN, Kathy J, Maryam A, Hei Sook S (2008) Identification and functional characterization of adipose-specific phospholipase A2 (AdPLA). J Biol Chem 283(37):25428–25436

Faulk CK, Holt GJ (2006) Responses of cobia Rachycentron canadum larvae to abrupt or gradual changes in salinity. Aquaculture 254(1–4):275–283

Gibbons TC, Metzger DC, Healy TM, Schulte PM (2017) Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats. Mol Ecol 26(10)

Grabherr MG, Haas BJ, Moran Y, Levin JZ, Thompson DA, Ido A, Xian A, Lin F, Raktima R, Qiandong Z (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652

Guo B, Tang Z, Wu C, Xu K, Qi P Transcriptomic analysis reveal an efficient osmoregulatory system in Siberian sturgeon Acipenser baeri in response to salinity stress. Sci Rep

Halestrap AP (2013) Monocarboxylic acid transport. Compr Physiol 3(4):1611–1643

Higashimoto Y, Nakao N, Ohkubo T, Tanaka M, Nakashima K (2001) Structure and tissue distribution of prolactin receptor mRNA in Japanese flounder (Paralichtys olivaceus): conserved and preferential expression in osmoregulatory organs. Gen Comp Endocrinol 123(2):170–179

Ho SN (2010) Intracellular water homeostasis and the mammalian cellular osmotic stress response. J Cell Physiol 206(1):9–15

Hosoi M, Shinzato C, Takagi M, Hosoi-Tanabe S, Sawada H, Terasawa E, Toyohara H (2010) Taurine transporter from the giant Pacific oyster Crassostrea gigas : function and expression in response to hyper- and hypo-osmotic stress. Fish Sci 73(2):385–394

Hwang PP, Lee TH (2007) New insights into fish ion regulation and mitochondrion-rich cells. Comp Biochem Physiol A Mol Integr Physiol 148(3):479–497

Jia Y, Lin F, Hongkun Z, Yong Z, Jie C, Zengjin Z, Jing W, Shengting L, Ruiqiang L, Lars B (2006) WEGO: a web tool for plotting GO annotations. Nucl Acids Res 34(Web Server issue):W293–W297

Koteliansky V, Lee A-H, Glimcher LH, Hur KY, So J-S et al (2012) Silencing of lipid metabolism genes through ire1α-mediated Mrna decay lowers plasma lipids in mice. Cell Metab 16(4):487–499

Lai KP, Li JW, Wang SY, Chiu MY, Tse A, Lau K, Si L, Au WT, Tse KF, Wong KC (2015) Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. BMC Genomics 16(1):135

Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967

Masamrekh R, Kuzikov A, Veselovsky A, Toropygin I, Shkel T, Strushkevich N, Gilep A, Usanov S, Archakov A, Shumyantseva V (2018) Interaction of 17α-hydroxylase, 17(20)-lyase (CYP17A1) inhibitors - abiraterone and galeterone - with human sterol 14α-demethylase (CYP51A1). J Inorg Biochem S0162013417308334

Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods

Nguyen TV, Jung H, Nguyen TM, Hurwood D, Mather P (2016) Evaluation of potential candidate genes involved in salinity tolerance in striped catfish ( Pangasianodon hypophthalmus ) using an RNA-Seq approach. Mar Genomics 25:75–88

Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley SK, Leyh TS (2003) The kinetic mechanism of phosphomevalonate kinase. J Biol Chem 278(7):4510–4515

Ricardo LS, James Tony L, Zelionara Pereira B, Adalto B, Nery LEM (2003) Lipids as energy source during salinity acclimation in the euryhaline crab Chasmagnathus granulata dana, 1851 (crustacea-grapsidae). J Exp Zool A Comp Exp Biol 295A(2):200–205

Ronkin D, Seroussi E, Nitzan T, Doron-Faigenboim A, Cnaani A (2015) Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species. Comp Biochem Physiol D: Genom Proteomics 13:35–43

Scarborough PE, Ma J, Qu W, Zeldin DC (1999) P450 subfamily CYP2J and their role in the bioactivation of arachidonic acid in extrahepatic tissues*. Drug Metab Rev 31(1):205–234

Si Y, Wen H, Li Y, He F, Li J, Li S, He H (2018) Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis. BMC Genomics 19(1):464

Silve S, Dupuy PH, Labit-Lebouteiller C, Kaghad M, Chalon P, Rahier A, Taton M, Lupker J, Shire D, Loison G (1996) Emopamil-binding protein, a mammalian protein that binds a series of structurally diverse neuroprotective agents, exhibits delta8-delta7 sterol isomerase activity in yeast. J Biol Chem 271(37):22434–22440

Thanh NM, Jung H, Lyons RE, Njaci I, Yoon BH, Chand V, Tuan NV, Thu VTM, Mather P (2015) Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus). Mar Genomics 23:87–97

Toru U, Ikuyo I, Nozomu K, Asuka I, Kazuhito T, Xing-Hua J, Nobukazu A, Junken A, Hiroyuki A, Natsuo U (2012) Regulation of peroxisomal lipid metabolism by catalytic activity of tumor suppressor H-rev107. J Biol Chem 287(4):2706

Tseng YC, Hwang PP (2008) Some insights into energy metabolism for osmoregulation in fish ☆. Comp Biochem Physiol Toxicol Pharmacol 148(4):419–429

Wang Z, Gerstein M, Snyder M RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63

Wong KS, Ozaki H, Suzuki Y, Iwasaki W, Takei Y (2014) Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach. BMC Genomics 15(1):1134

Wu Z, Gu B, Wang Z, Chen G (2009) Effects of salinity on growth and energy budget of juvenile cobia, Rachycentron canadum. J World Aquacult Soc 40(3):374–382

Xu Z, Gan L, Li T, Xu C, Chen K, Wang X, Qin JG, Chen L, Li E (2015) Transcriptome profiling and molecular pathway analysis of genes in association with salinity adaptation in Nile Tilapia Oreochromis niloticus. PLoS One 10(8):e0136506

Yang Y, Cheng JZ, Singhal SS, Saini M, Pandya U, Awasthi S, Awasthi YC (2001) Role of glutathione S-transferases in protection against lipid peroxidation. Overexpression of hGSTA2-2 in K562 cells protects against hydrogen peroxide-induced apoptosis and inhibits JNK and caspase 3 activation. J Biol Chem 276(22):19220–19230

Yau-Chung H, Chao-Kai K, Cheng-Hao T, Tsung-Han L (2015) Transcriptomic analysis of metabolic pathways in milkfish that respond to salinity and temperature changes. PLoS One 10(8):e0134959

Yi B, Qianfeng Z, Guofang Z (2014) RNA-Seq technology and its application in fish transcriptomics. Omics J Integr Biol 18(2):98

Yoshida Y, Aoyama Y, Noshiro M, Gotoh O (2000) Sterol 14-demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily. Biochem Biophys Res Commun 273(3):799–804

Zhang X, Wen H, Wang H, Ren Y, Zhao J, Li Y (2017) RNA-Seq analysis of salinity stress-responsive transcriptome in the liver of spotted sea bass (Lateolabrax maculatus). PLoS One 12(3):e0173238