Introns in, introns out in plant gene families: A genomic approach of the dynamics of gene structure

Journal of Structural and Functional Genomics

Volumn 3, Issue 1-4, 2003, Pages 111-116

  Lecharny, Alain ^a   Boudet, Nathalie ^a   Gy, Isabelle ^a   Aubourg, Sébastien ^a,b   Kreis, Martin ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

^b CNRS   (France)

Author keywords

Arabidopsis; Gene families; Intron; Structure

Indexed keywords

AMINO ACID SEQUENCE; ARABIDOPSIS; EVOLUTION; EXON; GENE DUPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENE TRANSFER; INTRON; MULTIGENE FAMILY; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; REVIEW;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE TRANSFER, HORIZONTAL; INTRONS; MULTIGENE FAMILY; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 0037266831     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1022614001371     Document Type: Review

References (44)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195.
2. AGI, Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
3. Aubourg, S., Takvorian, A., Chéron, A., Kreis, M. and Lecharny, A. (1997) Structure, organization and putative function of the genes identified within a 23-kb fragment from Arabidopsis thaliana chromosome IV. Gene, 199, 241-253.
4. Aubourg, S., Chéron, A., Kreis, M. and Lecharny, A. (1998) Structure and expression of an asparaginyl-tRNA synthetase gene located on chromosome IV of Arabidopsis thaliana and adjacent to a novel gene of 15 exons. Biochim. Biophys. Acta, 1398, 225-231.
5. Aubourg, S., Picaud, A., Kreis, M. and Lecharny, A. (1999) Structure and expression of three src2 homologues and a novel subfamily of flavoprotein monooxygenase genes revealed by the analysis of a 25 kb fragment from Arabidopsis thaliana chromosome IV. Gene, 230, 197-205.
6. Aubourg, S., Kreis, M. and Lecharny, A. (1999) The DEAD box RNA helicase family in Arabidopsis thaliana. Nucleic Acids Res., 27, 628-636.
7. Aubourg, S., Lecharny, A. and Bohlmann, J. (2002) Genomic analysis of the terpenoid synthase (AtTPS) gene of Arabidopsis thaliana. Mol. Genet. Genomics, 267, 730-745.
8. Betts, M.J., Guigo, R., Agarwal, P. and Russel, R.B. (2001) Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution. EMBO J., 20, 5354-5360.
9. Blanc, G., Barakat, A., Guyot, R., Cooke, R. and Delseny, M. (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell, 12, 1093-1102.
10. Bolle, C., Herrmann, R.G., and Oelmuller, R. (1996) Intron sequences are involved in the plastid- and light-dependent expression of the spinach PsaD gene. Plant J., 10, 919-924.
11. Boudet, N., Aubourg, S., Toffano-Nioche, C., Kreis, M. and Lecharny, A. (2001) Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila. Genome Res., 11, 2101-2114.
12. Brown, N.P., Whittaker, A.J., Newell, W.R., Pawlings, C.J. and Beck, S. (1995) Identification and analysis of multigene families by comparison of exon fingerprints. J. Mol. Biol., 249, 342-359.
13. Dornelas, M.C., Lejeune, B., Dron, M. and Kreis, M. (1998) The Arabidopsis shaggy-related protein kinase (ASK) gene family: structure, organisation and evolution. Gene, 212, 249-257.
14. Dornelas, M.C., Wittich, P., von Recklinghausen, I., vanLammeren, A. and Kreis, M. (1999) Characterization of three novel members of the Arabidopsis SHAGGY-related protein kinase (ASK) multigene family. Plant Mol. Biol., 39, 137-147.
15. European Union Chromosome 3 Arabidopsis Sequencing Consortium; The Institute for Genomic Research and Kazusa DNA Research Institute. (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature, 408, 820-821.
16. Frugoli, J.A., McPeek, M.A., Thomas, T.L. and McLung, C.R. (1998) Intron loss and gain during evolution of the catalase gene family in angiosperms. Genetics, 149, 355-365.
17. Fu, H., Kim, S.Y. and Park, W.D. (1995a) High-level tuber expression and sucrose inducibility of a potato Sus4 sucrose synthase gene require 5′ and 3′ flanking sequences and the leader intron. Plant Cell, 7, 1387-1394.
