Abstract
Schizothorax prenanti (S. prenanti) is an indigenous fish species and is popularly cultured in southwestern China. In recent years, intensive farming of S. prenanti and water quality deterioration has increased the susceptibility of this fish to various pathogens, including Aeromonas hydrophila (A. hydrophila), which has caused severe damage to S. prenanti production. However, the understanding of molecular immune response of S. prenanti to A. hydrophila infection is still lacking. In order to better comprehend the S. prenanti time series immune response process against A. hydrophila, we conducted the first transcriptomic comparison in S. prenanti spleen at 4, 24, and 48 h after the infection challenge of A. hydrophila against their control counterparts. In total, 628 million clean reads were obtained from 18 libraries and assembled into 262,745 transcripts. After eliminating sequence redundancy, 69,373 unigenes with an average length of 1476 bp were obtained. Comparative analysis revealed 1890 unigenes with significantly differential expression, including 172, 455, 589 upregulated and 27, 676, 551 unigenes downregulated genes for 4, 24, and 48 h post-infection, respectively. Differentially expressed genes (DEGs) were validated using qPCR for 15 randomly selected genes. Enrichment and pathway analysis of DEGs was carried out to understand the functions of the immune-related genes. Our results revealed that many important functional genes relating to complement and coagulation cascades, chemokine signaling pathway, toll-like receptor signaling pathway, NOD-like receptor signaling pathway and leukocyte transendothelial migration were regulated during the infection of A. hydrophila, and the expression of those genes reflected the transcriptome profiles during the challenging stages.
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Aijaz S, Balda MS, Matter K (2006) Tight junctions: molecular architecture and function. Int Rev Cytol 248:261–298
Altschul S, Madden T, Schaffer A et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Beck BH, Farmer BD, Straus DL, Li C, Peatman E (2012) Putative roles for a rhamnose binding lectin in Flavobacterium columnare pathogenesis in channel catfish Ictalurus punctatus. Fish Shellfish Immunol 33:1008–1015
Bonecchi R, Garlanda C, Mantovani A, Riva F (2016) Cytokine decoy and scavenger receptors as key regulators of immunity and inflammation. Cytokine 87:37–45
Chadzinska M, Baginski P, Kolaczkowska E, Savelkoul HFJ, Lidy Verburg-van Kemenade BM (2008) Expression profiles of matrix metalloproteinase 9 in teleost fish provide evidence for its active role in initiation and resolution of inflammation. Immunology 125:601–610
Chatchaiphan S, Srisapoome P, Kim J-H, Devlin RH, Na-Nakorn U (2017) De novo transcriptome characterization and growth-related gene expression profiling of diploid and triploid bighead catfish (Clarias macrocephalus Günther, 1864). Mar Biotechnol 19:36–48
Chong C-R, Chan WPA, Nguyen TH, Liu S, Procter NEK, Ngo DT, Sverdlov AL, Chirkov YY, Horowitz JD (2014) Thioredoxin-interacting protein: pathophysiology and emerging pharmacotherapeutics in cardiovascular disease and diabetes. Cardiovasc Drugs Ther 28:347–360
Colwell R, Macdonell M, Deley J (1986) Proposal to recognize the family Aeromonadaceae fam-Nov. Int J Syst Bacteriol 36:473–477
Conesa A, Götz S, García-Gómez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Copeland DL, Duff RJ, Liu Q, Prokop J, Londraville RL (2011) Leptin in teleost fishes: an argument for comparative study. Front Physiol 2:26
Ding R (1994) The fishes of Sichuan (Chinese). Sichuan Publishing House of Science and Technology, Chengdu, Sichuan, China
Du X, Li Y, Li D et al (2017) Transcriptome profiling of spleen provides insights into the antiviral mechanism in Schizothorax prenanti after poly (I: C) challenge. Fish Shellfish Immunol 62:13–23
Du Z, Huang X, Wang K et al (2011) Isolation and identification of etiology of skin ulcer in Schizothorax prenanti (Chinese). J Sichuan Agric Univ:274–279
Du Z, Wang K, Li Z, Fan L (2003) The first reports of disease control and prevention in Schizothorax prenanti (Chinese). China Fish 82–83
Geng Y, Wang KY, Huang XL, Chen DF, Li CW, Ren SY, Liao YT, Zhou ZY, Liu QF, du ZJ, Lai WM (2012) Streptococcus agalactiae, an emerging pathogen for cultured Ya-fish, Schizothorax prenanti, in China. Transbound Emerg Dis 59:369–375
