Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoni

International Journal for Parasitology

Volumn 40, Issue 6, 2010, Pages 743-749

  Venancio, Thiago M ^a,c   Wilson, R Alan ^b   Verjovski Almeida, Sergio ^a   DeMarco, Ricardo ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b UNIVERSITY OF YORK   (United Kingdom)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Genome; Retrotransposons; Schistosoma japonicum; Schistosoma mansoni

Indexed keywords

DNA; FLATWORM; GENOME; PARASITE; SCHISTOSOMIASIS; SPECIATION (BIOLOGY);

AFRICA; ARTICLE; ASIA; CLADISTICS; CONTROLLED STUDY; EVOLUTION; EVOLUTIONARY ADAPTATION; GENETIC CONSERVATION; HYPOTHESIS; LONG TERMINAL REPEAT; NONHUMAN; PARASITE MIGRATION; RETROPOSON; SCHISTOSOMA JAPONICUM; SCHISTOSOMA MANSONI; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; TRANSPOSON;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA, HELMINTH; EVOLUTION, MOLECULAR; GENOMICS; PHYLOGENY; RECOMBINATION, GENETIC; RETROELEMENTS; SCHISTOSOMA JAPONICUM; SCHISTOSOMA MANSONI; SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINAL REPEAT SEQUENCES;

SCHISTOSOMA; SCHISTOSOMA JAPONICUM; SCHISTOSOMA MANSONI; SCHISTOSOMATIDAE; VERTEBRATA;

EID: 77951297976     PISSN: 00207519     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijpara.2009.11.013     Document Type: Article

References (30)

