Gene duplication in the genome of parasitic Giardia lamblia

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Sun, Jun ^a,b   Jiang, Huifeng ^a,c   Flores, Roberto ^c   Wen, Jianfan ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTE; EVOLUTIONARY BIOLOGY; GENOMICS; LIFESTYLE; PARASITE; PARASITISM; PROTOZOAN;

EUKARYOTA; EUTHERIA; GIARDIA; GIARDIA INTESTINALIS; PROTISTA; PROTOZOA; VERTEBRATA;

PROTOZOAL PROTEIN;

ARTICLE; EVOLUTION; GENE DUPLICATION; GENETICS; GENOME; GIARDIA LAMBLIA;

EVOLUTION; GENE DUPLICATION; GENOME, PROTOZOAN; GIARDIA LAMBLIA; PROTOZOAN PROTEINS;

EID: 77649223873     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-49     Document Type: Article

References (52)

1. Giardiasis surveillance - United States, 1998-2002. MC Hlavsa JC Watson MJ Beach, MMWR Surveill Summ 2005 54 1 9 16 15674189
2. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. ML Sogin JH Gunderson HJ Elwood RA Alonso DA Peattie, Science (New York, NY) 1989 243 4887 75 77
3. Kingdom protozoa and its 18 phyla. T Cavalier-Smith, Microbiol Rev 1993 57 4 953 994 8302218
4. Cell biology of the primitive eukaryote Giardia lamblia. FD Gillin DS Reiner JM McCaffery, Annu Rev Microbiol 1996 50 679 705 10.1146/annurev.micro. 50.1.679 8905095
5. Identification of a Giardia krr1 homolog gene and the secondarily anucleolate condition of Giaridia lamblia. DD Xin JF Wen D He SQ Lu, Molecular biology and evolution 2005 22 3 391 394 10.1093/molbev/msi052 15548749
6. Oxygen content of transmembrane proteins over macroevolutionary time scales. C Acquisti J Kleffe S Collins, Nature 2007 445 7123 47 52 10.1038/nature05450 17183269
7. Biology of Giardia lamblia. RD Adam, Clinical microbiology reviews 2001 14 3 447 475 10.1128/CMR.14.3.447-475.2001 11432808
8. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. HG Morrison AG McArthur FD Gillin SB Aley RD Adam GJ Olsen AA Best WZ Cande F Chen MJ Cipriano, et al. Science (New York, NY) 2007 317 5846 1921 1926
9. Evolution by gene duplication. S Ohno, Berlin, New York,: Springer-Verlag 1970
10. The origin of new genes: glimpses from the young and old. M Long E Betran K Thornton W Wang, Nature reviews 2003 4 11 865 875 14634634
11. Gene gain and gene loss in streptococcus: is it driven by habitat? PR Marri W Hao GB Golding, Molecular biology and evolution 2006 23 12 2379 2391 10.1093/molbev/msl115 16966682
12. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. JO Andersson AM Sjogren LA Davis TM Embley AJ Roger, Curr Biol 2003 13 2 94 104 10.1016/S0960-9822(03)00003-4 12546782
13. Evolution by gene duplication: an update. J Zhang, Trends in Ecology & Evolution 2003 2003 6 292 298
14. Role of duplicate genes in genetic robustness against null mutations. Z Gu LM Steinmetz X Gu C Scharfe RW Davis WH Li, Nature 2003 421 6918 63 66 10.1038/nature01198 12511954 (Pubitemid 36077084)
15. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. Y Gilad M Przeworski D Lancet, PLoS biology 2004 2 1 5 10.1371/journal.pbio.0020005 14737185
16. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. CT Hittinger A Rokas SB Carroll, Proceedings of the National Academy of Sciences of the United States of America 2004 101 39 14144 14149 10.1073/pnas.0404319101 15381776
17. Rapid evolution in a pair of recent duplicate segments of rice. H Jiang D Liu Z Gu W Wang, Journal of experimental zoology Part B 2007 308 1 50 57 10.1002/jez.b.21122 (Pubitemid 46302790)
18. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. Rice Chromosomes 11 and 12 Sequencing Consortia, BMC biology 2005 3 20 10.1186/1741-7007-3-20 16188032
19. How did Saccharomyces evolve to become a good brewer? J Piskur E Rozpedowska S Polakova A Merico C Compagno, Trends Genet 2006 22 4 183 186 10.1016/j.tig.2006.02.002 16499989
20. Relaxation of yeast mitochondrial functions after whole-genome duplication. H Jiang W Guan D Pinney W Wang Z Gu, Genome Res 2008 18 9 1466 1471 10.1101/gr.074674.107 18669479
21. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. J Zhang YP Zhang HF Rosenberg, Nature genetics 2002 30 4 411 415 10.1038/ng852 11925567
22. Synonymous codon usage variation among Giardia lamblia genes and isolates. B Lafay PM Sharp, Molecular biology and evolution 1999 16 11 1484 1495 10555279
23. Frequency of variant antigens in Giardia lamblia. TE Nash SM Banks DW Alling JW Merritt Jr JT Conrad, Exp Parasitol 1990 71 4 415 421 10.1016/0014-4894(90)90067-M 1699782
