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Transcriptomic Analysis of Compromise Between Air-Breathing and Nutrient Uptake of Posterior Intestine in Loach (Misgurnus anguillicaudatus), an Air-Breathing Fish

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Abstract

Dojo loach (Misgurnus anguillicaudatus) is an air-breathing fish species by using its posterior intestine to breathe on water surface. So far, the molecular mechanism about accessory air-breathing in fish is seldom addressed. Five cDNA libraries were constructed here for loach posterior intestines form T01 (the initial stage group), T02 (mid-stage of normal group), T03 (end stage of normal group), T04 (mid-stage of air-breathing inhibited group), and T05 (the end stage of air-breathing inhibited group) and subjected to perform RNA-seq to compare their transcriptomic profilings. A total of 92,962 unigenes were assembled, while 37,905 (40.77 %) unigenes were successfully annotated. 2298, 1091, and 3275 differentially expressed genes (fn1, ACE, EGFR, Pxdn, SDF, HIF, VEGF, SLC2A1, SLC5A8 etc.) were observed in T04/T02, T05/T03, and T05/T04, respectively. Expression levels of many genes associated with air-breathing and nutrient uptake varied significantly between normal and intestinal air-breathing inhibited group. Intraepithelial capillaries in posterior intestines of loaches from T05 were broken, while red blood cells were enriched at the surface of intestinal epithelial lining with 241 ± 39 cells per millimeter. There were periodic acid-schiff (PAS)-positive epithelial mucous cells in posterior intestines from both normal and air-breathing inhibited groups. Results obtained here suggested an overlap of air-breathing and nutrient uptake function of posterior intestine in loach. Intestinal air-breathing inhibition in loach would influence the posterior intestine’s nutrient uptake ability and endothelial capillary structure stability. This study will contribute to our understanding on the molecular regulatory mechanisms of intestinal air-breathing in loach.

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References

  • Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang HZ, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LL (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32:D115–D119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arai K, Fujimoto T (2013) Genomic constitution and atypical reproduction in polyploid and unisexual lineages of the Misgurnus Loach, a Teleost Fish. Cytogenet Genome Res 140:226–240

    Article  CAS  PubMed  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Astrof S, Hynes RO (2009) Fibronectins in vascular morphogenesis. Angiogenesis 12(2):165–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bautch VL (2012) VEGF-directed blood vessel patterning: from cells to organism. Cold Spring Harb Perspect Med 2:2196–2207

    Article  Google Scholar 

  • Cao XJ, Wang WM (2009) Histology and mucin histochemistry of the digestive tract of yellow catfish, Pelteobagrus fulvidraco. Anat Histol Embryol 38:254–261

    Article  CAS  PubMed  Google Scholar 

  • Chávez-Mardones J, Gallardo-Escárate C (2015) Next-generation transcriptome profiling of the salmon louse Caligus rogercresseyi exposed to deltamethrin (Alpha Max™): discovery of relevant genes and sex-related differences. Mar Biotechnol 17:793–810

    Article  PubMed  Google Scholar 

  • Chen X, Mei J, Wu JJ, Jing J, Ma WG, Zhang J, Dan C, Wang WM, Gui JF (2015) A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish. Mar Biotechnol 17:190–198

    Article  CAS  PubMed  Google Scholar 

  • Deng YY, Li JQ, Wu SF, Zhu YP, Chen YW, He FC (2006) Integrated nr database in protein annotation system and its localization. Comput Eng 32:71–74

    Google Scholar 

  • Ema M, Taya S, Yokotani N, Sogawa K, Matsuda Y, Fujii-Kuriyama Y (1997) A novel bHLH-PAS factor with close sequence similarity to hypoxia-inducible factor 1 regulates VEGF expression and is potentially involved in lung and vascular development. Proc Natl Acad Sci U S A 94:4273–4278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fatigati V, Murphy RA (1984) Actin and tropomyosin variants in smooth muscles. Dependence on tissue type. J Biol Chem 259:14383–14388

    CAS  PubMed  Google Scholar 

  • Flatt JF, Hélène G, Burton NM, Borgese F, Tomlinson RJ, Forsyth RJ, Baldwin SA, Levinson BE, Quittet P, Aguilar-Martinez P, Delaunay J, Stewart GW, Bruce LJ (2011) Stomatin-deficient cryohydrocytosis results from mutations in SLC2A1: a novel form of GLUT1 deficiency syndrome. Blood 118:5267–5277

