Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae

Abstract

Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.

Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat and Athila). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin.

Conclusions: The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin.

Figure 1

Assembling the retroelement dataset. (a) Flow chart for the generation of the dataset. The shaded region denotes steps coordinated by the RetroMap software. (Eprobe refers to a BLAST query sequence) (b) LTR prediction. The innermost direct repeats identified in sequences flanking the original BLAST hit are assigned as LTRs. The repeats delimit the boundaries of the full-length LTR retrotransposons.

Figure 2

Arabidopsis thaliana Metaviridae and Pseudoviridae reverse transcriptase diversity. Phylogenetic trees used in this figure are adapted from [14,18]. Each tree is based on ClustalX [56] alignments of reverse transcriptase domains for elements in a given family. Neighbor-joining trees (10,000 bootstrap repetitions) were generated using MEGA2 [57]. The non-LTR retrotransposon Ta11 served as the root for both trees. The three Metaviridae sublineages are boxed.

Figure 3

Physical distribution of full-length A. thaliana retroelements. The five A. thaliana chromosomes are designated as Ath1-5. Triangles indicate the location of a particular retroelement on the chromosome. Non-LTR retrotransposons are in black, Pseudoviridae in gray, and Metaviridae in white. Vertical bars on the chromosome show the precise location of the retroelement. Regions of heterochromatin are represented as follows: telomeres and NORs (on Ath2 and Ath4) by rounded chromosome ends; centromeres by hourglass shapes; heterochromatic knobs (on Ath4 and Ath5) by narrowed stretches on chromosome bars. The relatively short chromosome 5 knob is barely visible to the right of the centromere. The inset more clearly depicts heterochromatic regions that are obscured by element insertions. Chromosomes are drawn to scale.

Figure 4

Chromosomal distribution of LTRs for the Metaviridae and Pseudoviridae families in A. thaliana. Chromosomes are displayed as in Figure 3. In addition, solo LTRs are drawn as open triangles. The upper chromosome depicts the distribution of Pseudoviridae, the lower the distribution of Metaviridae. In contrast to Figure 3, shading is not used to distinguish between the families.

Figure 5

Relative ages of A. thaliana LTR retroelement lineages. (a) Box-plot showing the age distribution of Pseudoviridae full-length elements contrasted with those of the Metaviridae. The position of the median is shown as a gray bar in the box that delimits the boundaries of the lower and upper quartiles. Data points more than 1.5 times the inter-quartile range above the upper quartile or below the lower quartile are indicated by individual horizontal lines. Ages were calculated as described in Materials and methods. (b) Relative-age box-plots of Metaviridae sublineages. Permutation test p-values for the significance of the displayed age distributions are shown below each box-plot.