Proceedings of the XLVII Italian Society of Agricultural Genetics - SIGA Annual Congress

Verona, Italy - 24/27 September, 2003

ISBN 88-900622-4-X

Poster Abstract - 5.36

ABUNDANCE, DISTRIBUTION AND PHYLOGENETIC RELATIONSHIP OF LTR-RETROTRANSPOSONS IN THE RICE (ORYZA SATIVA L.) GENOME

A. ZUCCOLO, M. MORGANTE

Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine

retrotransposon, Long Terminal Repeats, recombination, expansion, reduction

The analysis of the repetitive component of a genome can serve two different purposes: on one hand it can shed light on the evolutionary history of the genome, on the other it can be of great help for an accurate annotation of a genomic sequence. The rice genome (1C = 420 Mbp) is being completely sequenced but the knowledge of the composition of its repetitive component is still lacking. In order to study LTR-retroelements distribution and phylogeny in Oryza sativa L., 343 PAC and BAC clones sequenced by the Rice Genome Program were initially considered. An overall non redundant sequence space of 43 Mbp was analysed. The identification of complete LTR-retrotransposons was carried out on the basis of the results of dot matrix analysis to reveal the presence of the LTR (Long Terminal Repeats). 314 complete elements were identified and classified as members of the Ty3-gypsy family (230 elements) or Ty1-copia (73 elements) family; 11 elements were not classified because of the lack of the pol domain. Elements were classified into subfamilies on the basis of LTR sequence similarity. An overall estimate of the distribution of partial and complete LTR-retroelements in the rice genome was obtained using similarity searches on a larger set of sequenced BACs spanning more then half of the rice genome (303 Mbp) and on the entire sequence of chromosome 1. Almost 16.4% of the genome fraction considered is represented by LTR-retrotransposons that seem to be evenly dispersed across the genome. Solo LTRs that are the result of different types of recombination events are almost 2 times more frequently found than entire elements, showing that mechanisms are active that can reduce genome size. In order to understand the evolution of the rice genome in comparison to that of the maize genome a phylogenetic analysis of elements using conserved domains from both species was performed that revealed differential amplification of some subfamilies in the two species. Sequence divergence between the LTRs from each element was used to estimate the time of their insertion into the genome. Most elements appear to have inserted less that 5 million years ago.