Distribution of microsatellites in relation to coding sequences within the Arabidopsis thaliana genome

Plant Science

Volumn 157, Issue 1, 2000, Pages 97-104

  Casacuberta, Elena ^a   Puigdomènech, Pere ^a   Monfort, Amparo ^a  

^a DEPT OF ENVIRONMENTAL CHEMISTRY   (Spain)

Author keywords

Arabidopsis thaliana; Length polymorphism; Microsatellites

Indexed keywords

DNA MARKER; MICROSATELLITE DNA;

ARABIDOPSIS; ARTICLE; CHROMOSOME SIZE; EXON; GENE NUMBER; GENE STRUCTURE; GENETIC CODE; GENETIC POLYMORPHISM; GENOME; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; REGULATOR GENE;

ARABIDOPSIS THALIANA;

EID: 0343193135     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-9452(00)00271-5     Document Type: Article

References (33)

1. Goffeau et al., The yeast genome directory, Nature 387 (1997) 1-105.
2. The Caenorhabditis elegans sequencing consortium: genome sequence of the nematode C. elegans: a platform for investigating biology, Science 282 (1998) 2012-2022.
3. Mayer K., Schuller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Dusterhoft A., Stiekema W., Entian K.D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L., Rieger M., Weichselgartner M., de Simone V., Obermaier B., Mache R., Muller M., Kreis M., Delseny M., Puigdomenech P., Watson M., McCombie W.R., et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 402:1999;769-777.
4. Lin X., Kaul S., Rounsley S., Shea T.P., Benito M.I., Town C.D., Fujii C.Y., Mason T., Bowman C.L., Barnstead M., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Venter J.C., et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 402:1999;761-768.
5. Dean C., Schimdt R. Plant genomes: a current molecular description. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:1995;395-418.
6. SanMiguel P., Tikonov A., jin Y.-k, et al. Nested retrotransposons in the intergenic regions of the maize genome. Science. 274:1996;765-767.
7. Bevan M., Bancroft I., Bent E., et al. The Arabidopsis genome project analyses of 1.9 Mb of contiguous sequence from chromosome IV of Arabidopsis thaliana. Nature. 391:1998;485-488.
8. Tsay Y.-F., Frank M.J., Page T., Dean C., Crawford N.M. Identification of a mobile endogenous transposon in Arabidopsis thaliana. Nature. 260:1993;342-344.
9. Voytas D.F., Ausubel F.M. A copia-like transposable element family in Arabidopsis thaliana. Nature. 336:1988;242-244.
10. Konieczny A., Voytas D.F., Cummings M.P., Ausubel F.M. A superfamily of Arabidopsis thaliana retrotransposons. Genetics. 127:1991;801-809.
11. Pélissier T., Tutois S., Deragon J.M., Tourmente S., Genestier S., Picard G. Athila, a new retroelement from Arabidopsis thaliana. Plant Mol. Biol. 29:1995;441-452.
12. Wright D.A., Ke N., Smalle J., Hauge B.M., Goodman H.M., Voytas D.F. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics. 142:1996;569-578.
13. Casacuberta E., Casacuberta J.M., Puigdomenech P., Monfort A. Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterization of the Emigrant family of elements. Plant J. 16:1998;79-85.
14. Bell C.J., Ecker J. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 19:1994;137-144.
15. Morgante M., Olivieri A.M. PCR-amplified microsatellites as markers in plant genetics. Plant J. 3:1993;175-182.
16. McCouch S.R., Chen X., Panaud O., et al. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol. Biol. 35:1997;89-99.
17. Struss D., Plieske J. The use of microsatellite markers for detection of genetic diversity in barley populations. Theor. Appl. Genet. 97:1998;308-315.
18. Loridon K., Cournoyer B., Goubely C., Depeiges A., Picard G. Length polymorphism and allele structure of trinucleotide microsatellites in natural accessions of Arabidopsis thaliana. Theor. Appl. Genet. 97:1998;591-604.
19. Hardtke C.S., Müller J., Berleth T. Genetic similarity among Arabidopsis thaliana ecotypes by DNA sequence comparison. Plant Mol. Biol. 32:1996;915-922.
20. Innan H., Terauchi R., Miyashit N.T. microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics. 146:1997;1441-1452.
21. Burge C.B., Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:1997;78-94.
22. Burge C.B., Karlin S. Finding the genes in genomic DNA. Curr. Opin. Struc. Biol. 8:1998;346-354.
23. Xu Y., Mural R.I., Shah M., Uberbacher E.C. Recognizing exons in genomic sequences using GRAIL II. Genetic Engineering, Principles and methods. 1994a;241-253 Plenum, London.
24. Xu Y., Mural R.I., Uberbacher E.C. Constructing gene models from accurately predicted exons: an application of dynamic programming. Computer Applications in the Biosciences. 1994b;613-623.
25. Dellaporta S.L., Wood J., Hicks J.B. Molecular Biology of Plants: A Laboratory Course Manual. 1984;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
26. Chen M., Bennetzen J.L. Sequence composition and organization in the Sh2/A1 - homologous region of rice. Plant Mol. Biol. 32:1996;999-1001.
27. Vendramin G.G., Ziegenhagen B. Characterization and inheritance of polymorphic plastid microsatellites in Abies. Genome. 40:1997;857-864.
28. Lagercrantz U., Ellegren H., Andersson L. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucl. Acids Res. 21:1993;1111-1115.
29. Smith G.P. Evolution of repeated DNA sequences by unequal crossover. Science. 191:1976;528-535.
30. Levinson G., Gutman G.A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:1987;203-221.
31. Granok H., Leibovitch B.A., Shaffer C.D., Elgin S.C.R. Chromatin Ga-ga over GAGA factor. Curr. Biol. 5:1995;238-241.
32. Wilkins R.C., Lis J.T. Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation. Nucl. Acids Res. 25:1997;3963-3968.
33. Hebsgaard S.M., Korning P.G., Tolstrup N., Engelbrecht J., Rouze P., Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucl. Acids Res. 24:1996;3439-3452.