Whole Genome Mapping and Re-Organization of the Nuclear and Mitochondrial Genomes of Babesia microti Isolates

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Cornillot, Emmanuel ^a,b   Dassouli, Amina ^c,d   Garg, Aprajita ^c   Pachikara, Niseema ^c   Randazzo, Sylvie ^d   Depoix, Delphine ^d,h   Carcy, Bernard ^d   Delbecq, Stéphane ^d   Frutos, Roger ^a,e   Silva, Joana C ^f   Sutton, Richard ^c   Krause, Peter J ^g   Mamoun, Choukri Ben ^c  

^a University of Montpellier I and II   (France)

^b LIRMM   (France)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIV MONTPELLIER   (France)

^e INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

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

^g YALE UNIVERSITY   (United States)

^h MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BABESIA MICROTI; CELL NUCLEUS; CHROMOSOME STRUCTURE; GENE IDENTIFICATION; GENE MAPPING; GENE STRUCTURE; GENETIC ORGANIZATION; GENETIC STRAIN; GENOME; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEAR GENOME; NUCLEOTIDE SEQUENCE; PARASITE ISOLATION; STRAIN DIFFERENCE; TELOMERE;

ANIMALS; BABESIA MICROTI; GENOME, MITOCHONDRIAL; GENOME, PROTOZOAN;

EID: 84883414669     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0072657     Document Type: Article

References (50)

