The Genomic Organization of Retrotransposons in Brassica oleracea
- 243 Downloads
We have investigated the copy numbers and genomic organization of five representative reverse transcriptase domains from retrotransposons in Brassica oleracea. Two non-homologous Pseudoviridae (Ty1/copia-like) elements, two Metaviridae (Ty3/gypsy-like) elements (one related to the Athila family) and one Retroposinae (LINE) element were hybridized to a gridded BAC library, “BoB”. The results indicated that the individual LTR retrotransposons (copia and gypsy-like) were represented by between 90 and 320 copies in the haploid genome, with only evidence of a single location for the LINE. Sequence analysis of the same elements against genome survey sequence gave estimates of between 60 and 570, but no LINE was found. There was minimal evidence for clustering between any of these retroelements: only half the randomly expected number of BACs hybridized to both LTR-retrotransposon families. Fluorescent in situ hybridization showed that each of the retroelements had a characteristic genomic distribution. Our results suggest there are preferential sites and perhaps control mechanisms for the insertion or excision of different retrotransposon groups.
KeywordsBAC library copia fluorescent in situ hybridization (FISH) gypsy LINE reverse transcriptase
Unable to display preview. Download preview PDF.
- The Arabidopsis Genome Initiative2000Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature108796815Google Scholar
- Babula, D., Kaczmarek, M., Barakat, A., Delseny, M., Quiros, C.F., Sadowski, J. 2003Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative mapMol. Gen. Genomics268656665Google Scholar
- Cheng, Z., Presting, G.G., Robin Buell, C., Wing, R.A., Jiang, J. 2001High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of riceGenetics15717491757PubMedGoogle Scholar
- Chèvre, A.-M., Eber, F., Baranger, A., Renard, M. 1997Gene flow from transgenic cropsNature389924Google Scholar
- Gish, W.R., 2005. WU-BLAST archives: http://blast.wustl.edu
- Lavie, L., Prieto, J-L., Tatout, C., Deragon, J-M. 2002Bali1A, a possible LINE partner for the SINE S1 in Brassica napusGenome letters1123130Google Scholar
- Lukashin, A.V., Borodovsky, M. 1998GeneMark.hmm: new solutions for gene findingNucleic Acids Res.25955964Google Scholar
- Peterson-Burch, B., Nettleton, D. and Voytas, D.F., 2004. Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biology 5(10), R78:http://genomebiology.com/2004/5/10/R78
- Schwarzacher, T., Heslop-Harrison, J.S.(P.) 2000Practical In Situ HybridizationBIOS Scientific Publishers LtdOxford, UKGoogle Scholar
- U, N.1935Genomic analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilisationJpn. J. Bot.7389452Google Scholar
- Warwick, S.I., Francis, A., La Fleche, J., 2003. Guide to Wild Germplasm of Brassica and Allied Crops (tribe Brassiceae, Brassicaceae) 2nd Edition. http://www.brassica.info/crucifer%20genetics/brass00.pdf