Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta)

Plant Journal

Volumn 56, Issue 4, 2008, Pages 562-574

  Novikova, Olga ^a   Mayorov, Vladimir ^b   Smyshlyaev, Georgiy ^c   Fursov, Michail ^d   Adkison, Linda ^b   Pisarenko, Olga ^e   Blinov, Alexander ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b MERCER UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^d Novosibirsk Center of Information Technologies 'UniPro'   (Russian Federation)

^e RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

Chromodomain containing Gypsy; LTR retrotransposons; Mosses; Phylogeny; Physcomitrella patens

Indexed keywords

BRYOPHYTA; BRYOPHYTES; EUKARYOTA; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS; TRACHEOPHYTA;

PLANT RNA;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENETICS; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOSS; PHYLOGENY; PLANT GENE; PLANT GENOME; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; BRYOPHYTA; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; RETROELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, PLANT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TERMINAL REPEAT SEQUENCES;

EID: 58149269509     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2008.03621.x     Document Type: Article

References (49)

1. Akita, M. and Valkonen, J.P. (2002) A novel gene family in moss (Physcomitrella patens) shows sequence homology and a phylogenetic relationship with the TIR-NBS class of plant disease resistance genes. J. Mol. Evol. 55, 595-605.
2. Bowen, N.J. and Jordan, I.K. (2002) Transposable elements and the evolution of eukaryotic complexity. Curr. Issues Mol. Biol. 4, 65-76.
3. Chaparro, C., Guyot, R., Zuccolo, A., Piégu, B. and Panaud, O. (2007) RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 35(Database issue), D66-D70.
4. Dej, K.J., Gerasimova, T., Corces, V.G. and Boeke, J.D. (1998) A hotspot for the Drosophila gypsy retroelement in the ovo locus. Nucleic Acids Res. 26, 4019-4025.
5. Deka, N., Willard, C.R., Wong, E. and Schmid, C.W. (1988) Human transposon-like elements insert at a preferred target site: evidence for a retrovirally mediated process. Nucleic Acids Res. 16, 1143-1151.
6. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
7. Fedoroff, N.V. (1999) Transposable elements as a molecular evolutionary force. Ann. N Y Acad. Sci. 870, 251-264.
8. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
9. Feschotte, C., Jiang, N. and Wessler, S.R. (2002) Plant transposable elements: where genetics meets genomics. Genetics, 3, 329-341.
10. Finnegan, D.J. (1992) Transposable elements. Curr. Opin. Genet. Dev. 2, 861-867.
11. Friesen, N., Brandes, A. and Heslop-Harrison, J.S. (2001) Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol. Biol. Evol. 18, 1176-1188.
12. Gao, X., Hou, Y., Ebina, H., Levin, H.L. and Voytas, D.F. (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18, 359-369.
13. Goodwin, T.J. and Poulter, R.T. (2001) The DIRS1 group of retrotransposons. Mol. Biol. Evol. 18, 2067-2082.
14. Gorinsek, B., Gubensek, F. and Kordis, D. (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol. 21, 781-798.
15. Havecker, E.R., Gao, X. and Voytas, D.F. (2004) The diversity of LTR retrotransposons. Genome Biol. 5, 225.
16. Hirochika, H. and Hirochika, R. (1993) Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn. J. Genet. 68, 35-46.
17. Hirochika, H., Fukuchi, A. and Kikuchi, F. (1992) Retrotransposon families in rice. Mol. Gen. Genet. 233, 209-216.
18. Ignatov, M.S., Afonina, O.M., Ignatova, E.A. et al. (2006) Checklist of mosses of East Europe and North Asia. Arctoa, 15, 1-130.
19. Jordan, I.K., Matyunina, L.V. and McDonald, J.F. (1999) Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc. Natl Acad. Sci. USA, 96, 12621-12625.
20. Kidwell, M.G. and Lisch, D.R. (2000) Transposable elements and host genome evolution. Trends Ecol. Evol. 15, 95-99.
21. Kim, J.M., Vanguri, S., Boeke, J.D., Gabriel, A. and Voytas, D.F. (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8, 464-478.
