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 - 3.12

SEQUENCE CHARACTERISATION OF A VERY LARGE PLANT GENOME (NORWAY SPRUCE, PICEA ABIES (L.) KARST.)

A. ZUCCOLO, F. CATTONARO, I. JURMAN, M. VIZZI, M. MORGANTE

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

retrotransposon, ripetitive DNA, amplification, methylation

Genome expansion by amplification of repetitive sequences is a well described phenomenon. LTR-retrotransposons are the major contributors to the expansion in plants. Very large genomes (greater than 1*10¹⁰ bp per haploid genome) have however not yet been analysed at the sequence level to understand how the expansion was achieved, whether by amplification to very high copy number of a limited number of repeats or by amplification to lower copy numbers of a very large number of different repeats. The family Pinaceae in the Gymnosperms provides for an interesting case study because on one hand Gymnosperms are not yet well characterized at the genome level and on the other hand all species within the family have very large genomes.

In order to take a wide and comprehensive approach to the study of the structure of the Norway spruce (Picea abies (L.) Karst.) genome, seven different genomic libraries were constructed and used as source of clones to be sequenced. Three of them were screened to isolate by hybridisation a set of highly repetitive sequences: the 119 sequences obtained were characterised in silico and by Southern blot. Two other libraries were made using methylation sensitive enzymes to look at the hyper- and hypomethylated fractions respectively. Finally two libraries were made using randomly sheared (nebulised) genomic DNA to provide a random sample of the genome in one case and a random sample of its hypomethylated fraction in the other. Over 4000 sequences corresponding to more than 2 Mbp have been obtained from these last two libraries.

Sequence analyses on all libraries reveal that: a) at least 70% of the genome is made of repetitive sequences; b) repetitive DNA is hypermethylated in Norway spruce; c) LTR retrotransposons are the major component of the repetitive fraction while other classes, although all present, are not abundant (LINEs, SINEs, tandem repeats); d) no single family of retrotransposons makes up a large fraction of the genome, while many families seem to have amplified to high levels.

These results provide a different model for genome expansion in Gymnosperms from the one that seems to apply to cereals where single LTR families often make up 10% or more of their large genomes. We will discuss the results in light of the evolutionary history of Gymnosperms.