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Marine Biotechnology

, Volume 11, Issue 3, pp 317–326 | Cite as

Functional Annotation and Analysis of Expressed Sequence Tags from the Hepatopancreas of Mitten Crab (Eriocheir sinensis)

  • Hui Jiang
  • Yi-Mei Cai
  • Li-Qiao Chen
  • Xiao-Wei Zhang
  • Song-Nian Hu
  • Qun WangEmail author
Original Article

Abstract

Due to its popularity as a traditional food, intensive harvesting of the mitten crab (Eriocheir sinensis) is common and has lead to an increase in disease incidence, resulting in catastrophic losses to crab aquaculture. The hepatopancreas of E. sinensis is not only an important digestive organ but also an indispensable immune organ. We constructed a nonnormalized cDNA library from the hepatopancreas of E. sinensis and acquired 3,297 high-quality expressed sequence tags representing 1,178 unigenes. More than half of these unigenes were novel genes for this species; the remaining had homologs in public databases, which is of great importance for future functional research. We also investigated the association of these genes with immune processes for insight into one of the main functions of the hepatopancreas besides metabolism. Despite the relatively low sampling scalar of our cDNA library, we were able to demonstrate several important properties of the hepatopancreatic transcriptome and identified numerous genes that were closely associated with immune responses. These results might serve as the basis for an in-depth genomics study of E. sinensis, including transcriptome analysis, physical mapping, and whole genome sequencing.

Keywords

Eriocheir sinensis Hepatopancreas Expressed sequence tag Invertebrates Innate immunity 

Notes

Acknowledgements

This research was supported by grants from the National Nature Science Foundation of China (no. 30671607), the Key Basic Research Project (06DJ14003) from the Science and Technology Commission of the Shanghai Municipal Government, Zhejiang Key Science and Technology Program (2005C12006-1), and the Specialized Project for the Key Technology Research of Agricultural Restructuring from the Ministry of Agriculture.

Supplementary material

10126_2008_9146_Fig1_ESM.gif (57 kb)
Supplementary file 1

ESTs assigned in contigs; 45% of the contigs yielded by Phrap were formed by two EST sequences and nearly 16% of the contigs were constructed by more than ten ESTs (GIF 57.0 kb)

10126_2008_9146_Fig1_ESM.tif (275 kb)
High resolution image file (TIFF 275 KB)
10126_2008_9146_MOESM3_ESM.doc (54 kb)
Supplementary file 2 The total list of unigenes involved in GO mapping at the second level based on the categories of cellular component, molecular function, and biological process (DOC 53.5 KB)
10126_2008_9146_MOESM4_ESM.doc (76 kb)
Supplementary file 3 Genes expressed at a high level in the library (DOC 76.0 KB)
10126_2008_9146_MOESM5_ESM.doc (132 kb)
Supplementary file 4 The total list of unigenes involved in GO mapping at the third level based on the categories of cellular component, molecular function, and biological process (DOC 132 KB)
10126_2008_9146_MOESM6_ESM.doc (101 kb)
Supplementary file 5 Genes potentially included in stress defense and immune response mechanisms (DOC 101 KB)

