Getting the most out of parasitic helminth transcriptomes using HelmDB: Implications for biology and biotechnology

Biotechnology Advances

Volumn 31, Issue 8, 2013, Pages 1109-1119

  Mangiola, Stefano ^a   Young, Neil D ^a   Korhonen, Pasi ^a   Mondal, Alinda ^a   Scheerlinck, Jean Pierre ^a   Sternberg, Paul W ^b   Cantacessi, Cinzia ^a   Hall, Ross S ^a   Jex, Aaron R ^a   Gasser, Robin B ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Annotation improvement; Bioinformatics; Genomics; Parasitic helminths (nematode and trematode); Systems biology; Transcriptomics

Indexed keywords

ANNOTATION-IMPROVEMENT; GENOMICS; PARASITIC HELMINTHS (NEMATODE AND TREMATODE); SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

ANIMALS; BIOINFORMATICS; BIOTECHNOLOGY; DATABASE SYSTEMS; DISEASE CONTROL; GENES;

DISEASES;

ANNELID; BIOINFORMATICS; BIOLOGY; BIOTECHNOLOGY; DATABASE; DISEASE; DRUG; GENOMICS; NEMATODE; PARASITISM; PATHOGENICITY; PRIORITIZATION; VACCINE;

ANIMALIA; NEMATODA; TREMATODA; VERMES;

HELMINTH PROTEIN; TRANSCRIPTOME;

ANIMAL; ANNOTATION-IMPROVEMENT; BIOINFORMATICS; BIOLOGY; BIOTECHNOLOGY; DATA BASE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENOMICS; HELMINTH; MOLECULAR GENETICS; PARASITIC HELMINTHS (NEMATODE AND TREMATODE); REVIEW; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

ANNOTATION-IMPROVEMENT; BIOINFORMATICS; GENOMICS; PARASITIC HELMINTHS (NEMATODE AND TREMATODE); SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

ANIMALS; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HELMINTH PROTEINS; HELMINTHS; MOLECULAR SEQUENCE ANNOTATION; TRANSCRIPTOME;

EID: 84887993159     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2012.12.004     Document Type: Review

References (85)