1. Arkhipova I.R., Pyatkov K.I., Meselson M., Evgen'ev M.B. Retroelements containing introns in diverse invertebrate taxa. Nat. Genet. 2003, 33:123-124.
2. Berriman M., Haas B.J., LoVerde P.T., Wilson R.A., Dillon G.P., Cerqueira G.C., Mashiyama S.T., Al-Lazikani B., Andrade L.F., Ashton P.D., Aslett M.A., Bartholomeu D.C., Blandin G., Caffrey C.R., Coghlan A., Coulson R., Day T.A., Delcher A., DeMarco R., Djikeng A., Eyre T., Gamble J.A., Ghedin E., Gu Y., Hertz-Fowler C., Hirai H., Hirai Y., Houston R., Ivens A., Johnston D.A., Lacerda D., Macedo C.D., McVeigh P., Ning Z., Oliveira G., Overington J.P., Parkhill J., Pertea M., Pierce R.J., Protasio A.V., Quail M.A., Rajandream M.A., Rogers J., Sajid M., Salzberg S.L., Stanke M., Tivey A.R., White O., Williams D.L., Wortman J., Wu W., Zamanian M., Zerlotini A., Fraser-Liggett C.M., Barrell B.G., El-Sayed N.M. The genome of the blood fluke Schistosoma mansoni. Nature 2009, 460:352-358.
3. Betran E., Long M. Expansion of genome coding regions by acquisition of new genes. Genetica 2002, 115:65-80.
4. Biedler J., Tu Z. Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity. Mol. Biol. Evol. 2003, 20:1811-1825.
5. Biemont C., Vieira C. Genetics: junk DNA as an evolutionary force. Nature 2006, 443:521-524.
6. Brindley P.J., Laha T., McManus D.P., Loukas A. Mobile genetic elements colonizing the genomes of metazoan parasites. Trends Parasitol. 2003, 19:79-87.
7. DeMarco R., Kowaltowski A.T., Machado A.A., Soares M.B., Gargioni C., Kawano T., Rodrigues V., Madeira A.M.B.N., Wilson R.A., Menck C.F.M., Setubal J.C., Dias-Neto E., Leite L.C.C., Verjovski-Almeida S. Saci-1, -2 and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. J. Virol. 2004, 78:2967-2978.
8. DeMarco R., Machado A.A., Bisson-Filho A.W., Verjovski-Almeida S. Identification of 18 new transcribed retrotransposons in Schistosoma mansoni. Biochem. Biophys. Res. Commun. 2005, 333:230-240.
9. Drew A.C., Brindley P.J. A retrotransposon of the non-long terminal repeat class from the human blood fluke Schistosoma mansoni. Similarities to the chicken-repeat-1-like elements of vertebrates. Mol. Biol. Evol. 1997, 14:602-610.
10. Drew A.C., Minchella D.J., King L.T., Rollinson D., Brindley P.J. SR2 elements, non-long terminal repeat retrotransposons of the RTE-1 lineage from the human blood fluke Schistosoma mansoni. Mol. Biol. Evol. 1999, 16:1256-1269.
11. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
12. Goodier J.L., Kazazian H.H. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 2008, 135:23-35.
13. Kazazian H.H. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
14. Kryazhimskiy S., Tkacik G., Plotkin J.B. The dynamics of adaptation on correlated fitness landscapes. Proc. Natl. Acad. Sci. USA 2009, 106:18638-18643.
15. Laha T., Loukas A., Verity C.K., McManus D.P., Brindley P.J. Gulliver, a long terminal repeat retrotransposon from the genome of the oriental blood fluke Schistosoma japonicum. Gene 2001, 264:59-68.
16. Laha T., Brindley P.J., Smout M.J., Verity C.K., McManus D.P., Loukas A. Reverse transcriptase activity and untranslated region sharing of a new RTE-like, non-long terminal repeat retrotransposon from the human blood fluke, Schistosoma japonicum. Int. J. Parasitol. 2002, 32:1163-1174.
17. Laha T., Brindley P.J., Verity C.K., McManus D.P., Loukas A. Pido, a non-long terminal repeat retrotransposon of the chicken repeat 1 family from the genome of the Oriental blood fluke, Schistosoma japonicum. Gene 2002, 284:149-159.
18. Laha T., Loukas A., Smyth D.J., Copeland C.S., Brindley P.J. The fugitive LTR retrotransposon from the genome of the human blood fluke, Schistosoma mansoni. Int. J. Parasitol. 2004, 34:1365-1375.
19. Laha T., Kewgrai N., Loukas A., Brindley P.J. Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni. BMC Genomics 2005, 6:154.
20. Liu F., Zhou Y., Wang Z.Q., Lu G., Zheng H., Brindley P.J., McManus D.P., Blair D., Zhang Q.H., Zhong Y., Wang S., Han Z.G., Chen Z. The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature 2009, 460:345-351.
21. Lockyer A.E., Olson P.D., Ostergaard P., Rollinson D., Johnston D.A., Attwood S.W., Southgate V.R., Horak P., Snyder S.D., Le T.H., Agatsuma T., McManus D.P., Carmichael A.C., Naem S., Littlewood D.T. The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858. Parasitology 2003, 126:203-224.
22. Malik H.S., Burke W.D., Eickbush T.H. The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol. 1999, 16:793-805.
23. McFadden J., Knowles G. Escape from evolutionary stasis by transposon-mediated deleterious mutations. J. Theor. Biol. 1997, 186:441-447.
24. Morgan J.A., Dejong R.J., Adeoye G.O., Ansa E.D., Barbosa C.S., Bremond P., Cesari I.M., Charbonnel N., Correa L.R., Coulibaly G., D'Andrea P.S., De Souza C.P., Doenhoff M.J., File S., Idris M.A., Incani R.N., Jarne P., Karanja D.M., Kazibwe F., Kpikpi J., Lwambo N.J., Mabaye A., Magalhaes L.A., Makundi A., Mone H., Mouahid G., Muchemi G.M., Mungai B.N., Sene M., Southgate V., Tchuente L.A., Theron A., Yousif F., Zanotti-Magalhaes E.M., Mkoji G.M., Loker E.S. Origin and diversification of the human parasite Schistosoma mansoni. Mol. Ecol. 2005, 14:3889-3902.
25. Oliver K.R., Greene W.K. Transposable elements: powerful facilitators of evolution. BioEssays 2009, 31:703-714.
26. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 1988, 85:2444-2448.
27. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
28. SanMiguel P., Gaut B.S., Tikhonov A., Nakajima Y., Bennetzen J.L. The paleontology of intergene retrotransposons of maize. Nat Genet 1998, 20:43-45.
29. Tajima F., Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 1984, 1:269-285.
30. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.