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. 2012 Feb 7;3(1):2.
doi: 10.1186/1759-8753-3-2.

The Predominantly Selfing Plant Arabidopsis Thaliana Experienced a Recent Reduction in Transposable Element Abundance Compared to Its Outcrossing Relative Arabidopsis Lyrata

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The Predominantly Selfing Plant Arabidopsis Thaliana Experienced a Recent Reduction in Transposable Element Abundance Compared to Its Outcrossing Relative Arabidopsis Lyrata

Nicole de la Chaux et al. Mob DNA. .
Free PMC article

Abstract

Background: Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences.

Results: We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated.

Conclusions: Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs.

Figures

Figure 1
Figure 1
Relationship between copy numbers in A. thaliana and A. lyrata for each family. The panels show data for different TE classes, as indicated above each panel. The diagonal black line represents the line of equal copy numbers in both species. Families with a higher copy number in A. thaliana and A. lyrata thus correspond to points below and above the diagonal line, respectively. Families discussed in the text are highlighted and labeled by black arrows.
Figure 2
Figure 2
Copy number distribution of TEs in both genomes. The figure shows a histogram of element copy number (horizontal axis) divided into families shared between the two genomes and unique families (inset). Dark grey bars represent the number of families in A. thaliana and light grey bars in A. lyrata. The dashed lines of the same shading indicate the average copy number per family for the respective species. We note that for each copy number value on the horizontal axis, the bars for both A. thaliana and A. lyrata originate at a value of zero on the vertical axis. Thus, bars are not stacked, despite their visual appearance, and do not represent the sum of copies in both species. We used this format to ensure visual clarity despite the large number of bars in each histogram. Notice the different vertical scales for shared and unique families.
Figure 3
Figure 3
Average insertion time distribution for each family. The average insertion time was calculated based on the average nucleotide divergence between all copies of one family. (a) Histogram for shared families; (b) histogram for unique families. The percentage of families with a given age are represented by dark grey bars for A. thaliana and light grey bars for A. lyrata. The mean average insertion time for shared families is 11.1 Mya for A. thaliana and 9 Mya for A. lyrata, respectively. For unique families it is 6.7 and 5.5 Mya, respectively. The mean of the average insertion time for shared families is significantly smaller in A. lyrata (P <10-15, Wilcoxon rank sum test). Notice the different scales for shared and unique families.
Figure 4
Figure 4
Insertion time distribution for all elements. A histogram of the number of elements with a given insertion time (horizontal axis). Values on the vertical axis are given as percent of the total number of elements. Elements in A. thaliana are represented by dark grey bars, and elements in A. lyrata by light grey bars. For visual clarity, the figure only shows elements with an insertion time less than 15 Mya. Only few elements were inserted even earlier. The inset shows the frequency of elements younger than 2 million years. The double-headed arrow indicates the approximate time range when selfing arose in A. thaliana [36,39]. We note that for each copy number value on the horizontal axis, the bars for both A. thaliana and A. lyrata originate at a value of zero on the vertical axis. Thus, bars are not stacked, despite their visual appearance, and do not represent the sum of copies in both species. We used this format to ensure visual clarity despite the large number of bars in each histogram.
Figure 5
Figure 5
Insertion time distribution for elements belonging to families unique to one genome. Analogous to Figure 4, but only for families unique to one of the two genomes. The figure shows a histogram of the number of elements with a given insertion time (horizontal axis). Values on the vertical axis are given as percent of the total number of elements. Elements unique to A. thaliana are represented by dark grey bars, and elements unique to A. lyrata by light grey bars. For A. thaliana only 363 elements belong to families unique to this species. We note that for each copy number value on the horizontal axis, the bars for both A. thaliana and A. lyrata originate at a value of zero on the vertical axis. Thus, bars are not stacked, despite their visual appearance, and do not represent the sum of copies in both species. We used this format to ensure visual clarity despite the large number of bars.

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