References

  1. Abernathy JW, Xu P, Li P, Xu DH, Kucuktas H, Klesius P, Arias C, Liu Z (2007) Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis. BMC Genomics 8:176PubMedCrossRefGoogle Scholar
  2. Argraves WS, Greene LM, Cooley MA, Gallagher WM (2003) Fibulins: physiological and disease perspectives. EMBO Rep 4:1127–1131PubMedCrossRefGoogle Scholar
  3. 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. The Gene Ontology Consortium. Nat Genet 25:25–29PubMedCrossRefGoogle Scholar
  4. Borkovic SS, Pavlovic SZ, Kovacevic TB, Stajn AS, Petrovic VM, Saicic ZS (2008) Antioxidant defence enzyme activities in hepatopancreas, gills and muscle of spiny cheek crayfish (Orconectes limosus) from the River Danube. Comp Biochem Physiol C Toxicol Pharmacol 147:122–128PubMedCrossRefGoogle Scholar
  5. Brouwer M, Hoexum-Brouwer T, Cashon RE (1993) A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies. Biochem J 294(Pt 1):219–225PubMedGoogle Scholar
  6. Chen Dw, Zhang M, Shrestha S (2007) Compositional characteristics and nutritional quality of Chinese mitten crab (Eriocheir sinensis). Food Chem 103:1343–1349CrossRefGoogle Scholar
  7. Clavero-Salas A, Sotelo-Mundo RR, Gollas-Galvan T, Hernandez-Lopez J, Peregrino-Uriarte AB, Muhlia-Almazan A, Yepiz-Plascencia G (2007) Transcriptome analysis of gills from the white shrimp Litopenaeus vannamei infected with white spot syndrome virus. Fish Shellfish Immunol 23:459–472PubMedCrossRefGoogle Scholar
  8. De La Vega E, O’leary NA, Shockey JE, Robalino J, Payne C, Browdy CL, Warr GW, Gross PS (2008) Anti-lipopolysaccharide factor in Litopenaeus vannamei (LvALF): a broad spectrum antimicrobial peptide essential for shrimp immunity against bacterial and fungal infection. Mol Immunol 45:1916–1925CrossRefGoogle Scholar
  9. Dong B, Xiang JH (2007) Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation. Aquaculture 272:208–215CrossRefGoogle Scholar
  10. Douglas SE, Knickle LC, Kimball J, Reith ME (2007) Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species. BMC Genomics 8:144PubMedCrossRefGoogle Scholar
  11. English TE, Storey KB (2003) Freezing and anoxia stresses induce expression of metallothionein in the foot muscle and hepatopancreas of the marine gastropod Littorina littorea. J Exp Biol 206:2517–2524PubMedCrossRefGoogle Scholar
  12. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194PubMedGoogle Scholar
  13. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  14. Fujiwara S, Hirokawa Y, Takatsuka Y, Suda K, Asamizu E, Takayanagi T, Shibata D, Tabata S, Tsuzuki M (2007) Gene expression profiling of coccolith-bearing cells and naked cells in haptophyte Pleurochrysis haptonemofera with a cDNA macroarray system. Mar Biotechnol (NY) 9:550–560CrossRefGoogle Scholar
  15. Gai Y, Zhao J, Song L, Li C, Zheng P, Qiu L, Ni D (2008) A prophenoloxidase from the Chinese mitten crab Eriocheir sinensis: gene cloning, expression and activity analysis. Fish Shellfish Immunol 24:156–167PubMedCrossRefGoogle Scholar
  16. Gueguen Y, Cadoret JP, Flament D, Barreau-Roumiguiere C, Girardot AL, Garnier J, Hoareau A, Bachere E, Escoubas JM (2003) Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas. Gene 303:139–145PubMedCrossRefGoogle Scholar
  17. Hagner-Holler S, Kusche K, Hembach A, Burmester T (2005) Biochemical and molecular characterisation of hemocyanin from the amphipod Gammarus roeseli: complex pattern of hemocyanin subunit evolution in Crustacea. J Comp Physiol B 175:445–452PubMedCrossRefGoogle Scholar
  18. Haidle L, Janssen JE, Gharbi K, Moghadam HK, Ferguson MM, Danzmann RG (2008) Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol (NY) 10:579–592CrossRefGoogle Scholar
  19. Hoffmann JA, Kafatos FC, Janeway CA, Ezekowitz RA (1999) Phylogenetic perspectives in innate immunity. Science 284:1313–1318PubMedCrossRefGoogle Scholar
  20. Imjongjirak C, Amparyup P, Tassanakajon A, Sittipraneed S (2007) Antilipopolysaccharide factor (ALF) of mud crab Scylla paramamosain: molecular cloning, genomic organization and the antimicrobial activity of its synthetic LPS binding domain. Mol Immunol 44:3195–3203PubMedCrossRefGoogle Scholar
  21. Jayaraj SS, Thiagarajan R, Arumugam M, Mulainadhan P (2007) Isolation, purification and characterization of β 1, 3-glucan binding protein from the plasma of marine mussel Perna viridis. Fish Shellfish Immunol 24:715–725PubMedCrossRefGoogle Scholar