22. Kordis, D. (2005) A genomic perspective on the chromodomain-containing retrotransposons: chromoviruses. Gene, 347, 161-173.
23. Kumar, A. and Bennetzen, J.L. (1999) Plant retrotransposons. Annu. Rev. Genet. 33, 479-532.
24. Kumar, S., Tamura, K. and Nei, M. (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 5, 150-163.
25. Kumekawa, N., Ohtsubo, E. and Ohtsubo, H. (1999) Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom. Genes Genet. Syst. 74, 299-307.
26. Langdon, T., Seago, C., Mende, M., Legett, M., Thomas, H., Forster, J.W., Thomas, H., Jones, R.N. and Jenkins, G. (2000) Retrotransposon evolution in diverse plant genomes. Genetics, 156, 313-325.
27. Liu, R., Vitte, C., Ma, J., Mahama, A.A., Dhliwayo, T., Lee, M. and Bennetzen, J.L. (2007) A GeneTrek analysis of the maize genome. Proc. Natl Acad. Sci. USA, 104, 11844-11849.
28. Malik, H.S. and Eickbush, T.H. (1999) Modular evolution of the integrase domain in the Ty3/gypsy class of LTR retrotransposons. J. Virol. 73, 5186-5190.
29. Marín, I. and Lloréns, C. (2000) Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol. Biol. Evol. 17, 1040-1049.
30. McClure, M.A., Smith, C. and Elton, P. (1996) Parameterization studies for the SAM and HMMER methods of hidden Markov model generation. Proc. Int. Conf. Intell. Syst. Mol. Biol. 4, 155-164.
31. Miller, J.T., Dong, F., Jackson, S.A., Song, J. and Jiang, J. (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics, 150, 1615-1623.
32. Murray, M.G. and Thompson, W.F. (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321-4325.
33. Nishiyama, T., Fujita, T., Shin-I, T. et al. (2003) Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc. Natl Acad. Sci. USA, 100, 8007-8012.
34. Peterson-Burch, B.D. and Voytas, D.F. (2002) Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol. Biol. Evol. 19, 1832-1845.
35. Rensing, S.A., Fritzowsky, D., Lang, D. and Reski, R. (2005) Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens. BMC Genomics, 6, 43.
36. Rensing, S.A., Lang, D., Zimmer, A.D. et al. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319, 64-69.
37. Renzaglia, K.S., Duff, R.J.T., Nickrent, D.L. and Garbary, D.J. (2002) Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 769-793.
38. Reski, R. and Frank, W. (2005) Moss (Physcomitrella patens) functional genomics - Gene discovery and tool development, with implications for crop plants and human health. Brief Funct. Genomic Proteomic, 4, 48-57.
39. Stenøien, H.K. (2007) Compact genes are highly expressed in the moss Physcomitrella patens. J. Evol. Biol. 20, 1223-1229.
40. Suoniemi, A., Taskanen, J. and Schulman, A.H. (1998) Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J. 13, 699-705.
41. Telesnitsky, A. and Goff, S.P. (1997) Reverse transcriptase and the generation of retroviral DNA. In Retroviruses (Coffin, J.M., Hughes, S.H. and Varmus, H.E., eds). Cold Spring Harbor: Cold Spring Laboratory Press, pp. 121-160.
42. Terol, J., Castillo, M.C., Bargues, M., Pérez-Alonso, M. and de Frutos, R. (2001) Structural and evolutionary analysis of the copia-like elements in the Arabidopsis thaliana genome. Mol. Biol. Evol. 18, 882-892.
43. Terzian, C., Ferraz, C., Demaille, J. and Bucheton, A. (2000) Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup. Mol. Biol. Evol. 17, 908-914.
44. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
45. Vallee, B.L. and Auld, D.S. (1993) Cocatalytic zinc motifs in enzyme catalysis. Proc. Natl Acad. Sci. USA, 90, 2715-2718.
46. Vitte, C. and Panaud, O. (2005) LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet. Genome Res. 110, 91-107.
47. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E. and Keller, B. (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26, 307-316.
48. Wicker, T., Sabot, F., Hua-Van, A. et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973-982.
49. Wright, D.A. and Voytas, D.F. (1998) Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics, 149, 703-715.