1. Abubucker S., Martin J., Taylor C.M., Mitreva M. HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PLoS One 2011, 6:e21832.
2. Albert R. Scale-free networks in cell biology. J Cell Sci 2005, 118:4947-4957.
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
4. Anderson R.C. Nematode Parasites of Vertebrates. Their development and transmission 2000, CABI Publishing, Wallingford, UK.
5. Aoki K., Ogata Y., Shibata D. Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 2007, 48:381-390.
6. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
7. Berriman M., Haas B.J., LoVerde P.T., Wilson R.A., Dillon G.P., Cerqueira G.C., et al. The genome of the blood fluke Schistosoma mansoni. Nature 2009, 460:352-358.
8. Bethony J., Brooker S., Albonico M., Geiger S.M., Loukas A., Diemert D., et al. Soil-transmitted helminth infections: ascariasis, trichuriasis, and hookworm. Lancet 2006, 367:1521-1532.
9. Brooker S., Clements A.C., Bundy D.A. Global epidemiology, ecology and control of soil-transmitted helminth infections. Adv Parasitol 2006, 62:221-261.
10. Butland G., Babu M., Diaz-Mejia J.J., Bohdana F., Phanse S., Gold B., et al. eSGA: E. coli synthetic genetic array analysis. Nat Methods 2008, 5:789-795.
11. Cantacessi C., Jex A.R., Hall R.S., Young N.D., Campbell B.E., Joachim A., et al. A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. Nucleic Acids Res 2010, 38:e171.
12. Cantacessi C., Mitreva M., Campbell B.E., Hall R.S., Young N.D., Jex A.R., et al. First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. Infect Genet Evol 2010, 10:1199-1207.
13. Cantacessi C., Mitreva M., Jex A.R., Young N.D., Campbell B.E., Hall R.S., et al. Massively parallel sequencing and analysis of the Necator americanus transcriptome. PLoS Negl Trop Dis 2010, 4:e684.
14. Cantacessi C., Gasser R.B., Strube C., Schnieder T., Jex A.R., Hall R.S., et al. Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention. Biotechnol Adv 2011, 29:261-271.
15. Cantacessi C., Young N.D., Nejsum P., Jex A.R., Campbell B.E., Hall R.S., et al. The transcriptome of Trichuris suis-first molecular insights into a parasite with curative properties for key immune diseases of humans. PLoS One 2011, 6:e23590.
16. Cantacessi C., Campbell B.E., Gasser R.B. Key strongylid nematodes of animals - impact of next-generation transcriptomics on systems biology and biotechnology. Biotechnol Adv 2012, 30:469-488.
17. Cantacessi C., Campbell B.E., Jex A.R., Young N.D., Hall R.S., Ranganathan S., et al. Bioinformatics meets parasitology. Parasite Immunol 2012, 34:265-275.
18. Cantacessi C., Campbell B.E., Jex A.R., Hall R.S., Young N.D., Nolan M.J., et al. Recent progress in transcriptomics of key gastrointestinal nematodes of animals - fundamental research toward new intervention strategies. Parasitic Helminths - Targets, Screens, Drugs and Vaccines; Drug discovery in infectious diseases (PM Selzer, series editor) 2012, 61-72. Wiley-VCH Verlag GmbH & Co. C.R. Caffrey (Ed.).
19. Coles G.C. The future of veterinary parasitology. Vet Parasitol 2001, 98:31-39.
20. Costanzo M., Baryshnikova A., Bellay J., Kim Y., Spear E.D., Sevier C.S., et al. The genetic landscape of a cell. Science 2010, 327:425-431.
21. Defoin-Platel M., Hassani-Pak K., Rawlings C. Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. Asp Appl Biol 2011, 107:79-87.
22. Dimmer E.C., Huntley R.P., Alam-Faruque Y., Sawford T., O'Donovan C., Martin M.J., et al. The UniProt-GO annotation database in 2011. Nucleic Acids Res 2012, 40:D565-D570.
23. Elsworth B., Wasmuth J., Blaxter M. NEMBASE4: the nematode transcriptome resource. Int J Parasitol 2011, 41:881-894.
24. Fairweather I. Reducing the future threat from (liver) fluke: realistic prospect or quixotic fantasy?. Vet Parasitol 2011, 180:133-143.
25. Finn R.D., Clements J., Eddy S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39:W29-W37.
26. Garber M., Grabherr M.G., Guttman M., Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011, 8:469-477.
27. Gasser R.B., Bott N.J., Chilton N.B., Hunt P., Beveridge I. Toward practical, DNA-based diagnostic methods for parasitic nematodes of livestock-bionomic and biotechnological implications. Biotechnol Adv 2008, 26:325-334.
28. Geldhof P., Visser A., Clark D., Saunders G., Britton C., Gilleard J., et al. RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects. Parasitology 2007, 134:609-619.