  22. Kam CM, Gotz MG, Koot G, Mcguire M, Thiele D, Hudig D, Powers JC (2004) Design and evaluation of inhibitors for dipeptidyl peptidase I (cathepsin C). Arch Biochem Biophys 427:123–134PubMedCrossRefGoogle Scholar
  23. Kim SK, Park PJ, Kim JB, Shahidi F (2002) Purification and characterization of a collagenolytic protease from the filefish, Novoden modestrus. J Biochem Mol Biol 35:165–171PubMedGoogle Scholar
  24. Kocabas AM, Li P, Cao D, Karsi A, He C, Patterson A, Ju Z, Dunham RA, Liu Z (2002) Expression profile of the channel catfish spleen: analysis of genes involved in immune functions. Mar Biotechnol (NY) 4:526–536CrossRefGoogle Scholar
  25. La Claire JW 2nd (2006) Analysis of expressed sequence tags from the harmful alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta). Mar Biotechnol (NY) 8:534–546CrossRefGoogle Scholar
  26. Larade K, Storey KB (2004) Accumulation and translation of ferritin heavy chain transcripts following anoxia exposure in a marine invertebrate. J Exp Biol 207:1353–1360PubMedCrossRefGoogle Scholar
  27. Lee SY, Lee BL, Soderhall K (2004) Processing of crayfish hemocyanin subunits into phenoloxidase. Biochem Biophys Res Commun 322:490–496PubMedCrossRefGoogle Scholar
  28. Li C, Zhao J, Song L, Mu C, Zhang H, Gai Y, Qiu L, Yu Y, Ni D, Xing K (2008a) Molecular cloning, genomic organization and functional analysis of an anti-lipopolysaccharide factor from Chinese mitten crab Eriocheir sinensis. Dev Comp Immunol 32:784–794PubMedGoogle Scholar
  29. Li E, Chen L, Zeng C, Yu N, Xiong Z, Chen X, Qin JG (2008b) Comparison of digestive and antioxidant enzymes activities, haemolymph oxyhemocyanin contents and hepatopancreas histology of white shrimp, Litopenaeus vannamei, at various salinities. Aquaculture 274:80–86CrossRefGoogle Scholar
  30. Lofgren SE, Miletti LC, Steindel M, Bachere E, Barracco MA (2008) Trypanocidal and leishmanicidal activities of different antimicrobial peptides (AMPs) isolated from aquatic animals. Exp Parasitol 118:197–202PubMedCrossRefGoogle Scholar
  31. Luo T, Zhang X, Shao Z, Xu X (2003) PmAV, a novel gene involved in virus resistance of shrimp Penaeus monodon. FEBS Lett 551:53–57PubMedCrossRefGoogle Scholar
  32. Luo T, Li F, Lei K, Xu X (2007) Genomic organization, promoter characterization and expression profiles of an antiviral gene PmAV from the shrimp Penaeus monodon. Mol Immunol 44:1516–1523PubMedCrossRefGoogle Scholar
  33. Missirlis F, Kosmidis S, Brody T, Mavrakis M, Holmberg S, Odenwald WF, Skoulakis EM, Rouault TA (2007) Homeostatic mechanisms for iron storage revealed by genetic manipulations and live imaging of Drosophila ferritin. Genetics 177:89–100PubMedCrossRefGoogle Scholar
  34. Muhlia-Almazan A, Sanchez-Paz A, Garcia-Carreno FL (2008) Invertebrate trypsins: a review. J Comp Physiol B 178:655–672PubMedCrossRefGoogle Scholar
  35. Multhoff G (2007) Heat shock protein 70 (Hsp70): membrane location, export and immunological relevance. Methods 43:229–237PubMedCrossRefGoogle Scholar
  36. Nagoshi H, Inagawa H, Morii K, Harada H, Kohchi C, Nishizawa T, Taniguchi Y, Uenobe M, Honda T, Kondoh M, Takahashi Y, Soma G (2006) Cloning and characterization of a LPS-regulatory gene having an LPS binding domain in kuruma prawn Marsupenaeus japonicus. Mol Immunol 43:2061–2069PubMedCrossRefGoogle Scholar
  37. Padhi A, Verghese B (2008) Detecting molecular adaptation at individual codons in the pattern recognition protein, lipopolysaccharide- and beta-1,3-glucan-binding protein of decapods. Fish Shellfish Immunol 24:638–648PubMedCrossRefGoogle Scholar
  38. Paraoan L, Grierson I, Maden BE (2000) Analysis of expressed sequence tags of retinal pigment epithelium: cystatin C is an abundant transcript. Int J Biochem Cell Biol 32:417–426PubMedCrossRefGoogle Scholar
  39. Pinho GL, Da Rosa CM, Maciel FE, Bianchini A, Yunes JS, Proenca LA, Monserrat JM (2005) Antioxidant responses and oxidative stress after microcystin exposure in the hepatopancreas of an estuarine crab species. Ecotoxicol Environ Saf 61:353–360PubMedCrossRefGoogle Scholar
  40. Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X, Liu Z (2007) Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics 8:157PubMedCrossRefGoogle Scholar
  41. Reusch TB, Veron AS, Preuss C, Weiner J, Wissler L, Beck A, Klages S, Kube M, Reinhardt R, Bornberg-Bauer E (2008) Comparative analysis of expressed sequence tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress. Mar Biotechnol (NY) 10:297–309CrossRefGoogle Scholar
