Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis)

Genetica

Volumn 133, Issue 1, 2008, Pages 37-46

  Wang, Shi ^a   Bao, Zhenmin ^a   Hu, Xiaoli ^a   Shao, Mingyu ^a   Zhang, Lingling ^a   Hu, Jingjie ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

CFG1; Chlamys farreri; Methylation; Patinopecten yessoensis; PYG1; Retrotransposon; Scallop

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; GENE DOSAGE; GENE EXPRESSION REGULATION; GENETICS; METHYLATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROMOTER REGION; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCALLOP; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; GENE DOSAGE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; METHYLATION; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PECTINIDAE; PHYLOGENY; PROMOTER REGIONS (GENETICS); RETROELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

CHLAMYS FARRERI; CHLAMYS NIPPONENSIS; MIZUHOPECTEN YESSOENSIS; POECILIIDAE; XIPHOPHORUS MACULATUS;

EID: 41549115861     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-007-9180-3     Document Type: Article

References (36)

1. Arkhipova I, Meselson M (2000) Transposable elements in sexual and ancient taxa. Proc Natl Acad Sci USA 97:14473-14477
2. Boeke JD, Corces VG (1989) Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol 43:403-434
3. Bowen NJ, McDonald JG (1999) Genomic analysis of Caenorhabditis elegans reveals ancient families of retrovirus-like elements. Genome Res 9:924-935
4. Capy P, Vitalis R, Langin T, Higuet D, Bazin C (1996) Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? J Mol Evol 42:359-368
5. Depicker A, van Montagu M (1997) Post-transcriptional gene silencing in plants. Curr Opin Cell Biol 9:372-382
6. English JJ, Mueller E, Baulcombe DC (1996) Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8:179-188
7. Gaffney PM, Pierce JC, Mackinley AG, Titchen DA, Glenn WK (2003) Pearl, a novel family of putative transposable elements in Bivalve mollusks. J Mol Evol 56:308-316
8. Gorelick RJ, Henderson LE, Hanser JP, Rein A (1988) Point mutants of Moloney murine leukemia virus that fail to package viral RNA: evidence for specific RNA recognition by a "zinc finger-like" protein sequence. Proc Natl Acad Sci USA 85:8420-8424
9. 4-Cys peptide binds metal ions: Spectroscopic studies and a proposed three-dimensional structure. Proc Natl Acad Sci USA 86:4047-4051
10. Havecker ER, Gao X, Voytas DF (2004) The diversity of LTR retrotransposons. Genome Biol 5:225
11. Hu X, Bao Z, Hu J, Shao M, Zhang L, Bi K, Zhan A, Huang X (2006) Cloning and characterization of tryptophan 2,3-dioxygenase gene of Zhikong scallop Chlamys farreri (Jones and Preston 1904). Aquac Res 37:1187-1194
12. Ingelbrecht I, van Houdt H, van Montagu M, Depicker A (1994) Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. Proc Natl Acad Sci USA 91:10502-10506
13. Jentoft JE, Smith LM, Fu X, Johnson M, Leis J (1988) Conserved cysteine and histidine residues of the avian myeloblastosis virus nucleocapsid protein are essential for viral replication but are not "zinc-binding fingers". Proc Natl Acad Sci USA 85:7094-7098
14. Kazazian HH Jr. (2004) Mobile elements: drivers of genome evolution. Science 303:1626-1632
15. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479-532
16. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
17. Laha T, Loukas A, Verity CK, McManus DP, Brindley PJ (2001) Gulliver, a long terminal repeat retrotransposon from the genome of the oriental blood fluke Schistosoma japonicum. Gene 264:59-68
18. Laha T, Loukas A, Smyth DJ, Copeland CS, Brindley PJ (2004) The fugitive LTR retrotransposon from the genome of the human blood fluke, Schistosoma japonicum. Int J Parasitol 34:1365-1375
19. Malik HS, Eickbush TH (1999) Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol 73:5186-5189
20. McDonald JF (1995) Transposable elements: possible catalysts of organismic evolution. Trends Ecol Evol 10:123-126
21. Michaille J-J, Mathavan S, Gaillard J, Garel A (1990) The complete sequence of mag, a new retrotransposon in Bombyx mori. Nucleic Acids Res 18:674
22. Pearl LH, Taylor WR (1987) A structural model for the retroviral proteases. Nature 329:351-354
23. Reese MG (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26:51-56
24. Rose RR, Doolittle WF (1983) Molecular mechanisms of speciation. Science 220:157-162
25. Sijen T, Wellink J, Hiriart JB, van Kammen A (1996) RNA-mediated virus resistance: Role of repeated transgenes and delineation of targeted regions. Plant Cell 8:2277-2294
26. Springer MS, Davidson EH, Britten RJ (1991) Retroviral-like element in a marine invertebrate. Proc Natl Acad Sci USA 88:8401-8404
27. Springer MS, Britten RJ (1993) Phylogenetic relationships of reverse transcriptase and RNaseH sequences and aspects of genome structure in the gypsy group of retrotransposons. Mol Biol Evol 10:1370-1379
28. Stam M, Mol JNM, Kooter JM (1997) The silence of genes in transgenic plants. Ann Bot 79:3-12
29. Thompson JD, Higgins DG, Gibson TJ (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
30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
31. van den Boogaart T, Lomonossoff GP, Davies JW (1998) Can we explain RNA-mediated virus resistance by homology-dependent gene silencing? Mol Plant-Microbe Interact 11:717-723
32. van Houdt H, Ingelbrecht I, van Montagu M, Depicker A (1997) Post-transcriptional silencing of a neomycin phospho-transferase II transgene correlates with the accumulation of unproductive RNAs and with increased cytosine methylation of 3′ flanking regions. Plant J 12:379-392
33. Volff J-N, Korting C, Altschmied J, Duschl J, Sweeney K, Wichert K, Froschauer A, Schartl M (2001) Jule from the fish Xiphophorus is the first complete vertebrate Ty3/Gypsy retrotransposon from the Mag family. Mol Biol Evol 18:101-111
34. Walsh CP, Chaillet JR, Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20:116-117
35. Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353-3362
36. Zhang L, Bao Z, Cheng J, Li H, Huang X, Wang S, Zhang C, Hu J (2007) Fosmid library construction and initial analysis of end sequences in Zhikong scallop (Chlamys farreri). Mar Biotechnol. doi: 10.1007/s10126-007-9014-4