Hostname: page-component-586b7cd67f-2brh9 Total loading time: 0 Render date: 2024-11-24T07:21:08.577Z Has data issue: false hasContentIssue false
  • English
  • Français

Limitations of the Echinococcus granulosus genome sequence assemblies for analysis of the gene family encoding the EG95 vaccine antigen

Published online by Cambridge University Press:  27 November 2017

Charles G. Gauci ,
Cristian A. Alvarez Rojas ,
Conan Chow  and
Marshall W. Lightowlers
Charles G. Gauci*
Affiliation:
Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
Cristian A. Alvarez Rojas
Affiliation:
Faculty of Veterinary Science, Centre for Animal Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
Conan Chow
Affiliation:
Genera Biosystems, 1 Dalmore Drive, Scoresby, Victoria 3179, Australia
Marshall W. Lightowlers
Affiliation:
Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
*
Author for correspondence: Charles G. Gauci, E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Echinococcus granulosus is an important zoonotic parasite that is distributed worldwide. The EG95 vaccine was developed to assist with control of E. granulosus transmission through the parasite's livestock intermediate hosts. The vaccine is based on a recombinant antigen encoded by a gene which is a member of a multi-gene family. With the recent availability of two E. granulosus draft genomes, we sought to map the eg95 gene family to the genomes. We were unable to map unequivocally any of the eg95 gene family members which had previously been characterized by cloning and sequencing both strands of genomic DNA fragments. Our inability to map EG95-related genes to the genomes has revealed limitations in the assembled sequence data when utilized for gene family analyses. This study contrasts with the expectations expressed in often high-profile publications describing draft genomes of parasitic organisms, highlighting deficiencies in currently available genomic resources for E. granulosus and provides a cautionary note for research which seeks to utilize these genome datasets.

