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, 13 (2), 137-44

A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome

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A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome

Guillaume Blanc et al. Genome Res.

Abstract

The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing of ancestral large-scale duplication events. Here, using more appropriate methodology and a more recent version of the genome sequence annotation, we investigate the scale and timing of segmental duplications in Arabidopsis. We used protein sequence similarity searches to detect duplicated blocks in the genome, used the level of synonymous substitution between duplicated genes to estimate the relative ages of the blocks containing them, and analyzed the degree of overlap between adjacent duplicated blocks. We conclude that the Arabidopsis lineage underwent at least two distinct episodes of duplication. One was a polyploidy that occurred much more recently than estimated previously, before the Arabidopsis/Brassica rapa split and probably during the early emergence of the crucifer family (24-40 Mya). An older set of duplicated blocks was formed after the monocot/dicot divergence, and the relatively low level of overlap among these blocks indicates that at least some of them are remnants of a larger duplication such as a polyploidy or aneuploidy.

Figures

Figure 1.
Figure 1.
Map of duplicated regions identified in the Arabidopsis genome. Red and blue colored boxes depict recent and old sister regions, respectively, as defined by the analysis of the level of synonymous substitutions between duplicated genes. Lines link paired blocks. Centromeres are shown as circles. An interactive version of this map is available at http://wolfe.gen.tcd.ie/athal/dup.
Figure 2.
Figure 2.
Box plots of Ks values (Yang 1999) estimated from duplicated genes located in sister regions. The central box depicts the middle 50% of the data between the 25th and 75th percentile for each pair of duplicated blocks, and the enclosed horizontal line represents the median value of the distribution. Asterisks outside of the main bodies of data indicate extreme values.
Figure 3.
Figure 3.
Map of duplicated regions identified in the Arabidopsis pseudo ancestral genome. The vertical line represents a single chromosome containing 20,187 genes ordered according to a procedure that merged the recent blocks (see text) to approximate the ancestral Arabidopsis genome before the last polyploidy event. Red boxes depict the sections of the pseudo genome corresponding to merged sister regions. Other shaded boxes at right represent duplicated regions identified in the pseudo ancestral genome (colors are used for clarity and do not depict any age classification). Curved lines link paired regions, and circles depict the regions corresponding to the centromeres in the real genome.
Figure 4.
Figure 4.
Position of the duplication events in the tree of life. (A) Phylogenetic relationships between the analyzed plant species. The arrow marks the probable position of the recent large-scale duplication event identified in this analysis. (B) Distribution of Ks values obtained from sets of orthologous sequences between Arabidopsis and selected plant species and between paralogous sequences in recent and old Arabidopsis blocks. The numbers of sequences orthologous to Arabidopsis are 252 for Brassica rapa, 1358 for cotton, 1741 for Medicago, 1465 for tomato, and 1026 for rice. The paralog Ks distributions are for 2617 and 576 gene pairs occurring in recent duplicated blocks, and blocks identified in the pseudo ancestral genome, respectively. The vertical lines depict the positions of the modes of the distributions obtained from Arabidopsis paralogous genes.

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