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652
Huang S, Cao X, Tian X (2016) Transcriptomic analysis of compromise between air-breathing and nutrient uptake of posterior intestine in loach (Misgurnus anguillicaudatus), an air-breathing fish. Mar Biotechnol 18:521–533
Janda JM, Abbott SL (2010) The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev 23:35–73
Jiang Y, Feng S, Zhang S, Liu H, Feng J, Mu X, Sun X, Xu P (2016) Transcriptome signatures in common carp spleen in response to Aeromonas hydrophila infection. Fish Shellfish Immunol 57:41–48
Joseph SW, Carnahan A (1994) The isolation, identification, and systematics of the motile Aeromonas species. Annu Rev Fish Dis 4:315–343
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323
Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 32:816–827
Li Y, Lai S, Wang R, Zhao Y, Qin H, Jiang L, Li N, Fu Q, Li C (2017) RNA-Seq analysis of the antioxidant status and immune response of Portunus trituberculatus following aerial exposure. Mar Biotechnol 19:89–101
Liang J, Liu Y, Zhang X, Zhang X, Yue B, Song Z (2011) An observation of the loss of genetic variability in prenant’s schizothoracin, Schizothorax prenanti, inhabiting a plateau lake. Biochem Syst Ecol 39:361–370
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods 25:402–408
Lü A-J, Hu X-C, Wang Y, Zhu AH, Shen LL, Tian J, Feng ZZ, Feng ZJ (2015) Skin immune response in the zebrafish, Danio rerio (Hamilton), to Aeromonas hydrophila infection: a transcriptional profiling approach. J Fish Dis 38:137–150
Luo H, Xiao S, Ye H, Zhang Z, Lv C, Zheng S, Wang Z, Wang X (2016) Identification of immune-related genes and development of SSR/SNP markers from the spleen transcriptome of Schizothorax prenanti. PLoS One 11:e0152572
Magnadottir B (2010) Immunological control of fish diseases. Mar Biotechnol 12:361–379
Moltó A, Olivé A (2010) Anti-IL-1 molecules: new comers and new indications. Joint Bone Spine 77:102–107
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Mu Y, Ding F, Cui P, Ao J, Hu S, Chen X (2010) Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics 11:506
Nakasugi K, Crowhurst R, Bally J, Waterhouse P (2014) Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PLoS One 9:e91776
Rauschmayr T, Groves RW, Kupper TS (1997) Keratinocyte expression of the type 2 interleukin 1 receptor mediates local and specific inhibition of interleukin 1-mediated inflammation. Proc Natl Acad Sci U S A 94:5814–5819
Robinson N, Sahoo PK, Baranski M, Mahapatra KD, Saha JN, Das S, Mishra Y, Das P, Barman HK, Eknath AE (2012) Expressed sequences and polymorphisms in Rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. Mar Biotechnol 14:620–633
Singh V, Chaudhary DK, Mani I, Jain R, Mishra BN (2013) Development of diagnostic and vaccine markers through cloning, expression, and regulation of putative virulence-protein-encoding genes of Aeromonas hydrophila. J Microbiol (Seoul, Korea) 51:275–282
Song J, Song Z, Yue B, Zheng W (2006) Assessing genetic diversity of wild populations of Prenant’s schizothoracin, Schizothorax prenanti, using AFLP markers. Environ Biol Fish 77:79–86
Song K, Li L, Zhang G (2017a) Bias and correction in RNA-seq data for marine species. Mar Biotechnol 19:541–550
Song X, Hu X, Sun B, Bo Y, Wu K, Xiao L, Gong C (2017b) A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila. Sci Rep 7:40777
Sun F, Peatman E, Li C, Liu S, Jiang Y, Zhou Z, Liu Z (2012) Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Dev Comp Immunol 38:169–180
Tran NT, Gao Z-X, Zhao H-H, Yi SK, Chen BX, Zhao YH, Lin L, Liu XQ, Wang WM (2015) Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila. Fish Shellfish Immunol 45:72–82
Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138
Wei R, Liu T, Zhou C, Zhang XD, Yuan DY, Wang T, Lin FJ, Chen H, Wu HW, Li ZQ (2013a) Identification, tissue distribution and regulation of preproghrelin in the brain and gut of Schizothorax prenanti. Regul Pept 186:18–25
Wei R, Yuan D, Wang T, Zhou CW, Lin FJ, Chen H, Wu HW, Yang SY, Wang Y, Liu J, Gao YD, Li ZQ (2013b) Characterization, tissue distribution and regulation of agouti-related protein (AgRP) in a cyprinid fish (Schizothorax prenanti). Gene 527:193–200