29. Gerstein M.B., Lu Z.J., Van Nostrand E.L., Cheng C., Arshinoff B.I., Liu T., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010, 330:1775-1787.
30. Gossett R.E., Frolov A.A., Roths J.B., Behnke W.D., Kier A.B., Schroeder F. Acyl-CoA binding proteins: multiplicity and function. Lipids 1996, 31:895-918.
31. Goud G.N., Zhan B., Ghosh K., Loukas A., Hawdon J., Dobardzic A., et al. Cloning, yeast expression, isolation, and vaccine testing of recombinant Ancylostoma-secreted protein (ASP)-1 and ASP-2 from Ancylostoma ceylanicum. J Infect Dis 2004, 189:919-929.
32. Hewitson J.P., Grainger J.R., Maizels R.M. Helminth immunoregulation: the role of parasite secreted proteins in modulating host immunity. Mol Biochem Parasitol 2009, 167:1-11.
33. Hotez P.J., Bundy D.A.P., Beegle K., Brooker S., Drake L., de Silva N., et al. Helminth infections: soil-transmitted helminth infections and schistosomiasis. Disease control priorities in developing countries 2006, World Bank, Washington, DC. 2nd ed. D.T. Jamison, J.G. Breman, A.R. Measham, G. Alleyne, M. Claeson, D.B. Evans (Eds.).
34. Hotez P.J., Fenwick A., Savioli L., Molyneux D.H. Rescuing the bottom billion through control of neglected tropical diseases. Lancet 2009, 373:1570-1575.
35. Huber W., Carey V.J., Long L., Falcon S., Gentleman R. Graphs in molecular biology. BMC Bioinformatics 2007, 8(Suppl. 6):S8.
36. Jex A.R., Lim Y.A., Bethony J.M., Hotez P.J., Young N.D., Gasser R.B. Soil-transmitted helminths of humans in Southeast Asia-towards integrated control. Adv Parasitol 2011, 74:231-265.
37. Jex A.R., Liu S., Li B., Young N.D., Hall R.S., Li Y., et al. Ascaris suum draft genome. Nature 2011, 479:529-533.
38. Kanehisa M., Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
39. Kaplan N., Vaaknin A., Linial M. PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res 2003, 31:5617-5626.
40. Kinch L.N., Grishin N.V. Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. Protein Sci 2006, 15:2669-2674.
41. Kuzniar A., van Ham R.C., Pongor S., Leunissen J.A. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 2008, 24:539-551.
42. Li W., Godzik A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
43. Lun Z.R., Gasser R.B., Lai D.H., Li A.X., Zhu X.Q., Yu X.B., et al. Clonorchiasis: a key foodborne zoonosis in China. Lancet Infect Dis 2005, 5:31-41.
44. Lustigman S., Geldhof P., Grant W.N., Osei-Atweneboana M.Y., Sripa B., Basanez M.G. A research agenda for helminth diseases of humans: basic research and enabling technologies to support control and elimination of helminthiases. PLoS Negl Trop Dis 2012, 6:e1445.
45. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
46. Martin J., Abubucker S., Heizer E., Taylor C.M., Mitreva M. Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. Nucleic Acids Res 2012, 40:D720-D728.
47. Mas-Coma S., Valero M.A., Bargues M.D. Chapter 2. Fasciola, lymnaeids and human fascioliasis, with a global overview on disease transmission, epidemiology, evolutionary genetics, molecular epidemiology and control. Adv Parasitol 2009, 69:41-146.
48. McKerrow J.H., Caffrey C., Kelly B., Loke P., Sajid M. Proteases in parasitic diseases. Annu Rev Pathol 2006, 1:497-536.
49. McQuilton P., St Pierre S.E., Thurmond J. FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Res 2012, 40:D706-D714.
50. Miller J.L., Harupa A., Kappe S.H., Mikolajczak S.A. Plasmodium yoelii macrophage migration inhibitory factor is necessary for efficient liver-stage development. Infect Immun 2012, 80:1399-1407.
51. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628.
52. Mummery-Widmer J.L., Yamazaki M., Stoeger T., Novatchkova M., Bhalerao S., Chen D., et al. Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Nature 2009, 458:987-992.
53. Olson S.A. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 2002, 3:87-91.
54. Palumbo E. Association between schistosomiasis and cancer: a review. Infect Dis Clin Pract 2007, 15:145-148.
55. Park J.K., Kim K.H., Kang S., Kim W., Eom K.S., Littlewood D.T. A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes). BMC Evol Biol 2007, 7:11.
56. Pruitt K.D., Tatusova T., Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-D65.
57. Pruitt K.D., Tatusova T., Brown G.R., Maglott D.R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 40:D130-D135.
58. Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., et al. The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-D301.
59. Roberts L.S., Janovy J.J. Foundations of parasitology 2000, W.C.B Company, U.K. 5th ed.
60. Robin X., Turck N., Hainard A., Tiberti N., Lisacek F., Sanchez J.C., et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011, 12:77.
61. Rollinson D. A wake up call for urinary schistosomiasis: reconciling research effort with public health importance. Parasitology 2009, 136:1593-1610.
62. Rollinson D., Knopp S., Levitz S., Stothard J.R., Tchuente L.A., Garba A., et al. Time to set the agenda for schistosomiasis elimination. Acta Trop 2012, [Epub ahead of print].
63. Roy S., Ernst J., Kharchenko P.V., Kheradpour P., Negre N., Eaton M.L., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797.
64. Sackett D., Holmes P. Assessing the economic cost of endemic disease on the profitability of Australian beef cattle and sheep producers 2006, 119. Meat and Livestock Australia Limited, [ISBN 1741910021].
65. Salavati R., Najafabadi H.S. Sequence-based functional annotation: what if most of the genes are unique to a genome?. Trends Parasitol 2010, 26:225-229.
66. Sayers E.W., Barrett T., Benson D.A., Bolton E., Bryant S.H., Canese K., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2012, 40:D13-D25.
67. Shoemaker B.A., Panchenko A.R. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 2007, 3:e43.
68. Sripa B., Kaewkes S., Sithithaworn P., Mairiang E., Laha T., Smout M., et al. Liver fluke induces cholangiocarcinoma. PLoS Med 2007, 4:e201.
69. Swets J.A. Measuring the accuracy of diagnostic systems. Science 1988, 240:1285-1293.
70. The Gene Ontology Consortium Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29.
71. The Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature 2009, 460:345-351.
72. Tong A.H., Lesage G., Bader G.D., Ding H., Xu H., Xin X., et al. Global mapping of the yeast genetic interaction network. Science 2004, 303:808-813.
73. Wang Z., Zhang X.C., Le M.H., Xu D., Stacey G., Cheng J. A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One 2011, 6:e17906.
74. Wolstenholme A.J., Fairweather I., Prichard R., von Samson-Himmelstjerna G., Sangster N.C. Drug resistance in veterinary helminths. Trends Parasitol 2004, 20:469-476.
75. Xie C., Mao X., Huang J., Ding Y., Wu J., Dong S., et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 2011, 39:W316-W322.
76. Yook K., Harris T.W., Bieri T., Cabunoc A., Chan J., Chen W.J., et al. WormBase 2012: more genomes, more data, new website. Nucleic Acids Res 2012, 40:D735-D741.
77. Young N.D., Campbell B.E., Hall R.S., Jex A.R., Cantacessi C., Laha T., et al. Unlocking the transcriptomes of two carcinogenic parasites. Clonorchis sinensis and Opisthorchis viverrini. PLoS Negl Trop Dis 2010, 4:e719.
78. Young N.D., Hall R.S., Jex A.R., Cantacessi C., Gasser R.B. Elucidating the transcriptome of Fasciola hepatica - a key to fundamental and biotechnological discoveries for a neglected parasite. Biotechnol Adv 2010, 28:222-231.
79. Young N.D., Jex A.R., Cantacessi C., Hall R.S., Campbell B.E., Spithill T.W., et al. A portrait of the transcriptome of the neglected trematode, Fasciola gigantica-biological and biotechnological implications. PLoS Negl Trop Dis 2011, 5:e1004.
80. Young ND, Jex AR, Cantacessi C, Campbell BE, Gasser RB. Harnessing genomic technologies to explore the molecular biology of liver flukes-major implications for fundamental and applied research. In: Caffrey CR, editor. Parasitic helminths - targets, screens, drugs and vaccines; Drug discovery in infectious diseases (PM Selzer, series editor): Wiley-VCH Verlag GmbH & Co.; 2012. pp. 73-87.
81. Young N.D., Jex A.R., Li B., Liu S., Yang L., Xiong Z., et al. Whole-genome sequence of Schistosoma haematobium. Nat Genet 2012, 44:221-225.
82. Zdobnov E.M., Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.
83. Zerlotini A., Heiges M., Wang H., Moraes R.L., Dominitini A.J., Ruiz J.C., et al. SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res 2009, 37:D579-D582.
84. Zheng Q., Wang X.J. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 2008, 36:W358-W363.
85. Zhong W., Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 2006, 311:1481-1484.