Evidence of multiple retrotransposons in two litopenaeid species

Animal Genetics

Volumn 39, Issue 4, 2008, Pages 363-373

  Hizer, S E ^a   Tamulis, W G ^a   Robertson, L M ^a   Garcia, D K ^a  

^a CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

Litopenaeus; Phylogeny; Retrotransposon; RTE; Shrimp

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; EXPRESSED SEQUENCE TAG; GENETICS; GENOME; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PENAEIDAE; PHYLOGENY; POLYMERASE CHAIN REACTION; RETROPOSON; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENOME; MOLECULAR SEQUENCE DATA; PENAEIDAE; PHYLOGENY; POLYMERASE CHAIN REACTION; RETROELEMENTS; RNA-DIRECTED DNA POLYMERASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TERMINAL REPEAT SEQUENCES;

DECAPODA (CRUSTACEA); EUKARYOTA; LITOPENAEUS; LITOPENAEUS STYLIROSTRIS; LITOPENAEUS VANNAMEI; PENAEUS MONODON; PENELOPE;

EID: 47349101913     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2008.01739.x     Document Type: Article

References (62)

1. Alcivar-Warren A., Meehan-Meola D., Wang Y. et al. (2006) Isolation and mapping of telomeric pentanucleotide (TAACC)n repeats of the Pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization. Marine Biotechnology (New York, NY) 8, 467 80.
2. Arkhipova I.R., Pyatkov K.I., Meselson M. Evgen'ev M.B. (2003) Retroelements containing introns in diverse invertebrate taxa. Nature Genetics 33, 123 4.
3. Barbot W., Dupressoir A., Lazar V. Heidmann T. (2002) Epigenetic regulation of an IAP retrotransposon in the aging mouse: progressive demethylation and de-silencing of the element by its repetitive induction. Nucleic Acids Research 30, 2365 73.
4. Belancio V.P., Hedges D.J. Deininger P. (2006) LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Research 34, 1512 21.
5. Burke W.D., Malik H.S., Jones J.P. Eickbush T.H. (1999) The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Molecular Biology and Evolution 16, 502 11.
6. Craig N.L. (2002) Mobile DNA: An Introduction. In : Mobile DNA II (Ed. by N.L. Craig, R. Craigie, M. Gellert A.M. Lambowitz pp. 3 11. ASM Press, Washington, DC.
7. Cui L. Webb B.A. (1997) Homologous sequences in the Campoletis sonorensis polydnavirus genome are implicated in replication and nesting of the W segment family. Journal of Virology 71, 8504 13.
8. DeMarco R., Machado A.A., Bisson-Filho A.W. Verjovski-Almeida S. (2005) Identification of 18 new transcribed retrotransposons in Schistosoma mansoni. Biochemical and Biophysical Research Communications 333, 230 40.
9. Eickbush T.H. (1992) Transposing without ends: the non-LTR retrotransposable elements. The New Biologist 4, 430 40.
10. Eickbush T.H. (2002) R2 and Related Site-Specific Non-Long Terminal Repeat Retrotransposons. In : Mobile DNA II (Ed. by N.L. Craig, R. Craigie, M. Gellert A.M. Lambowitz pp. 813 35. ASM Press, Washington, DC.
11. Ejima Y. Yang L. (2003) Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Human Molecular Genetics 12, 1321 8.
12. Evgen'ev M.B. Arkhipova I.R. (2005) Penelope-like elements - a new class of retroelements: distribution, function and possible evolutionary significance. Cytogenetic and Genome Research 110, 510 21.
13. Felsenstein J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783 91.
14. Finnegan D.J. (1997) Transposable elements: how non-LTR retrotransposons do it. Current Biology 7, R245 8.
15. Furano A.V. (2000) The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Progress in Nucleic Acid Research and Molecular Biology 64, 255 94.
16. Gentles A.J., Kohany O. Jurka J. (2005) Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons. Molecular Biology and Evolution 22, 1983 91.
17. Glushkov S., Novikova O., Blinov A. Fet V. (2006) Divergent non-LTR retrotransposon lineages from the genomes of scorpions (Arachnida: Scorpiones). Molecular Genetics and Genomics 275, 288 96.
18. Gundersen-Rindal D.E. Lynn D.E. (2003) Polydnavirus integration in lepidopteran host cells in vitro. Journal of Insect Physiology 49, 453 62.
