Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

Abstract

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a "copy and paste" mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.

Figure 1.

Phylogenetic tree of six diploid Oryza species, established with the ADH2 gene. Only nodes with a bootstrap value >70% are shown. The tentative dates of the radiation event are given for each node. The computational methods are given in the Methods section.

Figure 2.

In silico reconstruction of Kangourou (A) and Wallabi (B) retrotransposons. The copies of the BES contigs are shown as horizontal lines (alternate black and gray according to their final position on the element). The schematic representation of the element assembled from O. australiensis BES is represented in gray. The schematic representation of the elements, as it is found in the O. australiensis sequenced BAC clones, is given in black at the bottom of the figures. The size scale in bp is given at the bottom.

Figure 3.

Physical map of three sequenced O. australiensis BAC clones. Black boxes represent predicted coding regions. Colored boxes represent different types of TEs as indicated on the figure. Numbers in parentheses indicate the estimated date of LTR-retrotransposon insertions (in million years) using the two molecular clocks MC1 and MC2 (see text). A,B,C correspond to the sequence of the BAC clones OA_59114, OA_AB10104J14, and OA_ABa0008H03, respectively.

Figure 4.

Southern hybridization of the three retrotransposons, RIRE1, Kangourou, and Wallabi on total genomic DNA of Oryza species digested with RsaI. The phylogenetic tree given on the figure is extrapolated from Ge et al. (1999). The direction of migration is from left to right.

Figure 5.

Phenetic relationships of RIRE1, Kangourou, and Wallabi in the genus Oryza: The neighbor-joining tree was constructed based on the alignments given in Supplemental data #3. For each tree, the dot shows the branch separating the O. australiensis sequences from the others. The number given near the dot corresponds to the bootstrap value. Color coding: black for the A-genome species; gray for O. punctata; orange forO. minuta; green for O. officinalis; blue for O. alta, and red for O. australiensis. The numbers of aligned sequences used to build the tree were as follows: for RIRE1: 752 O. australiensis sequences and 113 other Oryza sequences; for Kangourou: 570 O. australiensis sequences and 67 others; for Wallabi: 757 O. australiensis sequences and 422 others.

Figure 6.

Timing of the bursts of the three retrotransposons, RIRE1, Kangourou, and Wallabi: For each element, the curves represent the distribution of the observed divergence between each paralog (given at the bottom x-axis). Top x-axis represents the date of divergence in Mya translated from the observed divergence, using the two molecular clocks MC1 and MC2 (see Methods section). The groups of paralogs used to compute the pairwise distances are defined within the phenetic subgroups shown in the phenogrammes given in Supplemental data #4. The y-axis represents the total number of copy equivalent, i.e., (the frequency at which the divergence time occurred) × (the number of paralogs in the genome of O. australiensis, based on the dot-blot experiments, Table 1).

Figure 7.

Histograms of the most recent among all observed divergence computed for each paralog (compared with all others) of the three retrotransposons RIRE1, Kangourou, and Wallabi.