  42. Ried C, Wahl C, Miethke T, Wellnhofer G, Landgraf C, Schneider-Mergener J, Hoess A (1996) High affinity endotoxin-binding and neutralizing peptides based on the crystal structure of recombinant Limulus anti-lipopolysaccharide factor. J Biol Chem 271:28120–28127PubMedCrossRefGoogle Scholar
  43. Roux MM, Pain A, Klimpel KR, Dhar AK (2002) The lipopolysaccharide and beta-1,3-glucan binding protein gene is upregulated in white spot virus-infected shrimp (Penaeus stylirostris). J Virol 76:7140–7149PubMedCrossRefGoogle Scholar
  44. Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G (2008) Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol (NY) 10:227–233CrossRefGoogle Scholar
  45. Sekine H, Kenjo A, Azumi K, Ohi G, Takahashi M, Kasukawa R, Ichikawa N, Nakata M, Mizuochi T, Matsushita M, Endo Y, Fujita T (2001) An ancient lectin-dependent complement system in an ascidian: novel lectin isolated from the plasma of the solitary ascidian, Halocynthia roretzi. J Immunol 167:4504–4510PubMedGoogle Scholar
  46. Staszczak M (2008) The role of the ubiquitin-proteasome system in the response of the ligninolytic fungus Trametes versicolor to nitrogen deprivation. Fungal Genet Biol 45:328–337PubMedCrossRefGoogle Scholar
  47. Sun YD, Fu LD, Jia YP, Du XJ, Wang Q, Wang YH, Zhao XF, Yu XQ, Wang JX (2008) A hepatopancreas-specific C-type lectin from the Chinese shrimp Fenneropenaeus chinensis exhibits antimicrobial activity. Mol Immunol 45:348–361PubMedCrossRefGoogle Scholar
  48. Tharntada S, Somboonwiwat K, Rimphanitchayakit V, Tassanakajon A (2008) Anti-lipopolysaccharide factors from the black tiger shrimp, Penaeus monodon, are encoded by two genomic loci. Fish Shellfish Immunol 24:46–54PubMedCrossRefGoogle Scholar
  49. Turk D, Janjic V, Stern I, Podobnik M, Lamba D, Dahl SW, Lauritzen C, Pedersen J, Turk V, Turk B (2001) Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases. EMBO J 20:6570–6582PubMedCrossRefGoogle Scholar
  50. Vasta GR, Quesenberry M, Ahmed H, O’leary N (1999) C-type lectins and galectins mediate innate and adaptive immune functions: their roles in the complement activation pathway. Dev Comp Immunol 23:401–420PubMedCrossRefGoogle Scholar
  51. Verri T, Mandal A, Zilli L, Bossa D, Mandal PK, Ingrosso L, Zonno V, Vilella S, Ahearn GA, Storelli C (2001) D-glucose transport in decapod crustacean hepatopancreas. Comp Biochem Physiol A Mol Integr Physiol 130:585–606PubMedCrossRefGoogle Scholar
  52. Vizcaino JA, Gonzalez FJ, Suarez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutierrez S, Monte E, Llobell A, Rey M (2006) Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics 7:193PubMedCrossRefGoogle Scholar
  53. Von Schalburg KR, Leong J, Cooper GA, Robb A, Beetz-Sargent MR, Lieph R, Holt RA, Moore R, Ewart KV, Driedzic WR, Ten Hallers BF, Zhu B, De Jong PJ, Davidson WS, Koop BF (2008) Rainbow smelt (Osmerus mordax) genomic library and EST resources. Mar Biotechnol (NY) 10:487–491CrossRefGoogle Scholar
  54. Wang Y, Guo X (2007) Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica. Mar Biotechnol (NY) 9:500–511CrossRefGoogle Scholar
  55. Wisen S, Gestwicki JE (2008) Identification of small molecules that modify the protein folding activity of heat shock protein 70. Anal Biochem 374:371–377PubMedCrossRefGoogle Scholar
  56. 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 (NY) 10:388–403CrossRefGoogle Scholar
  57. Yeh HY, Klesius PH (2008) Channel catfish, Ictalurus punctatus, cyclophilin A and B cDNA characterization and expression analysis. Vet Immunol Immunopathol 121:370–377PubMedCrossRefGoogle Scholar
  58. Zhang L, Bao Z, Cheng J, Li H, Huang X, Wang S, Zhang C, Hu J (2007) Fosmid library construction and initial analysis of end sequences in Zhikong scallop (Chlamys farreri). Mar Biotechnol (NY) 9:606–612CrossRefGoogle Scholar
  59. Zheng K, Board PG, Fei X, Sun Y, Lv S, Yan G, Liu J, Shen J, Luo G (2008) A novel selenium-containing glutathione transferase zeta1-1, the activity of which surpasses the level of some native glutathione peroxidases. Int J Biochem Cell Biol 40:2090–2097PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Hui Jiang
    • 1
  • Yi-Mei Cai
    • 2
  • Li-Qiao Chen
    • 1
  • Xiao-Wei Zhang
    • 2
  • Song-Nian Hu
    • 2
  • Qun Wang
    • 1
    Email author
  1. 1.School of Life ScienceEast China Normal UniversityShanghaiChina
  2. 2.Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina

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