Comparative genomic analysis of simple sequence repeats in three Plasmodium species

Parasitology Research

Volumn 108, Issue 2, 2011, Pages 451-458

  Tyagi, Suchi ^a   Sharma, Meenu ^a   Das, Aparup ^a  

^a NATIONAL INSTITUTE OF MALARIA RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; GENOME SIZE; NONHUMAN; PLASMODIUM; PLASMODIUM FALCIPARUM; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; POPULATION ABUNDANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; RELATIVE DENSITY; SIMPLE SEQUENCE REPEAT; STRUCTURE ANALYSIS;

ANIMALS; CHROMOSOME MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; GENES, PROTOZOAN; GENOMICS; MINISATELLITE REPEATS; PLASMODIUM FALCIPARUM; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; SPECIES SPECIFICITY;

PLASMODIUM FALCIPARUM; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; TETRA;

EID: 79951770203     PISSN: 09320113     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00436-010-2086-5     Document Type: Article

References (64)

1. Bell GI, Jurka J (1997) The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process. J Mol Evol 44:414-421 (Pubitemid 27161338)
2. Cambareri EB, Jensen BC, Schabtach E, Selker EU (1989) Repeat-induced GC to AT mutations in Neurospora. Science 244:1571-1575
3. Carlton JM, Adams JH, Silva JC et al (2008) Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455:757-763
4. Caserta M, Verdone L (2002) Aspects of nucleosomal positional flexibility and fluidity. Chem Bio Chem 3:1172-1182 (Pubitemid 36005309)
5. Chernin J (2000) Parasite examples grouped according to life cycle. In: Wrigglesworth J (ed) Parasitology. CRC Press, London, p 51
6. Dieringer D, Schlotterer C (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 13:2242-2251
7. Durand PM, Oelofse AJ, Coetzer TL (2006) An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome. BMC Genomics 7:282
8. Ellegren H (2000a) Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24:400-402
9. Ellegren H (2000b) Microsatellite evolution: a battle between replication slippage and point mutation. Trends Genet 18:70
10. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435-445
11. Escalante AA, Ayala FJ (1994) Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. Proc Natl Acad Sci U S A 91:11373-11377 (Pubitemid 24356346)
12. Field D, Wills C (1998) Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc Natl Acad Sci U S A 95:1647-1652
13. Fondon JW, Garner HR (2004) Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci U S A 101:18058-18063
14. Galinski MR, Barnwell JW (2009) Monkey malaria kills four humans. Trends Parasitol 25:200-204
15. Gardner MJ, Hall N, Fung E et al (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498-511
16. Garnica DP, Pinzón AM, Quesada-Ocampo LM, Bernal AJ, Barreto E, Grünwald NJ, Restrepo S (2006) Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus. BMC Genomics 7:245
17. Grayburn WS, Selker EU (1989) A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication. Mol Cell Biol 9:4416-4421 (Pubitemid 19239610)
18. Guo X, Mrazek J (2008) Long simple sequence repeats in hostadapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes. J Mol Evol 67:497-509
19. Gupta A, Mehra P, Nitharwal R, Sharma A, Biswas AK, Dhar SK (2006) Analogous expression pattern of Plasmodium falciparum replication initiation proteins PfMCM4 and PfORC1 during the asexual and sexual stages of intraerythrocytic developmental cycle. FEMS Microbiol Lett 26:12-18 (Pubitemid 43999694)
20. Gur-Arie R, Cohen CJ, Eitan Y, Shelef L, Hallerman EM, Kashi Y (2000) Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res 10:62-71 (Pubitemid 30095256)
21. Hall DB, Holmlin RE, Barton JK (1996) Oxidative DNA damage through long-range electron transfer. Nature 382:731-735 (Pubitemid 26282182)
22. Hancock JM (1993) Evolution of sequences repetition and gene duplication in the TATA-binding protein TBP (TFIID). Nucleic Acids Res 21:2823-2830
23. Hancock JM (1996) Simple sequences and the expanding genome. BioEssays 18:421-425
24. Hancock JM (1999) Microsatellites and other simple sequences: genomic context and mutational mechanism. In: Goldstein DB, Schlotterer C (eds) Microsatellites: evolution and applications. Oxford University Press, Oxford, pp 1-7
25. Hefferon TW (2004) A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing. Proc Natl Acad Sci U S A 101:3504-3509
26. Hurst GDD, Werren JH (2001) The role of selfish genetic element in eukaryotic evolution. Nat Rev Genet 2:597-606 (Pubitemid 33674783)
27. Jayashree B, Punna P, Prasad P, Bantte K, Tom HC, Chandra S, Hoisington DA, Varshney RK (2006) A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation. In Silico Biol 6:607-620 (Pubitemid 47028649)
28. Jongwutiwes S, Putaporntip C, Iwasaki T, Sata T, Kanbara H (2004) Naturally acquired Plasmodium knowlesi malaria in human, Thailand. Emerg Infect Dis 10:2211-2213 (Pubitemid 39587350)
29. Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501-510 (Pubitemid 34415968)
