A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event

Genetics

Volumn 181, Issue 4, 2009, Pages 1183-1193

  Cheng, Xudong ^a,b   Zhang, Dongfeng ^a   Cheng, Zhukuan ^a   Keller, Beat ^c   Ling, Hong Qing ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; ARTICLE; GENE INSERTION; GENE SEQUENCE; GENETIC TRANSCRIPTION; INTROGRESSION; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PARSIMONY ANALYSIS; PHYLOGENY; PLANT GENOME; PRIORITY JOURNAL; PROTEIN DOMAIN; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIDER GENE; SOUTHERN BLOTTING; TOMATO; ARABIDOPSIS; CHROMOSOME MAP; GENE DOSAGE; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYSIOLOGY; SEQUENCE HOMOLOGY;

ARABIDOPSIS; LYCOPERSICON; LYCOPERSICON ESCULENTUM; SOLANACEAE;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME MAPPING; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE TRANSFER, HORIZONTAL; GENOME, PLANT; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; RETROELEMENTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOLANACEAE; TRANSCRIPTION, GENETIC;

EID: 67650321229     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.099150     Document Type: Article

References (50)

1. AKAMA, K., and S. TANIFUJI, 1989 Nucleotide sequence of a methionine initiator tRNA gene of Arabidopsis thaliana. Plant Mol. Biol. 13: 599-600.
2. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. ARABIDOPSIS GENOME INITIATIVE, 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. (Pubitemid 32016083)
4. BEGUIRISTAIN, T., M. A. GRANDBASTIEN, P. PUIGDOMENECH and J. M. CASACUBERTA, 2001 Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco: consequences for retrotransposon control and evolution in plants. Plant Physiol. 127: 212-221.
5. BERGTHORSSON, U., K. L. ADAMS, B. THOMASON and J. D. PALMER, 2003 Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197-201. (Pubitemid 36858687)
6. BLUME, B., C. S. BARRY, A. J. HAMILTON, M. BOUZAYEN and D. GRIERSON, 1997 Identification of transposon-like elements in non-coding regions of tomato ACC oxidase genes. Mol. Gen. Genet. 254: 297-303.
7. BOEKE, J. D., and V. G. CORCES, 1989 Transcription and reverse transcription of retrotransposons. Annu. Rev. Microbiol. 43: 403-434.
8. BROWN, J. C., and R. L. CHANEY, 1971 Effect of iron on the transport of citrate into the xylem of soybeans and tomatoes. Plant Physiol. 47: 836-840.
9. CHENG, X. D., L. L. DONG and H. Q. LING, 2004 Improvement on PCR-based cDNA and genomic library screening. Chinese H. Tech. Lett. 14: 32-37.
10. DIAO, X., M. FREELING and D. LISCH, 2006 Horizontal transfer of a plant transposon. PLoS Biol. 4: e5.
11. ELLIS, T. H., S. J. POYSER, M. R. KNOX, A. V. Vershinin and M. J. AMBROSE, 1998 Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol. Gen. Genet. 260: 9-19.
12. FLAVELL, A. J., E. DUNBAR, R. ANDERSON, S. R. PEARCE, R. HARTLEY et al., 1992 Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res. 20: 3639-3644.
13. FRAY, R. G., and D. GRIERSON, 1993 Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol. Biol. 22: 589-602.
14. FRIANT, S., T. HEYMAN, M. L. WILHELM and F. X. WILHELM, 1996 Extended interactions between the primer tRNAi (Met) and genomic RNA of the yeast Ty1 retrotransposon. Nucleic Acids Res. 24: 441-449. (Pubitemid 26085807)
15. HEDGES, S. B., 2002 The origin and evolution of model organisms. Nat. Rev. Genet. 3: 838-849.
16. JIANG, J., B. S. GILL, G. L. WANG, P. C. RONALD and D. C. WARD, 1995 Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc. Natl. Acad. Sci. USA 92: 4487-4491.
17. JIN, Y. K., and J. L. BENNETZEN, 1994 Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize. Plant Cell 6: 1177-1186. (Pubitemid 2137276)
18. JORDAN, I. K., and J. F. MCDONALD, 1998 Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup. Mol. Biol. Evol. 15: 1160-1171.
19. JORDAN, I. K., L. V. MATYUNINA and J. F. MCDONALD, 1999 Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc. Natl. Acad. Sci. USA 96: 12621-12625.
20. KUMAR, A., and J. L. BENNETZEN, 1999 Plant retrotransposons. Annu. Rev. Genet. 33: 479-532.