24. Variant-specific surface proteins of Giardia lamblia are zinc-binding proteins. TE Nash MR Mowatt, Proceedings of the National Academy of Sciences of the United States of America 1993 90 12 5489 5493 10.1073/pnas.90.12.5489 8516291
25. Antigenic variation in Giardia lamblia is regulated by RNA interference. CG Prucca I Slavin R Quiroga EV Elias FD Rivero A Saura PG Carranza HD Lujan, Nature 2008 456 7223 750 754 10.1038/nature07585 19079052
26. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694
27. Integrating robust clustering techniques in S-PLUS. A Struyf M Hubert PJ Rousseeuw, Computational Statistics & Data Analysis 1997 26 1 17 37
28. Selectionism and neutralism in molecular evolution. M Nei, Molecular biology and evolution 2005 22 12 2318 2342 10.1093/molbev/msi242 16120807
29. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Z Yang R Nielsen, Molecular biology and evolution 2000 17 1 32 43 10666704
30. An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids Res 2002 30 7 1575 1584 10.1093/nar/30.7.1575 11917018
31. Cell and molecular biology: concepts and experiments. G Karp Pvd Geer, Hoboken, NJ: John Wiley 4 2005
32. The cytoskeleton of Giardia lamblia. HG Elmendorf SC Dawson JM McCaffery, International journal for parasitology 2003 33 1 3 28 10.1016/S0020-7519(02) 00228-X 12547343
33. Dynamic evolution of the innate immune system in Drosophila. TB Sackton BP Lazzaro TA Schlenke JD Evans D Hultmark AG Clark, Nature genetics 2007 39 12 1461 1468 10.1038/ng.2007.60 17987029
34. Gene map of the extended human MHC. R Horton L Wilming V Rand RC Lovering EA Bruford VK Khodiyar MJ Lush S Povey CC Talbot Jr MW Wright, et al. Nature reviews 2004 5 12 889 899 10.1038/nrg1489 15573121
35. Protein kinase R reveals an evolutionary model for defeating viral mimicry. NC Elde SJ Child AP Geballe HS Malik, Nature 2009 457 7228 485 489 10.1038/nature07529 19043403
36. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. M Remm CE Storm EL Sonnhammer, J Mol Biol 2001 314 5 1041 1052 10.1006/jmbi.2000.5197 11743721
37. Molecular evolution. W-H Li, Sunderland, Mass.: Sinauer Associates 1997
38. The evolutionary fate and consequences of duplicate genes. M Lynch JS Conery, Science (New York, NY) 2000 290 5494 1151 1155
39. Resolution of the early placental mammal radiation using Bayesian phylogenetics. WJ Murphy E Eizirik SJ O'Brien O Madsen M Scally CJ Douady E Teeling OA Ryder MJ Stanhope WW de Jong, et al. Science (New York, NY) 2001 294 5550 2348 2351 (Pubitemid 33140557)
40. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. JO Andersson AM Sjogren DS Horner CA Murphy PL Dyal SG Svard JM Logsdon Jr MA Ragan RP Hirt AJ Roger, BMC Genomics 2007 8 51 10.1186/1471-2164-8-51 17298675
41. Genome analysis of the platypus reveals unique signatures of evolution. WC Warren LW Hillier JA Marshall Graves E Birney CP Ponting F Grutzner K Belov W Miller L Clarke AT Chinwalla, et al. Nature 2008 453 7192 175 183 10.1038/nature06936 18464734
42. Comparative genomics of the eukaryotes. GM Rubin MD Yandell JR Wortman GL Gabor Miklos CR Nelson IK Hariharan ME Fortini PW Li R Apweiler W Fleischmann, et al. Science (New York, NY) 2000 287 5461 2204 2215
43. Evidence for karyogamy and exchange of genetic material in the binucleate intestinal parasite Giardia intestinalis. MK Poxleitner ML Carpenter JJ Mancuso CJ Wang SC Dawson WZ Cande, Science (New York, NY) 2008 319 5869 1530 1533
44. Antigenic variation in Giardia lamblia and the host's immune response. TE Nash, Philos Trans R Soc Lond B Biol Sci 1997 352 1359 1369 1375 10.1098/rstb.1997.0122 9355129
45. Biological selection of variant-specific surface proteins in Giardia lamblia. SM Singer HG Elmendorf JT Conrad TE Nash, J Infect Dis 2001 183 1 119 124 10.1086/317659 11087204
46. Epigenetic mechanisms are involved in the control of Giardia lamblia antigenic variation. L Kulakova SM Singer J Conrad TE Nash, Mol Microbiol 2006 61 6 1533 1542 10.1111/j.1365-2958.2006.05345.x 16968226
47. GiardiaDB database. http://www.giardiadb.org/giardiadb/
48. The National Center for Biotechnology Information. http://www.ncbi.nlm. nih.gov/
49. Ensembl. http://www.ensembl.org/index.html
50. Biological sequence analysis: probabilistic models of proteins and nucleic acids. R Durbin, Cambridge, U.K. New York: Cambridge University Press 1998
51. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Research 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147
52. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 10.1093/nar/22.22.4673 7984417