Keywords

Echinococcus granulosusEG95vaccinegenomegene
Type
Research Article
Information
Parasitology , Volume 145 , Issue 6 , May 2018 , pp. 807 - 813
Check for updates
Copyright
Copyright © Cambridge University Press 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alkan, C, Sajjadian, S and Eichler, EE (2011) Limitations of next-generation genome sequence assembly. Nature Methods 8, 61–65.Google Scholar
Alvarez Rojas, CA, Gauci, CG, Nolan, MJ, Harandi, MF and Lightowlers, MW (2012) Characterization of the eg95 gene family in the G6 genotype of Echinococcus granulosus. Molecular and Biochemical Parasitology 183, 115–121.CrossRefGoogle ScholarPubMed
Alvarez Rojas, CA, Romig, T and Lightowlers, MW (2014) Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge. International Journal for Parasitology 44, 9–18.Google Scholar
Bolger, ME, Arsova, B and Usadel, B (2017) Plant genome and transcriptome annotations: from misconceptions to simple solutions. Briefings in Bioinformatics. 1–13. doi: 10.1093/bib/bbw135.Google Scholar
Chow, C (2002) Characterization of the eg95 gene family encoding a host-protective antigen of Echinococcus granulosus, PhD Thesis, University of Melbourne, Australia.Google Scholar
Chow, C, Gauci, CG, Cowman, AF and Lightowlers, MW (2001) A gene family expressing a host-protective antigen of Echinococcus granulosus. Molecular and Biochemical Parasitology 118, 83–88.Google Scholar
Chow, C, Gauci, CG, Cowman, AF and Lightowlers, MW (2004) Echinococcus granulosus: oncosphere-specific transcription of genes encoding a host-protective antigen. Experimental Parasitology 106, 183–186.Google Scholar
Denton, JF, Lugo-Martinez, J, Tucker, AE, Schrider, DR, Warren, WC and Hahn, MW (2014) Extensive error in the number of genes inferred from draft genome assemblies. PLoS Computational Biology 10, e1003998.CrossRefGoogle ScholarPubMed
Doolittle, RF and Bork, P (1993) Evolutionarily mobile modules in proteins. Scientific American 269, 50–56.CrossRefGoogle ScholarPubMed
Florea, L, Souvorov, A, Kalbfleisch, TS and Salzberg, SL (2011) Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies. PLoS ONE 6, e21400.CrossRefGoogle Scholar
Goodswen, SJ, Barratt, JL, Kennedy, PJ and Ellis, JT (2015) Improving the gene structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico-derived vaccine. International Journal for Parasitology 45, 305–318.Google Scholar
Haag, KL, Gottstein, B and Ayala, FJ (2009) The EG95 antigen of Echinococcus spp. contains positively selected amino acids, which may influence host specificity and vaccine efficacy. PLoS ONE 4, e5362.CrossRefGoogle ScholarPubMed
Holroyd, N and Sanchez-Flores, A (2012) Producing parasitic helminth reference and draft genomes at the Wellcome Trust Sanger Institute. Parasite Immunology 34, 100–107.CrossRefGoogle ScholarPubMed
Koren, S and Phillippy, AM (2015) One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Current Opinion in Microbiology 23, 110–120.Google Scholar
Lightowlers, MW (2006) Cestode vaccines: origins, current status and future prospects. Parasitology 133(suppl.), S27–S42.CrossRefGoogle ScholarPubMed
Lightowlers, MW, Lawrence, SB, Gauci, CG, Young, J, Ralston, MJ, Maas, D and Health, DD (1996) Vaccination against hydatidosis using a defined recombinant antigen. Parasite Immunology 18, 457–462.Google Scholar
Lightowlers, MW, Jensen, O, Fernandez, E, Iriarte, JA, Woollard, DJ, Gauci, CG, Jenkins, DJ and Heath, DD (1999) Vaccination trials in Australia and Argentina confirm the effectiveness of the EG95 hydatid vaccine in sheep. International Journal for Parasitology 29, 531–534.CrossRefGoogle ScholarPubMed
Lightowlers, MW, Flisser, A, Gauci, CG, Heath, DD, Jensen, O and Rolfe, R (2000) Vaccination against cysticercosis and hydatid disease. Parasitology Today 16, 191–196.CrossRefGoogle ScholarPubMed
Lu, H, Giordano, F and Ning, Z (2016) Oxford Nanopore MinION Sequencing and Genome Assembly. Genomics Proteomics Bioinformatics 14, 265–279.Google Scholar
Lv, Z, Wu, Z, Zhang, L, Ji, P, Cai, Y, Luo, S, Wang, H and Li, H (2015) Genome mining offers a new starting point for parasitology research. Parasitology Research 114, 399–409.Google Scholar
Parra, G, Bradnam, K, Ning, Z, Keane, T and Korf, I (2009) Assessing the gene space in draft genomes. Nucleic Acids Research 37, 289–297.CrossRefGoogle ScholarPubMed
Rhoads, A and Au, KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13, 278–289.CrossRefGoogle ScholarPubMed
Schatz, MC, Witkowski, J and McCombie, WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biology 13, 243.CrossRefGoogle ScholarPubMed
Smyth, JD (1962) Chromosome number of Echinococcus granulosus. Journal of Parasitology 48, 544CrossRefGoogle Scholar
Spakulova, M, Orosova, M and Mackiewicz, JS (2011) Cytogenetics and chromosomes of tapeworms (Platyhelminthes, Cestoda). Advances in Parasitology 74, 177–230.CrossRefGoogle ScholarPubMed
Tsai, IJ, Zarowiecki, M, Holroyd, N, Garciarrubio, A, Sanchez-Flores, A, Brooks, KL, Tracey, A, Bobes, RJ, Fragoso, G, Sciutto, E, Aslett, M, Beasley, H, Bennett, HM, Cai, J, Camicia, F, Clark, R, Cucher, M, De Silva, N, Day, TA, Deplazes, P, Estrada, K, Fernandez, C, Holland, PW, Hou, J, Hu, S, Huckvale, T, Hung, SS, Kamenetzky, L, Keane, JA, Kiss, F, et al. (2013) The genomes of four tapeworm species reveal adaptations to parasitism. Nature 496, 57–63.Google Scholar
Zarowiecki, M and Berriman, M (2015) What helminth genomes have taught us about parasite evolution. Parasitology 142(suppl. 1), S85–S97.Google Scholar
Zhang, W, Li, J, You, H, Zhang, Z, Turson, G, Loukas, A and McManus, DP (2003) Short report: Echinococcus granulosus from Xinjiang, PR China: cDNAS encoding the EG95 vaccine antigen are expressed in different life cycle stages and are conserved in the oncosphere. American Journal of Tropical Medicine and Hygiene 68, 40–43.CrossRefGoogle ScholarPubMed
Zhang, W, Wang, S and McManus, DP (2014) Echinococcus granulosus genomics: a new dawn for improved diagnosis, treatment, and control of echinococcosis. Parasite 21, 66.Google Scholar
Zheng, H, Zhang, W, Zhang, L, Zhang, Z, Li, J, Lu, G, Zhu, Y, Wang, Y, Huang, Y, Liu, J, Kang, H, Chen, J, Wang, L, Chen, A, Yu, S, Gao, Z, Jin, L, Gu, W, Wang, Z, Zhao, L, Shi, B, Wen, H, Lin, R, Jones, MK, Brejova, B, Vinar, T, Zhao, G, McManus, DP, Chen, Z, Zhou, Y, et al. (2013) The genome of the hydatid tapeworm Echinococcus granulosus. Nature Genetics 45, 1168–1175.CrossRefGoogle ScholarPubMed