Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Lorenzi, Hernan ^a   Thiagarajan, Mathangi ^a   Haas, Brian ^b   Wortman, Jennifer ^c   Hall, Neil ^d   Caler, Elisabet ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

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

^d UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOMAL INSTABILITY; CONTROLLED STUDY; DNA STRUCTURE; ENTAMOEBA; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ENTAMOEBA INVADENS; ENTAMOEBA REPETITIVE ELEMENT 1; ENTAMOEBA REPETITIVE ELEMENT 2; EVOLUTIONARY ADAPTATION; GENE CLUSTER; GENE IDENTIFICATION; GENE MAPPING; GENE REARRANGEMENT; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES COMPARISON; SPECIES DIVERSITY; TRANSPOSON; ANIMAL; DNA SEQUENCE; EVOLUTION; GENETICS; LONG INTERSPERSED REPEAT; RETROPOSON; SHORT INTERSPERSED REPEAT;

ENTAMOEBA; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ENTAMOEBA INVADENS;

DNA BINDING PROTEIN; MARINER TRANSPOSASES; PROTOZOAL DNA; TRANSPOSASE;

ANIMALS; DNA, PROTOZOAN; DNA-BINDING PROTEINS; ENTAMOEBA; ENTAMOEBA HISTOLYTICA; EVOLUTION; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; REPETITIVE SEQUENCES, NUCLEIC ACID; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; TRANSPOSASES;

EID: 63149156216     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-595     Document Type: Article

References (36)