19. Han J.S. Boeke J.D. (2005) LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? Bioessays 27, 775 84.
20. Hizer S.E., Dhar A.K., Klimpel K.R. Garcia D.K. (2002) RAPD markers as predictors of infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance in shrimp (Litopenaeus stylirostris). Genome 45, 1 7.
21. Huang X. (1992) A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14, 18 25.
22. Iwashita S., Ueno S., Nakashima K. et al. (2006) A tandem gene duplication followed by recruitment of a retrotransposon created the paralogous bucentaur gene (bcntp97) in the ancestral ruminant. Molecular Biology and Evolution 23, 798 806.
23. Kim C., Rubin C.M. Schmid C.W. (2001) Genome-wide chromatin remodeling modulates the Alu heat shock response. Gene 276, 127 33.
24. Kimura R.H., Choudary P.V. Schmid C.W. (1999) Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Research 27, 3380 7.
25. Kimura R.H., Choudary P.V., Stone K.K. Schmid C.W. (2001) Stress induction of Bm1 RNA in silkworm larvae: SINEs, an unusual class of stress genes. Cell Stress Chaperones 6, 263 72.
26. Laha T., Brindley P.J., Smout M.J., Verity C.K., McManus D.P. Loukas A. (2002) Reverse transcriptase activity and untranslated region sharing of a new RTE-like, non-long terminal repeat retrotransposon from the human blood fluke, Schistosoma japonicum. International Journal for Parasitology 32, 1163 74.
27. Laha T., Kewgrai N., Loukas A. Brindley P.J. (2005) 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 6, 154.
28. Laha T., Kewgrai N., Loukas A. Brindley P.J. (2006) The dingo non-long terminal repeat retrotransposons from the genome of the hookworm, Ancylostoma caninum. Experimental Parasitology 113, 142 53.
29. Le Goff W., Guerin M., Chapman M.J. Thillet J. (2003) A CYP7A promoter binding factor site and Alu repeat in the distal promoter region are implicated in regulation of human CETP gene expression. Journal of Lipid Research 44, 902 10.
30. Lee J.T. (2003) X-chromosome inactivation: a multi-disciplinary approach. Seminars in Cell & Developmental Biology 14, 311 2.
31. Liu W.M., Chu W.M., Choudary P.V. Schmid C.W. (1995) Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Research 23, 1758 65.
32. Lyon M.F. (2003) The Lyon and the LINE hypothesis. Seminars in Cell & Developmental Biology 14, 313 8.
33. Lyozin G.T., Makarova K.S., Velikodvorskaja V.V., Zelentsova H.S., Khechumian R.R., Kidwell M.G., Koonin E.V. Evgen'ev M.B. (2001) The structure and evolution of Penelope in the virilis species group of Drosophila: an ancient lineage of retroelements. Journal of Molecular Evolution 52, 445 56.
34. Malik H.S. Eickbush T.H. (1998) The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Molecular Biology and Evolution 15, 1123 34.
35. Malik H.S., Burke W.D. Eickbush T.H. (1999) The age and evolution of non-LTR retrotransposable elements. Molecular Biology and Evolution 16, 793 805.
36. Matsumoto T., Takahashi H. Fujiwara H. (2004) Targeted nuclear import of open reading frame 1 protein is required for in vivo retrotransposition of a telomere-specific non-long terminal repeat retrotransposon, SART1. Molecular and Cellular Biology 24, 105 22.
37. McClintock B. (1984) The significance of responses of the genome to challenge. Science 226, 792 801.
38. Meehan D., Xu Z., Zuniga G. Alcivar-Warren A. (2003) High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda]. Marine Biotechnology (New York, NY) 5, 311 30.
39. Minchiotti G., Contursi C., Graziani F., Gargiulo G. Di Nocera P.P. (1994) Expression of Drosophila melanogaster F elements in vivo. Molecular and General Genetics 245, 152 9.
40. Morales J.F., Snow E.T. Murnane J.P. (2002) Environmental factors affecting transcription of the human L1 retrotransposon. I. Steroid hormone-like agents. Mutagenesis 17, 193 200.
41. Moran J.V., Holmes S.E., Naas T.P., DeBerardinis R.J., Boeke J.D. Kazazian H.H., Jr. (1996) High frequency retrotransposition in cultured mammalian cells. Cell 87, 917 27.