18. Fu, H., Kim, S.Y. and Park, W.D. (1995b) A potato Sus3 sucrose synthase gene contains a context-dependent 3′ element and a leader intron with both positive and negative tissue-specific effects. Plant Cell, 7, 1395-1403.
19. Gotoh, O. (1998) Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Mol. Biol. Evol., 15, 1447-1459.
20. Gy, I., Aubourg, S., Sherson, S., Cobett, C.S., Chéron, A., Kreis, M. and Lecharny, A. (1998) Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana. Gene, 209, 201-210.
21. Haouazine-Takvorian, N., Tymowska-Lalanne, Z., Takvorian, A., Tregear, J., Lejeune, B., Lecharny, A. and Kreis, M. (1997) Characterization of two members of the Arabidopsis thaliana gene family, AtBfruct3 and AtBfruct4, coding for vacuolar invertases. Gene, 197, 239-251.
22. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
23. Kinlaw, C.S. and Neale, D.B. (1997) Complex gene families in pine genomes. Trends Plant Sci., 2, 356-359.
24. Liss, M., Kirk, D.L., Beyser, K. and Fabry, S. (1997) Intron sequences provide a tool for high-resolution phylogenetic analysis of volvocine algae. Curr. Genet., 31, 214-227.
25. Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
26. Mironov, A.A., Fickett, J.W. and Gelfand, M.S. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288-1293.
27. Paquette, S.M., Bak, S. and Feyerreisen, R. (2000) Intron-exon organisation and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana. DNA Cell Biol., 19, 307-317.
28. Petrov, D.A., Sangster, T.A., Johnston, J.S., Hartl, D.L. and Shaw, K.L. (2000) Evidence for DNA loss as a determinant of genome size. Science, 287, 1060-1062.
29. Ride, J.P., Davies, E.M., Franklin, F.C.H. and Marshall, D.F. (1999) Analysis of Arabidopsis genome sequence reveals a large new gene family in plants. Plant Mol. Biol., 39, 927-932.
30. Riechmann, J.L. and Ratcliffe, O.J. (2000) A genomic perspective on plant transcription factors. Curr. Opin. Plant Biol., 3, 423-434.
31. Robertson, H.M. (1998) Two large families of chemoreceptor genes in the Nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss. Genome Res., 8, 449-463.
32. Rzhetsky, A., Ayala, F.J., Hsu, L.C., Chang, C. and Yoshida, A. (1997) Exon/intron structure of aldehyde dehydrogenase genes supports the 'introns-late' theory. Proc. Natl. Acad. Sci. USA, 94, 6820-6825.
33. Sanderfoot, A.A., Assaad, F.F. and Raikhel, N.V. (2000) The Arabidopsis genome. An abundance of soluble N-ethylmaleimide-sensitive factor adaptor protein receptors. Plant Physiol., 124, 1558-1569.
34. Sankoff, D. (2001) Gene and genome duplication. Curr. Opin. Genet. Dev., 11, 681-684.
35. Small, I.D. and Peeters, N. (2000) The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci., 25, 46-47.
36. The C. elegans Sequencing Consortium. (1998) Genome Sequence of the Nematode C. elegans. A Platform for Investigating Biology. Science, 282, 2012-2027.
37. Theologis A. et al. (2000) Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature, 408, 816-820.
38. Tavares, R., Aubourg, S., Lecharny, A. and Kreis, M. (2000) Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2. Plant Mol. Biol., 42, 703-717.
39. Tognolli, M., Overney, S., Penel, C., Greppin, H. and Simon, P. (2000) A genetic and enzymatic survey of Arabidopsis thaliana peroxidases. Plant Perox. Newslett., 14, 3-12.
40. Torki, M., Mandaron. P., Mache, R. and Falconet, D. (2000) Characterization of a ubiquitous expressed gene family encoding polygalacturonase in Arabidopsis thaliana. Gene, 242, 427-436.
41. Trapp, S.C., and Croteau, R.B. (2001) Genomic organization of plant terpene synthases and molecular evolutionary implications. Genetics, 158, 811-832.
42. Trotman, C.N.A. (1998) Introns-early: slipping lately? Trends Genet., 14, 132-134.
43. Vision, T.J., Brown, D.G. and Tanksley, S.D. (2000) The origin of genomic duplications in Arabidopsis. Science, 290, 2114-2117.
44. Wattler, S., Russ, A., Evans, M. and Nehls, M. (1998) A combined analysis of genomic and primary protein structure defines the phylogenetic relationship of new members of the T-box family. Genomics, 48, 24-33.