Wei R, Yuan D, Zhou C, Wang T, Lin F, Chen H, Wu H, Xin Z, Yang S, Chen D, Wang Y, Liu J, Gao Y, Li Z (2013c) Cloning, distribution and effects of fasting status of melanocortin 4 receptor (MC4R) in Schizothorax prenanti. Gene 532:100–107
Xu DH, Zhu Z, Wakefield MR, Xiao H, Bai Q, Fang Y (2016) The role of IL-11 in immunity and cancer. Cancer Lett 373:156–163
Xu X-Y, Shen Y-B, Fu J-J, Liu F, Guo SZ, Li JL (2013) Characterization of MMP-9 gene from grass carp (Ctenopharyngodon idella): an Aeromonas hydrophila-inducible factor in grass carp immune system. Fish Shellfish Immunol 35:801–807
Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B (2013) HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics 14:33
Yang Y, Yu H, Li H, Wang A (2016) Transcriptome profiling of grass carp (Ctenopharyngodon idellus) infected with Aeromonas hydrophila. Fish Shellfish Immunol 51:329–336
Ye H, He L, Cheng H et al (2014) Changes of cell immunity indexes in peripheral blood of Schizothorax prenanti injected with formalin-killed Aeromonas hydrophila. J Southwest Univ National (Nat Sci Ed) 36:28–35
Yuan D, Wang T, Zhou C, Lin F, Chen H, Wu H, Wei R, Xin Z, Li Z (2014a) Leptin and cholecystokinin in Schizothorax prenanti: molecular cloning, tissue expression, and mRNA expression responses to periprandial changes and fasting. Gen Comp Endocrinol 204:13–24
Yuan D, Zhou C, Wang T, Lin F, Chen H, Wu H, Wei R, Xin Z, Liu J, Gao Y, Chen D, Yang S, Wang Y, Pu Y, Li Z (2014b) Molecular characterization and tissue expression of peptide YY in Schizothorax prenanti: effects of periprandial changes and fasting on expression in the hypothalamus. Regul Pept 190–191:32–38
Zhang R, Zhang L, Ye X, Tian YY, Sun CF, Lu MX, Bai JJ (2013) Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae. Mol Biol Rep 40:5657–5668
Zhang X, Gao X, Wang J, Cao W (2015a) Extinction risk and conservation priority analyses for 64 endemic fishes in the upper Yangtze River, China. Environ Biol Fish 98:261–272
Zhang X, Wang S, Chen S, Chen Y, Liu Y, Shao C, Wang Q, Lu Y, Gong G, Ding S, Sha Z (2015b) Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection. Fish Shellfish Immunol 43:209–218
Zhou W, Zhang Y, Wen Y, Ji W, Zhou Y, Ji Y, Liu X, Wang W, Asim M, Liang X, Ai T, Lin L (2015) Analysis of the transcriptomic profilings of mandarin fish (Siniperca chuatsi) infected with Flavobacterium columnare with an emphasis on immune responses. Fish Shellfish Immunol 43:111–119
Zhu J, Li C, Ao Q, Tan Y, Luo Y, Guo Y, Lan G, Jiang H, Gan X (2015) Trancriptomic profiling revealed the signatures of acute immune response in tilapia (Oreochromis niloticus) following Streptococcus iniae challenge. Fish Shellfish Immunol 46:346–353
Zhu L, Nie L, Zhu G, Xiang LX, Shao JZ (2013) Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts. Dev Comp Immunol 39:39–62
Zhu Q, Zhang L, Li L, Que H, Zhang G (2016) Expression characterization of stress genes under high and low temperature stresses in the Pacific oyster, Crassostrea gigas. Mar Biotechnol 18:176–188
Zhuang M, Ai Z, Wu M (2007) Development of alpha-1-antitrypsin. J Microbiol 27:92–95
Acknowledgments
We thank Lingbing Zeng, in Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences, and Bin Chen, in College of Animal Science and Technology, Hunan Agricultural University, for providing constructive suggestions on the experiments. We also thank Genhua Yue and Baoqing Ye, Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 research link, National University of Singapore, for providing constructive suggestions on the manuscript.
Funding
This research was supported by the National Natural Science Foundation of China (31402302, 31602207), Fundamental Research Funds for the central Universities (XDJK2015C034, XDJK2017B008, XDJK2017C035), Scientific Research Initiation Project aided by a special fund, Southwest University Rongchang Campus (20700208), and the Youth Foundation of Southwest University Rongchang Campus (20700937, 20700938).
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Ye, H., Xiao, S., Wang, X. et al. Characterization of Spleen Transcriptome of Schizothorax prenanti during Aeromonas hydrophila Infection. Mar Biotechnol 20, 246–256 (2018). https://doi.org/10.1007/s10126-018-9801-0
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DOI: https://doi.org/10.1007/s10126-018-9801-0