21. KUMAR, A., S. R. PEARCE, K. MCLEAN, G. HARRISON, J. S. HESLOP-HARRISON et al., 1997 The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica 100: 205-217.
22. KUMAR, S., K. TAMURA and M. NEI, 2004 MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5: 150-163.
23. LI, L., X. CHENG and H.-Q. LING, 2004 Isolation and characterization of Fe(III)-chelate reductase gene LeFRO1 in tomato. Plant Mol. Biol. 54: 125-136.
24. LING, H.-Q., A. PICH, G. SCHOLZ and M. W. GANAL, 1996 Genetic analysis of two tomato mutants affected in the regulation of iron metabolism. Mol. Gen. Genet. 252: 87-92.
25. LING, H.-Q., P. BAUER, Z. BERECZKY, B. KELLER and M. GANAL, 2002 The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc. Natl. Acad. Sci. USA 99: 13938-13943.
26. LONG, M., S. J. DE SOUZA, C. ROSENBERG and W. GILBERT, 1996 Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor. Proc. Natl. Acad. Sci. USA 93: 7727-7731.
27. LONG, M., E. BETRAN, K. THORNTON and W. WANG, 2003 The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4: 865-875.
28. LOWE, T. M., and S. R. EDDY, 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
29. MA, J., K. M. DEVOS and J. L. BENNETZEN, 2004 Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
30. MARCHLER-BAUER, A., J. B. ANDERSON, C. DEWEESE-SCOTT, N. D. FEDOROVA, L. Y. GEER et al., 2003 CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31: 383-387.
31. NEUMANN, P., D. POZARKOVA and J. MACAS, 2003 Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol. Biol. 53: 399-410.
32. NUEZ, F., J. PROHENS and J. M. BLANCA, 2004 Relationships, origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations. Am. J. Bot. 91: 86-99.
33. OCHMAN, H., J. G. LAWRANCE and E. A. GROISMEN, 2000 Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. (Pubitemid 30337055)
34. PRICE, H. L., and A. W. DRINKARD, 1908 Inheritance in tomato hybrids. Virg. Agric. Exp. Stn. Bull. 177: 17-53.
35. PURUGGANAN, M. D., and S. R. WESSLER, 1995 Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA. Mol. Ecol. 4: 265-269.
36. RICO-CABANAS, L., and J. A. MARTINEZ-IZQUIERDO, 2007 CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis. Mol. Genet. Genomics 277: 365-377.
37. ROBERTSON, H. M., F. N. SOTO-ADAMES, K. K. O. R. WALDEN;, M. P. AYANCINI and D. J. LAMPE, 1998 The mariner transposons of animals: horizontally jumping genes, pp. 268-284 in Horizontal Gene Transfer, edited by M. SYVANEN and C. I. KADO. Chapman & Hall, London.
38. ROULIN, A., B. PIEGU, R. A. WING and O. PANAUD, 2008 Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J. 53: 950-959.
39. SANMIGUEL, P., A. TIKHONOV, Y. K. JIN, N. MOTCHOULSKAIA, D. ZAKHAROV et al., 1996 Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
40. SILVA, J. C., and M. G. KIDWELL, 2000 Horizontal transfer and selection in the evolution of P elements.Mol. Biol. Evol. 17: 1542-1557.
41. SILVA, J. C., E. L. LORETO and J. B. CLARK, 2004 Factors that affect the horizontal transfer of transposable elements. Curr. Issues Mol. Biol. 6: 57-71.
42. SONNHAMMER, E. L., and R. DURBIN, 1995 A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-GC10.
43. TANKSLEY, S. D., M. W. GANAL, J. P. PRINCE, M. C. DE VICENTE, M.W. BONIERBALE et al., 1992 High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.
44. VAN DER HOEVEN, R., C. RONNING, J. GIOVANNONI, G.MARTIN AND S. TANKSLEY, 2002 Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456.
45. WANG, W., H. ZHENG, C. FAN, J. LI, J. SHI et al., 2006 High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802.
46. WAUGH, R., K. MCLEAN, A. J. FLAVELL, S. R. PEARCE, A. KUMAR et al., 1997 Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253: 687-694.
47. WHITE, S. E., and J. F. DOEBLEY, 1999 The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics 153: 1455-1462.
48. WICKER, T., and B. KELLER, 2007 Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17: 1072-1081.
49. WU, H. K., 1967 Note on preparing of pachytene chromosomes by double mordants. Sci. Agric. 15: 40-44.
50. XIAO, H., N. JIANG, E. SCHAFFNER, E. J. STOCKINGER and E. VAN DER KNAAP, 2008 A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.