Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502 2012 and UKH1

Pathogens and Disease

Volumn 74, Issue 7, 2016, Pages

  Ifeonu, Olukemi O ^a   Chibucos, Marcus C ^a   Orvis, Joshua ^a   Su, Qi ^a   Elwin, Kristin ^b   Guo, Fengguang ^c   Zhang, Haili ^c   Xiao, Lihua ^d   Sun, Mingfei ^e   Chalmers, Rachel M ^b   Fraser, Claire M ^a   Zhu, Guan ^c   Kissinger, Jessica C ^f   Widmer, Giovanni ^g   Silva, Joana C ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b SINGLETON HOSPITAL   (United Kingdom)

^c TEXAS A AND M UNIVERSITY   (United States)

^d NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^e INSTITUTE OF ANIMAL SCIENCE   (China)

^f UNIVERSITY OF GEORGIA   (United States)

^g TUFTS UNIVERSITY   (United States)

Author keywords

Annotation; C. hominis TU502 2012; Cryptosporidium; Cryptosporidium baileyi; Cryptosporidium meleagridis; Genome assembly

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; CONTROLLED STUDY; CRYPTOSPORIDIUM BAILEYI; CRYPTOSPORIDIUM HOMINIS; CRYPTOSPORIDIUM MELEAGRIDIS; DENSITY GRADIENT; DNA SEQUENCE; GENE CLUSTER; GENE SEQUENCE; GENE STRUCTURE; GENETIC DIFFERENCE; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; NONHUMAN; OOCYST; POLYMORPHIC LOCUS; PRIORITY JOURNAL; SANGER SEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL GENE; BIOLOGY; CLASSIFICATION; CRYPTOSPORIDIUM; GENE EXPRESSION PROFILING; GENETICS; GENOME; GENOMICS; MOLECULAR GENETICS; PROCEDURES;

TRANSCRIPTOME;

COMPUTATIONAL BIOLOGY; CRYPTOSPORIDIUM; GENE EXPRESSION PROFILING; GENOME, PROTOZOAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE ANNOTATION; TRANSCRIPTOME;

EID: 84992361476     PISSN: None     EISSN: 2049632X     Source Type: Journal    
DOI: 10.1093/femspd/ftw080     Document Type: Article

References (23)

1. Abrahamsen MS, Templeton TJ, Enomoto S et al. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 2004;304:441-5.
2. Akiyoshi DE, Dilo J, Pearson C et al. Characterization of Cryptosporidium meleagridis of human origin passaged through different host species. Infect Immun 2003;71:1828-32.
3. Borodovsky M, Lomsadze A. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Curr Protoc Bioinform 2011;6:1-10.
4. Grinberg A, Widmer G. Cryptosporidium within-host genetic diversity: systematic bibliographical search and narrative overview. Int J Parasitol 2016;46:465-71.
5. Haas BJ, Salzberg SL, Zhu W et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 2008;9:R7.
6. Kotloff KL, Nataro JP, BlackwelderWC et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet 2013;382:209-22.
7. Lee E, Helt GA, Reese JT et al. Web Apollo: a web-based genomic annotation editing platform. Genome Biol 2013;14:R93.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.
9. McKenna A, Hanna M, Banks E et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Res 2010;20:1297- 303.
10. Parkhomchuk D, Borodina T, Amstislavskiy V et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009;37:e123.
11. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007;23:1061-7.
12. Ryan U, Fayer R, Xiao L. Cryptosporidium species in humans and animals: current understanding and research needs. Parasitology 2014;141:1667-85.
13. Stanke M, Steinkamp R, Waack S et al. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res 2004;32: W309-12.
14. Tretina K, Pelle R, Silva JC. Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva. BMC Genomics 2016;17:128.
15. Tzipori S. Cryptosporidiosis in perspective. Adv Parasitol 1988;27: 63-129.
16. Tzipori S, Rand W, Griffiths J et al. Evaluation of an animal model system for cryptosporidiosis: therapeutic efficacy of paromomycin and hyperimmune bovine colostrum-immunoglobulin. Clin Diagn Lab Immunol 1994;1: 450-63.
17. Upton SJ, Current WL. The species of Cryptosporidium (Apicomplexa: Cryptosporidiidae) infecting mammals. J Parasitol 1985;71:625-9.
18. Widmer G, Feng X, Tanriverdi S. Genotyping of Cryptosporidium parvum with microsatellite markers. Methods Mol Biol 2004;268:177-87.
19. Widmer G, Ras R, Chalmers RMet al. Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis. Environ Microbiol 2015;17:984-93.
20. Widmer G, Sullivan S. Genomics and population biology of Cryptosporidium species. Parasite Immunol 2012;34:61-71.
21. Xu P, Widmer G, Wang Y et al. The genome of Cryptosporidium hominis. Nature 2004;431:1107-12.
22. Zhang H, Guo F, Zhou H et al. Transcriptome analysis reveals unique metabolic features in the Cryptosporidium parvum Oocysts associated with environmental survival and stresses. BMC Genomics 2012;13:647.
23. Zimin AV, Marcais G, Puiu D et al. The MaSuRCA genome assembler. Bioinformatics 2013;29:2669-77.