42. Morrish T.A., Gilbert N., Myers J.S., Vincent B.J., Stamato T.D., Taccioli G.E., Batzer M.A. Moran J.V. (2002) DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nature Genetics 31, 159 65.
43. Morse B., Rotherg P.G., South V.J., Spandorfer J.M. Astrin S.M. (1988) Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature 333, 87 90.
44. Naas T.P., DeBerardinis R.J., Moran J.V., Ostertag E.M., Kingsmore S.F., Seldin M.F., Hayashizaki Y., Martin S.L. Kazazian H.H. (1998) An actively retrotransposing, novel subfamily of mouse L1 elements. The EMBO Journal 17, 590 7.
45. Neidhart M., Rethage J., Kuchen S., Kunzler P., Crowl R.M., Billingham M.E., Gay R.E. Gay S. (2000) Retrotransposable L1 elements expressed in rheumatoid arthritis synovial tissue: association with genomic DNA hypomethylation and influence on gene expression. Arthritis and Rheumatism 43, 2634 47.
46. Parish D.A., Vise P., Wichman H.A., Bull J.J. Baker R.J. (2002) Distribution of LINEs and other repetitive elements in the karyotype of the bat Carollia: implications for X-chromosome inactivation. Cytogenetic and Genome Research 96, 191 7.
47. Pyatkov K.I., Shostak N.G., Zelentsova E.S., Lyozin G.T., Melekhin M.I., Finnegan D.J., Kidwell M.G. Evgen'ev M.B. (2002) Penelope retroelements from Drosophila virilis are active after transformation of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 99, 16150 5.
48. Pyatkov K.I., Arkhipova I.R., Malkova N.V., Finnegan D.J. Evgen'ev M.B. (2004) Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proceedings of the National Academy of Sciences of the United States of America 101, 14719 24.
49. Ring M., Pfeifer T.A. Grigliatti T.A. (1996) Identification of a 5′ Truncated Non-LTR Retrotransposon, YAKPsl, from the Variegated Cutworm, Peridroma saucia, Using PCR. Insect Biochemistry and Molecular Biology 26, 511 8.
50. Saitou N. Nei M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406 25.
51. Saxton J.A. Martin S.L. (1998) Recombination between subtypes creates a mosaic lineage of LINE-1 that is expressed and actively retrotransposing in the mouse genome. Journal of Molecular Biology 280, 611 22.
52. Soifer H.S. Kasahara N. (2004) Retrotransposon-adenovirus hybrid vectors: efficient delivery and stable integration of transgenes via a two-stage mechanism. Current Gene Therapy 4, 373 84.
53. Tamura K., Dudley J., Nei M. Kumar S. (2007) mega4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution 24, 1596 9.
54. Tang K.F. Lightner D.V. (2006) Infectious hypodermal and hematopoietic necrosis virus (IHHNV)-related sequences in the genome of the black tiger prawn Penaeus monodon from Africa and Australia. Virus Research 118, 185 91.
55. Teng S.C., Kim B. Gabriel A. (1996) Retrotransposon reverse- transcriptase-mediated repair of chromosomal breaks. Nature 383, 641 4.
56. Thompson J.D., Higgins D.G. Gibson T.J. (1994) clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673 80.
57. de la Vega E., Degnan B.M., Hall M.R. Wilson K.J. (2007a) Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors. Fish & Shellfish Immunology 23, 1072 88.
58. de la Vega E., Hall M.R., Wilson K.J., Reverter A., Woods R.G. Degnan B.M. (2007b) Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon. Physiological Genomics 31, 126 38.
59. Volff J.N., Hornung U. Schartl M. (2001) Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements. Molecular Genetics and Genomics 265, 711 20.
60. White L.D. Jacobson J.W. (1996) Insertion of the retroposable element, jockey, near the Adh gene of Drosophila melanogaster is associated with altered gene expression. Genetical Research 68, 203 9.
61. Xu Z., Dhar A.K., Wyrzykowski J. Alcivar-Warren A. (1999) Identification of abundant and informative microsatellites from shrimp (Penaeus monodon) genome. Animal Genetics 30, 150 6.
62. Yang J., Malik H.S. Eickbush T.H. (1999) Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proceedings of the National Academy of Sciences of the United States of America 96, 7847 52.