Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Jerlström Hultqvist, Jon ^a   Franzén, Oscar ^b,c   Ankarklev, Johan ^a   Xu, Feifei ^d   Nohýnková, Eva ^e   Andersson, Jan O ^d   Svärd, Staffan G ^a   Andersson, Björn ^b,c  

^a UPPSALA UNIVERSITY   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c SCIENCE FOR LIFE LABORATORY   (Sweden)

^d UPPSALA UNIVERSITY   (Sweden)

^e CHARLES UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; NEK KINASE; PROTEIN HCMP; PROTEIN VSP; UNCLASSIFIED DRUG; CIRCULAR DNA; PROTOZOAL PROTEIN; PROTOZOAL RNA; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CHROMOSOME REARRANGEMENT; CHROMOSOME STRUCTURE; CONTROLLED STUDY; GENE IDENTIFICATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GIARDIA LAMBLIA; NONHUMAN; SEQUENCE HOMOLOGY; SWINE; WILD TYPE; ALLELE; COMPARATIVE STUDY; CONTIG MAPPING; DNA SEQUENCE; GENE; GENE EXPRESSION REGULATION; GENETICS; GENOME; GENOMICS; HETEROZYGOTE; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYADENYLATION; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY;

GIARDIA; GIARDIA INTESTINALIS; MAMMALIA; PROTOZOA;

ALLELES; CONSERVED SEQUENCE; CONTIG MAPPING; DNA, CIRCULAR; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENES, PROTOZOAN; GENOME, PROTOZOAN; GENOMICS; GIARDIA LAMBLIA; HETEROZYGOTE; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; PHYLOGENY; POLYADENYLATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTOZOAN PROTEINS; RNA, PROTOZOAN; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, DNA; SYNTENY;

EID: 77957326028     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-543     Document Type: Article

References (52)

