Significant Expansion of <em>Vicia pannonica</em> Genome Size Mediated by Amplification of a Single Type of Giant Retroelement
Abstract
Amplification and eventual elimination of dispersed repeats, especially those of the retroelement origin, account for most of the profound size variability observed among plant genomes. In most higher plants investigated so far, differential accumulation of various families of elements contributes to these differences. Here we report the identification of giant Ty3/gypsy-like retrotransposons from the legume plant Vicia pannonica, which alone make up ∼38% of the genome of this species. These retrotransposons have structural features of the Ogre elements previously identified in the genomes of pea and Medicago. These features include extreme size (25 kb), the presence of an extra ORF upstream of the gag–pol region, and a putative intron dividing the prot and rt coding sequences. The Ogre elements are evenly dispersed on V. pannonica chromosomes except for terminal regions containing satellite repeats, their individual copies show extraordinary sequence similarity, and at least part of them are transcriptionally active, which suggests their recent amplification. Similar elements were also detected in several other Vicia species but in most cases in significantly lower numbers. However, there was no obvious correlation of the abundance of Ogre sequences with the genome size of these species.
NUCLEAR genomes of higher plants differ considerably in their size, ranging from 0.1 pg (98 Mbp) in Fragaria viridis to 89.5 pg (87,686 Mbp) in Fritillaria davisii (Bennett and Leitch 2004). Even closely related species belonging to the same genus can display 5- to 10-fold differences in their haploid genome size, as it is, for example, in Phalenopsis, Scilla, or Vicia (Bennett and Leitch 2005). First investigations of this phenomenon using DNA reassociation kinetics (Chooi 1971; Flavellet al. 1974) revealed that genome size variation is mainly caused by differences in the proportion of repetitive DNA sequences. This was later confirmed by finding many families of repetitive sequences from a number of species. Among these, satellite repeats and retroelements have the most significant impact on genome size. Satellite repeats are organized as long arrays of tandemly repeated units (monomers). Although the monomer sequences are usually only tens to hundreds of nucleotides long (Macaset al. 2002), they can be amplified up to millions of copies (Katoet al. 1984; Inghamet al. 1993; Irifuneet al. 1995; Macaset al. 2000), making up to 20% of the genome (Inghamet al. 1993). However, in most plant species investigated so far, the majority of repetitive DNA is composed of various families of retroelements (reviewed in Kumar and Bennetzen 1999; Feschotteet al. 2002). This high proportion of retroelements within plant genomes is a consequence of their replicative (copy-and-paste) mode of transposition (retrotransposition), which generates a new copy of the element each time it is retrotransposed. Although the retroelements do not attain as high copy numbers as the satellite repeats, their impact on the genome size is more pronounced due to their considerable length, ranging from a few up to 14 kb (Hirochikaet al. 1992; Martinez-Izquierdoet al. 1997; Neumannet al. 2005). The recent discovery of a new group of giant retrotransposons, named Ogre elements, showed that the upper length limit of retrotransposons could be even longer. These Ty3/gypsy-like elements identified in pea (Pisum sativum) and Medicago truncatula are up to 22 kb long, and they occur at ∼10,000 copies in the pea genome, corresponding to at least 5% of its nuclear DNA (Neumannet al. 2003).
The genus Vicia (Fabaceae) includes >160 species differing considerably in their haploid nuclear DNA content (1.9–14.4 pg, corresponding to 1862–14,112 Mbp) (Bennett and Leitch 2005). Several studies revealed that there is a number of differentially amplified repeats of retroelement origin that significantly contribute to these differences (Pearceet al. 1996; Kumaret al. 1997; Nouzováet al. 2001; Hillet al. 2005). However, these studies described only partial retroelement sequences, which do not allow precise evaluation of the contribution that specific element families give to the evolution of the Vicia genome. In this work, we show that many of these partial sequences belong to a retrotransposon family closely related to the giant Ogre elements previously identified in pea and Medicago. We describe full-length Ogre-like elements isolated from the genome of Vicia pannonica and present data suggesting that significant expansion of the genome size in some Vicia species was caused by recent amplification of these elements.
Acknowledgments
We thank H. Štěpančíková for excellent technical assistance, M. Nouzová for help with DNA sequencing, and S. M. Rafelski and Lara Colton for assistance in preparation of the manuscript. This work was supported by grants GACR521/00/0655 and GACR521/02/P007 from the Czech Science Foundation, grant LC06004 from the Ministry of Education, Youth and Sports of the Czech Republic, and grant AVOZ50510513 from the Academy of Sciences of the Czech Republic.
Notes
Sequence data from this article have been deposited with the EMBL/GenBank Data libraries under accession no. AY936172.