    Article  CAS  PubMed  Google Scholar 

  • Fraser J, de Mello LV, Ward D, Rees HH, Williams DR, Fang Y, Brass A, Gracey AY, Cossins AR (2006) Hypoxia-inducible myoglobin expression in nonmuscle tissues. Proc Natl Acad Sci U S A 103(8):2977–2981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goncalves AF, Castro LF, Pereira-Wilson C, Coimbra J, Wilson JM (2007) Is there a compromise between nutrient uptake and gas exchange in the gut of Misgurnus anguillicaudatus, an intestinal air-breathing fish? Comp Biochem Physiol Part D Genomics Proteomics 2:345–355

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Groot JA, Albus H, Bakker R, Heukelom JSV, Zuidema T (1983) Electrical phenomena in fish intestine. In: Gilles-Baillien M, Gilles R (eds) Intestinal transport. Springer Berlin, Heidelberg, pp 321–340

    Chapter  Google Scholar 

  • Guo DC, Pannu H, Tran-Fadulu V, Papke CL, Yu RK, Avidan N, Bourgeois S, Estrera AL, Safi HJ, Sparks E, Amor D, Ades L, McConnell V, Willoughby CE, Abuelo D, Willing M, Lewis RA, Kim DH, Scherer S, Tung PP, Ahn C, Buja LM, Raman CS, Shete SS, Milewicz DM (2007) Mutations in smooth muscle alpha-actin (ACTA2) lead to thoracic aortic aneurysms and dissections. Nat Genet 39:1488–1493

    Article  CAS  PubMed  Google Scholar 

  • Hattori K, Dias S, Heissig B, Hackett NR, Lyden D, Tateno M, Hicklin DJ, Zhu ZP, Witte L, Crystal RG, Moore MAS, Rafii S (2001) Vascular endothelial growth factor and angiopoietin-1 stimulate postnatal hematopoiesis by recruitment of vasculogenic and hematopoietic stem cells. J Exp Med 193:1005–1014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Helbo S, Weber RE, Fago A (2013) Expression patterns and adaptive function diversity of vertebrate myoglobins. Biochim Biophys Acta 1834:1832–1839

    Article  CAS  PubMed  Google Scholar 

  • Jeuken M (1957) A study of the respiration of Misgurnus fossilus (L.), the pond loach. Thesis, University of Leiden, p 144

  • Jian W, Fu L, Koganti PP, Wang L, Hand JM, Ma H, Yao J (2016) Identification and functional prediction of large intergenic noncoding RNAs (lincRNAs) in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol 18:271–282

    Article  Google Scholar 

  • Johansen K (1970) Air-breathing in fish. Fish Physiol 4:361–411

    Article  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Yasushi O, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:277–280

    Article  Google Scholar 

  • Kikuchi G, Yoshida T, Noguchi M (2005) Heme oxygenase and heme degradation. Biochem Biophys Res Commun 338:558–567

    Article  CAS  PubMed  Google Scholar 

  • Koller G, Zill P, Fehr C, Pogarell O, Bondy B, Soyka M, Preuss UW (2009) No association of alcohol dependence with SLC6A5 and SLC6A9 glycine transporter polymorphisms. Addict Biol 14:506–508

    Article  CAS  PubMed  Google Scholar 

  • Lahlou B, Avella M (1993) Electrolyte transport mechanisms in fish intestine. In: Clauss W (ed) Ion transport in vertebrate colon, vol 16. Springer Berlin, Heidelberg, pp 1–25

    Chapter  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • McMahon BR, Burggren WW (1987) Respiratory physiology of intestinal air breathing in the teleost fish Misgurnus anguillicaudatus. J Exp Biol 133:371–393

    Google Scholar 

  • Munshi JS (1976) Gross and fine structure of the respiratory organs of air-breathing fish. In: Hughes GM (ed) Respiration of amphibious vertebrates. Academic, London, pp 73–104

    Google Scholar 

  • Nelson JS (2006) Fishes of the world, 4th edn. John Wiley & Sons, Hoboken

    Google Scholar 

  • Otrock ZK, Mahfouz RA, Makarem JA, Shamseddine AI (2007) Understanding the biology of angiogenesis: review of the most important molecular mechanisms. Blood Cell Mol Dis 39:212–220

    Article  CAS  Google Scholar 

  • Park JY, Kim IS, Kim SY (2003) Structure and mucous histochemistry of the intestinal respiratory tract of the mud loach, Misgurnus anguillicaudatus (Cantor). J Appl Ichthyol 19:2015–2219