1. Goto R, Panter-Brick C, Northrop-Clewes CA, Manahdhar R, Tuladhar NR. Poor Intestinal Permeability in Mildly Stunted Nepali Children: Associations with Weaning Practices and Giardia Lamblia Infection. British Journal of Nutrition 2002, 88:141-14910. 1079/BJN2002599, 10.1079/BJN2002599, 12171055.
2. Adam RD. Biology of Giardia lamblia. Clin Microbiol Rev 2001, 14:447-7510. 1128/CMR.14.3.447-475.2001, 10.1128/CMR.14.3.447-475.2001, 11432808.
3. LeChevallier MW, Norton WD, Lee RG. Occurrence of Giardia and Cryptosporidium spp. in surface water supplies. Appl Environ Microbiol 1991, 57:2610-2616. 183628, 1822675.
4. Craun GF, Calderon RL, Craun MF. Outbreaks associated with recreational water in the United States. International Journal of Environmental Health Research 2005, 15:24310. 1080/09603120500155716.
5. Wolfe MS. Giardiasis. Clin Microbiol Rev 1992, 5:93-100. 358225, 1735095.
6. Hellard ME, Sinclair MI, Hogg GG, Fairley CK. Prevalence of enteric pathogens among community based asymptomatic individuals. Journal of Gastroenterology and Hepatology 2000, 15:290-29310. 1046/j.1440-1746.2000.02089.x, 10.1046/j.1440-1746.2000.02089.x, 10764030.
7. Lloyd D, Harris JC. Giardia: highly evolved parasite or early branching eukaryote?. Trends in Microbiology 2002, 10:122-12710. 1016/S0966-842X(02)02306-5, 10.1016/S0966-842X(02)02306-5, 11864821.
8. Jiménez-García LF, Zavala G, Chávez-Munguía B, Ramos-Godínez MDP, López-Velázquez G, Segura-Valdez MDL, Montañez C, Hehl AB, Argüello-García R, Ortega-Pierres G. Identification of nucleoli in the early branching protist Giardia duodenalis. Int J Parasitol 2008, 38:1297-130410. 1016/j.ijpara.2008.04.012, 10.1016/j.ijpara.2008.04.012, 18625508.
9. Tovar J, Leon-Avila G, Sanchez LB, Sutak R, Tachezy J, van der Giezen M, Hernandez M, Muller M, Lucocq JM. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 2003, 426:172-17610. 1038/nature01945, 10.1038/nature01945, 14614504.
10. Andersson JO. Gene transfer and diversification of microbial eukaryotes. Annu Rev Microbiol 2009, 63:177-19310. 1146/annurev.micro.091208.073203, 10.1146/annurev.micro.091208.073203, 19575565.
11. Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JEJ, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG, Sogin ML. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 2007, 317:1921-192610. 1126/science.1143837, 10.1126/science.1143837, 17901334.
12. Bernander R, Palm JE, Svärd SG. Genome ploidy in different stages of the Giardia lamblia life cycle. Cell Microbiol 2001, 3:55-62. 10.1046/j.1462-5822.2001.00094.x, 11207620.
13. Adam RD. Biology of Giardia lamblia. Clin Microbiol Rev 2001, 14:447-47510. 1128/CMR.14.3.447-475.2001, 10.1128/CMR.14.3.447-475.2001, 88984, 11432808.
14. Le Blancq SM, Adam RD. Structural basis of karyotype heterogeneity in Giardia lamblia. Mol Biochem Parasitol 1998, 97:199-208. 10.1016/S0166-6851(98)00150-9, 9879898.
15. Andrews RH, Adams M, Boreham PF, Mayrhofer G, Meloni BP. Giardia intestinalis: electrophoretic evidence for a species complex. Int J Parasitol 1989, 19:183-190. 10.1016/0020-7519(89)90006-4, 2722391.
16. Monis PT, Caccio SM, Thompson RCA. Variation in Giardia: towards a taxonomic revision of the genus. Trends Parasitol 2009, 25:93-10010. 1016/j.pt.2008.11.006, 10.1016/j.pt.2008.11.006, 19135417.
17. Lalle M, Pozio E, Capelli G, Bruschi F, Crotti D, Cacciò SM. Genetic heterogeneity at the beta-giardin locus among human and animal isolates of Giardiaduodenalis and identification of potentially zoonotic subgenotypes. Int J Parasitol 2005, 35:207-21310. 1016/j.ijpara.2004.10.022, 10.1016/j.ijpara.2004.10.022, 15710441.
18. Thompson RCA, Monis PT. Variation in Giardia: implications for taxonomy and epidemiology. Adv Parasitol 2004, 58:69-13710. 1016/S0065-308X(04)58002-8, 10.1016/S0065-308X(04)58002-8, 15603762.
19. Cacciò SM, Thompson RCA, McLauchlin J, Smith HV. Unravelling Cryptosporidium and Giardia epidemiology. Trends Parasitol 2005, 21:430-43710. 1016/j.pt.2005.06.013, 10.1016/j.pt.2005.06.013, 16046184.
20. Sprong H, Cacciò SM, van der Giessen JWB, . on behalf of the ZOOPNET network and partners Identification of Zoonotic Genotypes of Giardia duodenalis. PLoS Negl Trop Dis 2009, 3:e55810. 1371/journal.pntd.0000558, on behalf of the ZOOPNET network and partners.
21. Andersson JO, Sjögren AM, Davis LAM, Embley TM, Roger AJ. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 2003, 13:94-104. 10.1016/S0960-9822(03)00003-4, 12546782.
22. Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG. Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?. PLoS Pathog 2009, 5:e100056010. 1371/journal.ppat.1000560.
23. Ey PL, Mansouri M, Kulda J, Nohýnková E, Monis PT, Andrews RH, Mayrhofer G. Genetic analysis of Giardia from hoofed farm animals reveals artiodactyl-specific and potentially zoonotic genotypes. J Eukaryot Microbiol 1997, 44:626-635. 10.1111/j.1550-7408.1997.tb05970.x, 9435134.
24. Birkeland SR, Preheim SP, Davids BJ, Cipriano MJ, Palm D, Reiner DS, Svärd SG, Gillin FD, McArthur AG. Transcriptome analyses of the Giardia lamblia life cycle. Mol Biochem Parasitol 2010, 10. 1016/j.molbiopara.2010.05.010Available: Accessed 29 June 2010., http://www.ncbi.nlm.nih.gov/pubmed/20570699
25. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 10.1093/nar/25.5.955, 146525, 9023104.
26. Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JEJ, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG, Sogin ML. Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science 2007, 317:1921-192610. 1126/science.1143837, 10.1126/science.1143837, 17901334.
27. Le Blancq SM. Chromosome rearrangements in Giardia lamblia. Parasitol Today (Regul Ed) 1994, 10:177-179. 10.1016/0169-4758(94)90021-3, 15275464.
28. Upcroft JA, Healey A, Upcroft P. Chromosomal duplication in Giardia duodenalis. Int J Parasitol 1993, 23:609-616. 10.1016/0020-7519(93)90167-W, 8225763.
29. Tůmová P, Hofstetrová K, Nohýnková E, Hovorka O, Král J. Cytogenetic evidence for diversity of two nuclei within a single diplomonad cell of Giardia. Chromosoma 2007, 116:65-7810. 1007/s00412-006-0082-4, 10.1007/s00412-006-0082-4, 17086421.
30. Le Blancq SM, Korman SH, Van der Ploeg LH. Spontaneous chromosome rearrangements in the protozoan Giardia lamblia: estimation of mutation rates. Nucleic Acids Res 1992, 20:4539-4545. 10.1093/nar/20.17.4539, 334182, 1408754.
31. Arkhipova IR, Morrison HG. Three retrotransposon families in the genome of Giardia lamblia: two telomeric, one dead. Proc Natl Acad Sci USA 2001, 98:14497-1450210. 1073/pnas.231494798, 10.1073/pnas.231494798, 64710, 11734649.
32. Lebbad M, Mattsson JG, Christensson B, Ljungström B, Backhans A, Andersson JO, Svärd SG. From mouse to moose: Multilocus genotyping of Giardia isolates from various animal species. Vet Parasitol 2010, 168:231-23910. 1016/j.vetpar.2009.11.003, 10.1016/j.vetpar.2009.11.003, 19969422.
33. Viguera E, Canceill D, Ehrlich SD. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J 2001, 20:2587-259510. 1093/emboj/20.10.2587, 10.1093/emboj/20.10.2587, 125466, 11350948.
34. Cooper MA, Adam RD, Worobey M, Sterling CR. Population genetics provides evidence for recombination in Giardia. Curr Biol 2007, 17:1984-198810. 1016/j.cub.2007.10.020, 10.1016/j.cub.2007.10.020, 17980591.
35. Andersson JO, Sjögren AM, Davis LAM, Embley TM, Roger AJ. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 2003, 13:94-104. 10.1016/S0960-9822(03)00003-4, 12546782.
36. Welch RA, Burland V, Plunkett G, Redford P, Roesch P, Rasko D, Buckles EL, Liou S, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HLT, Donnenberg MS, Blattner FR. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 2002, 99:17020-1702410. 1702410.1073/pnas.252529799, 10.1073/pnas.252529799, 139262, 12471157.
37. El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran A, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, Anupama A, Arner E, Aslund L, Attipoe P, Bontempi E, Bringaud F, Burton P, Cadag E, Campbell DA, Carrington M, Crabtree J, Darban H, da Silveira JF, de Jong P, Edwards K, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 2005, 309:409-41510. 1126/science.1112631, 10.1126/science.1112631, 16020725.
38. Koudela B, Nohýnková E, Vítovec J, Pakandl M, Kulda J. Giardia infection in pigs: detection and in vitro isolation of trophozoites of the Giardia intestinalis group. Parasitology 1991, 102(Pt 2):163-166. 10.1017/S0031182000062442, 1852483.
39. Chevreux B. MIRA sequence assembler , http://sourceforge.net/apps/mediawiki/mira-assembler/
40. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-21410. 1089/10665270050081478, 10.1089/10665270050081478, 10890397.
41. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
42. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
43. Badger JH, Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 1999, 16:512-524.
44. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D. Tablet--next generation sequence assembly visualization. Bioinformatics 2010, 26:401-40210. 1093/bioinformatics/btp666, 10.1093/bioinformatics/btp666, 2815658, 19965881.
45. Bininda-Emonds ORP. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 2005, 6:15610. 1186/1471-2105-6-156.
46. Carver TJ, Rutherford KM, Berriman M, Rajandream M, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21:3422-342310. 1093/bioinformatics/bti553, 10.1093/bioinformatics/bti553, 15976072.
47. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ, Sullivan S, Treatman C, Wang H. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res 2009, 37:D526-53010. 1093/nar/gkn631, 10.1093/nar/gkn631, 2686445, 18824479.
48. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
49. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-164510. 1101/gr.092759.109, 10.1101/gr.092759.109, 2752132, 19541911.
50. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-46310. 1093/bioinformatics/bti191, 10.1093/bioinformatics/bti191, 15608047.
51. Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 2004, 20:289-290. 10.1093/bioinformatics/btg412, 14734327.
52. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34:W369-37310. 1093/nar/gkl198, 10.1093/nar/gkl198, 1538909, 16845028.