1. Que X Reed SL Cysteine proteinases and the pathogenesis of amebiasis Clin Microbiol Rev 2000, 13(2):196-206. 100150 10755997
2. Bakre AA Rawal K Ramaswamy R Bhattacharya A Bhattacharya S The LINEs and SINEs of Entamoeba histolytica: Comparative analysis and genomic distribution Exp Parasitol 2005, 110(3):207-213. 15955314
3. Pritham EJ Feschotte C Wessler SR Unexpected diversity and differential success of DNA transposons in four species of entamoeba protozoans Mol Biol Evol 2005, 22(9):1751-1763. 15901838
4. Sharma R Bagchi A Bhattacharya A Bhattacharya S Characterization of a retrotransposon-like element from Entamoeba histolytica Mol Biochem Parasitol 2001, 116(1):45-53. 11463465
5. Shire AM Ackers JP SINE elements of Entamoeba dispar Mol Biochem Parasitol 2007, 152(1):47-52. 17178164
6. Deininger PL Moran JV Batzer MA Kazazian HH Jr Mobile elements and mammalian genome evolution Curr Opin Genet Dev 2003, 13(6):651-658. 14638329
7. Hedges DJ Deininger PL Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity Mutat Res 2007, 616(1-2):46-59. 1850990 17157332
8. Slotkin RK Martienssen R Transposable elements and the epigenetic regulation of the genome Nat Rev Genet 2007, 8(4):272-285. 17363976
9. Bertone P Trifonov V Rozowsky JS Schubert F Emanuelsson O Karro J Kao MY Snyder M Gerstein M Design optimization methods for genomic DNA tiling arrays Genome Res 2006, 16(2):271-281. 1361723 16365382
10. Singer MF Highly repeated sequences in mammalian genomes Int Rev Cytol 1982, 76:67-112. 6749748
11. Weiner AM SINEs and LINEs: The art of biting the hand that feeds you Curr Opin Cell Biol 2002. 14(3):343-350. 12067657
12. Loftus B Anderson I Davies R Alsmark UC Samuelson J Amedeo P Roncaglia P Berriman M Hirt RP Mann BJ The genome of the protist parasite Entamoeba histolytica Nature 2005, 433(7028):865-868. 15729342
13. Jurka J Kapitonov VV Pavlicek A Klonowski P Kohany O Walichiewicz J Repbase Update, a database of eukaryotic repetitive elements Cytogenet Genome Res 2005, 110(1-4):462-467. 16093699
14. Price AL Jones NC Pevzner PA De novo identification of repeat families in large genomes Bioinformatics (Oxford, England) 2005, 21(Suppl 1):i351-358. 15961478
15. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680. 308517 7984417
16. Ochman H Distinguishing the ORFs from the ELFs: Short bacterial genes and the annotation of genomes Trends Genet 2002. 18(7):335-337. 12127765
17. Nekrutenko A Makova KD Li WH The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study Genome research 2002, 12(1):198-202. 155263 11779845
18. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic acids research 2004, 32(5):1792-1797. 390337 15034147
19. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13(5):555-556. 9367129
20. Yang Z Nielsen R Goldman N Pedersen AM Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 2000, 155(1):431-449. 1461088 10790415
21. Schwartz S Zhang Z Frazer KA Smit A Riemer C Bouck J Gibbs R Hardison R Miller W PipMaker-a web server for aligning two genomic DNA sequences Genome Res 2000, 10(4):577-586. 310868 10779500
22. Sonnhammer EL Durbin R A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis Gene 1995, 167(1-2):GC1-10. 8566757
23. Neuveglise C Chalvet F Wincker P Gaillardin C Casaregola S Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings Eukaryot Cell 2005, 4(3):615-624. 1087794 15755923
24. Hamann A Feller F Osiewacz HD The degenerate DNA transposon Pat and repeat-induced point mutation (RIP) in Podospora anserina Mol Gen Genet 2000, 263(6):1061-1069. 10954093
25. Ferris PJ Characterization of a Chlamydomonas transposon, Gulliver, resembling those in higher plants Genetics 1989, 122(2):363-377. 1203708 2570007
26. Hacker J Hentschel U Dobrindt U Prokaryotic chromosomes and disease Science (New York, NY) 2003, 301(5634):790-793. 12907788
27. Bentley SD Vernikos GS Snyder LA Churcher C Arrowsmith C Chillingworth T Cronin A Davis PH Holroyd NE Jagels K Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18 PLoS genetics 2007, 3(2):e23. 1797815 17305430
28. Davis PH Zhang Z Chen M Zhang X Chakraborty S Stanley SL Jr Identification of a family of BspA like surface proteins of Entamoeba histolytica with novel leucine rich repeats Mol Biochem Parasitol 2006, 145(1):111-116. 1382194 16199101
29. Biessmann H Kasravi B Bui T Fujiwara G Champion LE Mason JM Comparison of two active HeT-A retroposons of Drosophila melanogaster Chromosoma 1994, 103(2):90-98. 8055715
30. Jensen S Cavarec L Dhellin O Heidmann T Retrotransposition of a marked Drosophila line-like I element in cells in culture Nucleic Acids Res 1994, 22(8):1484-1488. 308009 8190641
31. Haas BJ Delcher AL Mount SM Wortman JR Smith RK Jr Hannick LI Maiti R Ronning CM Rusch DB Town CD Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res 2003, 31(19):5654-5666. 206470 14500829
32. Stanley SL Jr Amoebiasis Lancet 2003, 361(9362):1025-1034. 12660071
33. Haque R Mondal D Duggal P Kabir M Roy S Farr BM Sack RB Petri WA Jr Entamoeba histolytica infection in children and protection from subsequent amebiasis Infect Immun 2006, 74(2):904-909. 1360358 16428733
34. Ali IK Clark CG Petri WA Jr Molecular epidemiology of amebiasis Infect Genet Evol 2008, 8(5):698-707. 18571478
35. Ali IK Mondal U Roy S Haque R Petri WA Jr Clark CG Evidence for a link between parasite genotype and outcome of infection with Entamoeba histolytica Journal of clinical microbiology 2007, 45(2):285-289. 1829016 17122021
36. Mukherjee C Clark CG Lohia A Entamoeba Shows Reversible Variation in Ploidy under Different Growth Conditions and between Life Cycle Phases PLoS neglected tropical diseases 2008, 2(8):e281. 2500184 18714361