1. Herwaldt BL, Linden JV, Bosserman E, Young C, Olkowska D, et al. (2011) Transfusion-associated babesiosis in the United States: a description of cases. Ann Intern Med 155: 509-519.
2. Vannier E, Krause PJ, (2012) Human babesiosis. N Engl J Med 366: 2397-2407.
3. Hatcher JC, Greenberg PD, Antique J, Jimenez-Lucho VE, (2001) Severe babesiosis in Long Island: review of 34 cases and their complications. Clin Infect Dis 32: 1117-1125.
4. Krause PJ, Gewurz BE, Hill D, Marty FM, Vannier E, et al. (2008) Persistent and relapsing babesiosis in immunocompromised patients. Clin Infect Dis 46: 370-376.
5. Cornillot E, Hadj-Kaddour K, Dassouli A, Noel B, Ranwez V, et al. (2012) Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. Nucleic Acids Res 40: 9102-9114.
6. Schnittger L, Rodriguez AE, Florin-Christensen M, Morrison DA, (2012) Babesia: a world emerging. Infect Genet Evol 12: 1788-1809.
7. Zahler M, Rinder H, Gothe R, (2000) Genotypic status of Babesia microti within the piroplasms. Parasitol Res 86: 642-646.
8. Shukla SK, Pantrangi M, Stahl B, Briska AM, Stemper ME, et al. (2012) Comparative whole-genome mapping to determine Staphylococcus aureus genome size, virulence motifs, and clonality. J Clin Microbiol 50: 3526-3533.
9. Tardy F, Baranowski E, Nouvel LX, Mick V, Manso-Silvan L, et al. (2012) Emergence of atypical Mycoplasma agalactiae strains harboring a new prophage and associated with an alpine wild ungulate mortality episode. Appl Environ Microbiol 78: 4659-4668.
10. van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, et al. (2007) Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 8: R52.
11. Kotewicz ML, Jackson SA, LeClerc JE, Cebula TA, (2007) Optical maps distinguish individual strains of Escherichia coli O157: H7. Microbiology 153: 1720-1733.
12. Jalan N, Aritua V, Kumar D, Yu F, Jones JB, et al. (2011) Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity. J Bacteriol 193: 6342-6357.
13. OpGen Technologies.
14. Gleason NN, Healy GR, Western KA, Benson GD, Schultz MG, (1970) The "Gray" strain of Babesia microti from a human case established in laboratory animals. J Parasitol 56: 1256-1257.
15. Depoix D, Carcy B, Jumas-Bilak E, Pages M, Precigout E, et al. (2002) Chromosome number, genome size and polymorphism of European and South African isolates of large Babesia parasites that infect dogs. Parasitology 125: 313-321.
16. Shukla SK, Kislow J, Briska A, Henkhaus J, Dykes C, (2009) Optical mapping reveals a large genetic inversion between two methicillin-resistant Staphylococcus aureus strains. J Bacteriol 191: 5717-5723.
17. Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7: e1002230.
18. Zhou S, Kile A, Kvikstad E, Bechner M, Severin J, et al. (2004) Shotgun optical mapping of the entire Leishmania major Friedlin genome. Mol Biochem Parasitol 138: 97-106.
19. Riley MC, Kirkup BC Jr, Johnson JD, Lesho EP, Ockenhouse CF, (2011) Rapid whole genome optical mapping of Plasmodium falciparum. Malar J 10: 252.
20. Jing J, Lai Z, Aston C, Lin J, Carucci DJ, et al. (1999) Optical mapping of Plasmodium falciparum chromosome 2. Genome Res 9: 175-181.
21. Corcoran LM, Thompson JK, Walliker D, Kemp DJ, (1988) Homologous recombination within subtelomeric repeat sequences generates chromosome size polymorphisms in P. falciparum. Cell 53: 807-813.
22. de Bruin D, Lanzer M, Ravetch JV, (1994) The polymorphic subtelomeric regions of Plasmodium falciparum chromosomes contain arrays of repetitive sequence elements. Proc Natl Acad Sci U S A 91: 619-623.
23. Figueiredo LM, Freitas-Junior LH, Bottius E, Olivo-Marin JC, Scherf A, (2002) A central role for Plasmodium falciparum subtelomeric regions in spatial positioning and telomere length regulation. EMBO J 21: 815-824.
24. Patarapotikul J, Langsley G, (1988) Chromosome size polymorphism in Plasmodium falciparum can involve deletions of the subtelomeric pPFrep20 sequence. Nucleic Acids Res 16: 4331-4340.
25. Pryde FE, Gorham HC, Louis EJ, (1997) Chromosome ends: all the same under their caps. Curr Opin Genet Dev 7: 822-828.
26. Scherf A, Figueiredo LM, Freitas-Junior LH, (2001) Plasmodium telomeres: a pathogen's perspective. Curr Opin Microbiol 4: 409-414.
27. Barry JD, Ginger ML, Burton P, McCulloch R, (2003) Why are parasite contingency genes often associated with telomeres? Int J Parasitol 33: 29-45.
28. Lanzer M, Fischer K, Le Blancq SM, (1995) Parasitism and chromosome dynamics in protozoan parasites: is there a connection? Mol Biochem Parasitol 70: 1-8.
29. Hikosaka K, Tsuji N, Watanabe Y, Kishine H, Horii T, et al. (2012) Novel type of linear mitochondrial genomes with dual flip-flop inversion system in apicomplexan parasites, Babesia microti and Babesia rodhaini. BMC Genomics 13: 622.
30. Gray MW, Lang BF, Burger G, (2004) Mitochondria of protists. Annu Rev Genet 38: 477-524.
31. Lang BF, Gray MW, Burger G, (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33: 351-397.
32. Nakajima R, Tsuji M, Oda K, Zamoto-Niikura A, Wei Q, et al. (2009) Babesia microti-group parasites compared phylogenetically by complete sequencing of the CCTeta gene in 36 isolates. J Vet Med Sci 71: 55-68.
33. Lau AO, (2009) An overview of the Babesia, Plasmodium and Theileria genomes: a comparative perspective. Mol Biochem Parasitol 164: 1-8.
34. Kappmeyer LS, Thiagarajan M, Herndon DR, Ramsay JD, Caler E, et al. (2012) Comparative genomic analysis and phylogenetic position of Theileria equi. BMC Genomics 13: 603.
35. Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, et al. (2012) Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. MBio 3: e00204-00212.
36. Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, et al. (2005) Genome of the host-cell transforming parasite Theileria annulata compared with T. parva. Science 309: 131-133.
37. Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, et al. (2005) Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309: 134-137.
38. Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, et al. (2007) Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog 3: 1401-1413.
39. Lodes MJ, Houghton RL, Bruinsma ES, Mohamath R, Reynolds LD, et al. (2000) Serological expression cloning of novel immunoreactive antigens of Babesia microti. Infect Immun 68: 2783-2790.
40. Homer MJ, Bruinsma ES, Lodes MJ, Moro MH, Telford S 3rd, et al. (2000) A polymorphic multigene family encoding an immunodominant protein from Babesia microti. J Clin Microbiol 38: 362-368.
41. McEachern MJ, Haber JE, (2006) Break-induced replication and recombinational telomere elongation in yeast. Annu Rev Biochem 75: 111-135.
42. Pfeiffer P, Goedecke W, Obe G, (2000) Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations. Mutagenesis 15: 289-302.
43. Valencia M, Bentele M, Vaze MB, Herrmann G, Kraus E, et al. (2001) NEJ1 controls non-homologous end joining in Saccharomyces cerevisiae. Nature 414: 666-669.
44. Pryde FE, Louis EJ, (1997) Saccharomyces cerevisiae telomeres. A review. Biochemistry (Mosc) 62: 1232-1241.
45. Preiser PR, Wilson RJ, Moore PW, McCready S, Hajibagheri MA, et al. (1996) Recombination associated with replication of malarial mitochondrial DNA. EMBO J 15: 684-693.
46. Gardner MJ, Hall N, Fung E, White O, Berriman M, et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
47. Hikosaka K, Kita K, Tanabe K, (2013) Diversity of mitochondrial genome structure in the phylum Apicomplexa. Mol Biochem Parasitol 188: 26-33.
48. Hikosaka K, Nakai Y, Watanabe Y, Tachibana S, Arisue N, et al. (2011) Concatenated mitochondrial DNA of the coccidian parasite Eimeria tenella. Mitochondrion 11: 273-278.
49. Hikosaka K, Watanabe Y, Kobayashi F, Waki S, Kita K, et al. (2011) Highly conserved gene arrangement of the mitochondrial genomes of 23 Plasmodium species. Parasitol Int 60: 175-180.
50. Kairo A, Fairlamb AH, Gobright E, Nene V, (1994) A 7.1 kb linear DNA molecule of Theileria parva has scrambled rDNA sequences and open reading frames for mitochondrially encoded proteins. EMBO J 13: 898-905.