30. Karaoglu H, Lee CMY, Meyer W (2005) Survey of simple sequence repeats in completed fungal genomes. Mol Biol Evol 22:639-649 (Pubitemid 40299513)
31. Kashi Y, King DG (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253-259
32. Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161-1167 (Pubitemid 32660663)
33. Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD (2008) The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 18:30-38
34. Kim TS, Booth JG, Gauch HG, Sun Q, Park J, Lee YH, Lee K (2008) Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inferences. BMC Genomics 9:31
35. King DG, Soller M, Kashi Y (1997) Evolutionary tuning knobs. Endeavour 21:36-40 (Pubitemid 27191080)
36. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci U S A 95:10774-10778 (Pubitemid 28413144)
37. Kuhlmann M, Borisova BE, Kaller M, Larsson P, Stach D, Na J, Eichinger L, Lyko F, Ambros V, Söderbom F, Hammann C, Nellen W (2005) Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Res 33:6405-6417 (Pubitemid 41742577)
38. Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985-998
39. Lai Y, Sun F (2003) The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol Biol Evol 20:2123-2131 (Pubitemid 38057776)
40. Li YC, Korol AB, Fahima T, Nevo E (2004)Microsatellites within genes: structure, function and evolution. Mol Biol Evol 21:991-1007 (Pubitemid 38658207)
41. Loire E, Praz F, Higuet D, Netter P, Achaz G (2009) Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR. Mol Biol Evol 26:111-121
42. Martinsen ES, Perkins SL, Schall JJ (2008) A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches. Mol Phylogenet Evol 47:261-273
43. Messier M, Li SH, Stewart CB (1996) The birth of microsatellites. Nature 381:483
44. Moran NA, McLaughlin HJ, Sorek R (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379-381
45. Moxon ER, Rainey PB,Nowak MA, Lenski RE (1994)Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 4:24-33
46. Pain A, Bohme U, Berry AE et al (2008) The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature 455:799-804
47. Perkins SL, Schall J (2002) A molecular phylogeny of malarial parasites recovered fromcytochrome b gene sequences. J Parasitol 88:972-978 (Pubitemid 35278746)
48. Phimpraphi W, Paul RE, Yimsamran S et al (2008) Longitudinal study of Plasmodium falciparum and Plasmodium vivax in a Karen population in Thailand. Malar J 7:99
49. Prasad MD, Muthulakshmi M, Madhu M, Archak S, Mita K, Nagaraju J (2005) Survey and analysis of microsatellites in the Silkworm, Bombyx mori: frequency, distribution, mutations, marker potential and their conservation in heterologous species. Genetics 169:197-214 (Pubitemid 40239164)
50. Pupko T, Graur D (1999) Evolution of microsatellites in the yeast Sacchaomyces cerevisiae: role of length and number of repeated units. J Mol Evol 48:313-316 (Pubitemid 29116076)
51. Richard GF, Dujon B (1997) Trinucleotide repeats in yeast. Res Microbiol 148:731-744
52. Sattabongkot J, Tsuboi T, Zollner GE, Sirichaisinthop J, Cui L (2004) Plasmodium vivax transmission: chances for control? Trends Parasitol 20:192-198
53. Schunk M, Kumma WP, Miranda IB, Osman ME, Roewer S, Alano A, Löscher T, Bienzle U, Mockenhaupt FP (2006) High prevalence of drug-resistance mutations in Plasmodium falciparum and Plasmodium vivax in southern Ethiopia. Malar J 5:54
54. Sen D, Gilbert W (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334:364-366
55. Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotech 25:490-498 (Pubitemid 350019510)
56. Singh B, Lee KS, Matusop A, Radhakrishnan A, Shamsul SSG, Cox- Singh J, Thomas A, Conway DJ (2004) A large focus of naturally acquired Plasmodium knowlesi infections in human beings. Lancet 363:1017-1024 (Pubitemid 38410774)
57. Singh V, Mishra N, Awasthi G, Dash AP, Das A (2009) Why is it important to study malaria epidemiology in India? Trends Parasitol 25:452-457
58. Su X, Carlton JM (2000) Genome display and typing of Plasmodium parasites using anchored polyA and polyT oligonucleotides. Exp Parasitol 94:273-278 (Pubitemid 30396155)
59. Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4:R13
60. Suter B, Schnappauf G, Thoma F (2002) Poly (dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promotors in vivo. Nucleic Acids Res 28:4083-4089
61. van Belkum A (1999) Short sequence repeats in microbial pathogenesis and evolution. Cell Mol Life Sci 56:729-734
62. van der Wel AM, Tomas AM, Kocken CHM, Malhotra P, Jase CJ (1997) Transfection of the primate malaria parasite Plasmodium knowlesi using entirely heterologous constructs. J Exp Med 85:1499-1503 (Pubitemid 27187607)
63. Volkman SK, Lozovsky E, Barry AE, Bedford T, Bethke L, Myrick A, Day KP, Hartl DL, Wirth DF, Sawyer SA (2007) Genomic heterogeneity in the density of non coding single nucleotide and microsatellite polymorphisms in Plasmodium falciparum. Gene 387:1-6 (Pubitemid 44959556)
64. Zhu HM, Li J, Zheng H (2006) Human natural infection of Plasmodium knowlesi. Chinese J parasitol parasitic diseases 24:70-71