Identification of Novel Retroid Agents in Danio Rerio, Oryzias Latipes, Gasterosteus Aculeatus and Tetraodon Nigroviridis

Overview

Journal Evol Bioinform Online

Publisher Sage Publications

Specialty Biology

Date 2009 May 23

PMID 19461980

Citations 9

Authors

Holly A Basta

Alex J Buzak

Marcella A McClure

Affiliations

Soon will be listed here.

Abstract

Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G. aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G. aculeatus.

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References

Petrov D . Mutational equilibrium model of genome size evolution. Theor Popul Biol. 2002; 61(4):531-44. DOI: 10.1006/tpbi.2002.1605. View

Benson D, Lipman D, Ostell J, Rapp B, Wheeler D . GenBank. Nucleic Acids Res. 1999; 28(1):15-8. PMC: 102453. DOI: 10.1093/nar/28.1.15. View

Kimmel C . Genetics and early development of zebrafish. Trends Genet. 1989; 5(8):283-8. DOI: 10.1016/0168-9525(89)90103-0. View

Temin H . Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts. Mol Biol Evol. 1985; 2(6):455-68. DOI: 10.1093/oxfordjournals.molbev.a040365. View

Mi S, Lee X, Li X, Veldman G, Finnerty H, Racie L . Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature. 2000; 403(6771):785-9. DOI: 10.1038/35001608. View

Samuelson L, Wiebauer K, Gumucio D, Meisler M . Expression of the human amylase genes: recent origin of a salivary amylase promoter from an actin pseudogene. Nucleic Acids Res. 1988; 16(17):8261-76. PMC: 338557. DOI: 10.1093/nar/16.17.8261. View

McClure M . Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol Biol Evol. 1991; 8(6):835-56. DOI: 10.1093/oxfordjournals.molbev.a040686. View

Wheeler D, Chappey C, Lash A, Leipe D, Madden T, Schuler G . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 1999; 28(1):10-4. PMC: 102437. DOI: 10.1093/nar/28.1.10. View

McClure M, Johnson M, Feng D, Doolittle R . Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny. Proc Natl Acad Sci U S A. 1988; 85(8):2469-73. PMC: 280018. DOI: 10.1073/pnas.85.8.2469. View

10.

Baranov P, Gesteland R, Atkins J . Recoding: translational bifurcations in gene expression. Gene. 2002; 286(2):187-201. DOI: 10.1016/s0378-1119(02)00423-7. View

11.

Xiong Y, Eickbush T . Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm. Cell. 1988; 55(2):235-46. DOI: 10.1016/0092-8674(88)90046-3. View

12.

McClure M, Richardson H, Clinton R, Hepp C, Crowther B, Donaldson E . Automated characterization of potentially active retroid agents in the human genome. Genomics. 2005; 85(4):512-23. DOI: 10.1016/j.ygeno.2004.12.006. View

13.

Jaillon O, Aury J, Brunet F, Petit J, Stange-Thomann N, Mauceli E . Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004; 431(7011):946-57. DOI: 10.1038/nature03025. View

14.

Shima A, Himmelbauer H, Mitani H, Furutani-Seiki M, Wittbrodt J, Schartl M . Fish genomes flying. Symposium on Medaka Genomics. EMBO Rep. 2003; 4(2):121-5. PMC: 1315840. DOI: 10.1038/sj.embor.embor743. View

15.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

16.

Fischer C, Ozouf-Costaz C, Crollius H, Dasilva C, Jaillon O, Bouneau L . Karyotype and chromosome location of characteristic tandem repeats in the pufferfish Tetraodon nigroviridis. Cytogenet Cell Genet. 2000; 88(1-2):50-5. DOI: 10.1159/000015484. View

17.

Kishi S, Uchiyama J, Baughman A, Goto T, Lin M, Tsai S . The zebrafish as a vertebrate model of functional aging and very gradual senescence. Exp Gerontol. 2003; 38(7):777-86. DOI: 10.1016/s0531-5565(03)00108-6. View

18.

Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E . GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats. Nucleic Acids Res. 2006; 34(9):e67. PMC: 3303178. DOI: 10.1093/nar/gkl335. View

19.

Driever W, Schier A, Neuhauss S, Malicki J, Stemple D, Stainier D . A genetic screen for mutations affecting embryogenesis in zebrafish. Development. 1996; 123:37-46. DOI: 10.1242/dev.123.1.37. View

20.

Hull R . Classifying reverse transcribing elements: a proposal and a challenge to the ICTV. International Committee on Taxonomy of Viruses. Arch Virol. 2002; 146(11):2255-61. DOI: 10.1007/s007050170036. View