    Article  Google Scholar 

  • Rawlings ND, Barrett AJ (1994) Families of serine peptidases. Methods Enzymol 244:19–61

    Article  CAS  PubMed  Google Scholar 

  • Roy S, Patel D, Khanna S, Gordillo GM, Biswas S, Friedman A, Sen CK (2007) Transcriptome-wide analysis of blood vessels laser captured from human skin and chronic wound-edge tissue. Proc Natl Acad Sci U S A 104:14472–14477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ryter SW, Alam J, Choi AM (2006) Heme oxygenase-1/carbon monoxide: from basic science to therapeutic applications. Physiol Rev 86:583–650

    Article  CAS  PubMed  Google Scholar 

  • Sarropoulou E, Galindo-Villegas J, García-Alcázar A, Kasapidis P, Mulero V (2012) Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. Mar Biotechnol 14:634–642

    Article  CAS  PubMed  Google Scholar 

  • Semenza GL (2001) Hypoxia-inducible factor 1: oxygen homeostasis and disease pathophysiology. Trends Mol Med 7:345–350

    Article  CAS  PubMed  Google Scholar 

  • Soonhag K (2002) Initial gene expression profile of rainbow trout (Oncorhynchus mykiss) intestine. Korean J Biol Sci 6:323–326

    Article  Google Scholar 

  • Suls A, Dedeken P, Goffin K, Van Esch H, Dupont P, Cassiman D, Kempfle J, Wuttke TV, Weber Y, Lerche H, Afawi Z, Vandenberghe W, Korczyn AD, Berkovic SF, Ekstein D, Kivity S, Ryvlin P, Claes LR, Deprez L, Maljevic S, Vargas A, Van Dyck T, Goossens D, Del-Favero J, Van Laere K, De Jonghe P, Van Paesschen W (2008) Paroxysmal exercise-induced dyskinesia and epilepsy is due to mutations in SLC2A1, encoding the glucose transporter GLUT1. Brain J Neurol 131:1831–1844

    Article  Google Scholar 

  • Takebe K, Nio J, Morimatsu M, Karaki S, Kuwahara A, Kato I, Iwanaga T (2005) Histochemical demonstration of a Na+-coupled transporter for short-chain fatty acids (Slc5a8) in the intestine and kidney of the mouse. Biomed Res 26:213–221

    Article  CAS  PubMed  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA (2000) The COG database: a tool for genome scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ulloa PE, Rincón G, Islas-Trejo A, Araneda C, Iturra P, Neira R, Medrano JF (2015) RNA sequencing to study gene expression and SNP variations associated with growth in zebrafish fed a plant protein-based diet. Mar Biotechnol 17:353–363

    Article  CAS  PubMed  Google Scholar 

  • Villars F, Bordenave L, Bareille R, Amedee J (2000) Effect of human endothelial cells on human bone marrow stromal cell phenotype: role of VEGF? J Cell Biochem 79:672–685

    Article  CAS  PubMed  Google Scholar 

  • Wynne JW, O’Sullivan MG, Cook MT, Stone G, Nowak BF, Lovell DR, Elliott NG (2008) Transcriptome analyses of amoebic gill disease-affected atlantic salmon (Salmo salar) tissues reveal localized host gene suppression. Mar Biotechnol 10:388–403

    Article  CAS  PubMed  Google Scholar 

  • Yi M, Ruoslahti E (2001) A fibronectin fragment inhibits tumor growth, angiogenesis, and metastasis. Proc Natl Acad Sci U S A 98:620–624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang JY, Yang RB, Yang XF, Fan QX, Wei KJ, Wang WM (2016) Ontogeny of the digestive tract in mud loach Misgurnus anguillicaudatus larvae. Aquac Res 47(4):1180–1190

Download references

Acknowledgments

This study was financially supported by National Natural Science Foundation of China (Project Number: 31201719) and the Fundamental Research Funds for the Central Universities of China (Project Number: 2662015PY033). We specially thank Dr. Mona Nasr Abd-elnaeim Hussein for revising our English writing.

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  1. College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 437000, Hubei, People’s Republic of China

    Songqian Huang, Xiaojuan Cao & Xianchang Tian

  2. Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Hubei, People’s Republic of China

    Xiaojuan Cao

  3. Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People’s Republic of China

    Xiaojuan Cao

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  1. Songqian Huang
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Correspondence to Xiaojuan Cao.

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Huang, S., Cao, X. & Tian, X. 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 (2016). https://doi.org/10.1007/s10126-016-9713-9

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  • DOI: https://doi.org/10.1007/s10126-016-9713-9

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