Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

The Diversity And Organization Of Retrotransposons In Brassica: Understanding Their Phylogeny And Evolution

Karine Alix¹ , Carol D Ryder³ , Jay Moore³ , Graham J King⁴ , Pat J S Heslop-Harrison²

¹  UMR de Génétique Végétale INRA/UPS/CNRS/INA P-G, Ferme du Moulon, 91190 Gif sur Yvette, France

²  Department of Biology, University of Leicester, Leicester LE1 7RH, UK

³  Warwick HRI, Wellesbourne, Warwick CV35 9EF, UK

⁴  Rothamsted Research, Harpenden, Hertfordshire, AL5 2QJ, UK

Retrotransposons are the most abundant, rapidly evolving and widely distributed component of most plant genomes. They belong to three major classes: two classes with long terminal repeats (LTRs) including Ty1/copia and Ty3/gypsy elements, and Long Interspersed Nuclear Elements (LINEs).
Using universal PCR primers, we isolated 79 fragments of retrotransposon reverse transcriptase (RT) fragments from the three diploid and three derived allotetraploid species of Brassica in the triangle of U. Sequence phylogeny showed that Ty1/copia and LINE elements were distinct, while a third clade was sub-divided into Ty3/gypsy, Athila and retrovirus-like branches, providing evidence that there are multiple and only distantly related lineages within this group. The parsimony trees showed no branches correlating with the known genome relationships for the six Brassica species, probably because members of all the retroelement families were present in the common ancestor. We hybridised five representative retrotransposon RT domains to a gridded BAC library from B. oleracea. Individual LTR-retrotransposons were represented by between 90 and 320 copies in the haploid genome, with only a few locations for the LINE, data that were confirmed by Genome Survey Sequence analyses. BAC screening and fluorescent in situ hybridization showed that each retrotransposon had a characteristic genomic distribution, suggesting no clustering of retroelements from different families.
The present study adds to our knowledge of the diversity, evolution and organization of Brassica retrotransposons. Based on their insertional polymorphisms and rapid recent evolution, retrotransposons have value to develop S-SAP, IRAP and insertional markers that will be useful in Brassica genomics.