Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?

Abstract

Tandemly arrayed genes (TAGs) are an important genomic component. However, most previous studies have focused on individual TAG families, and a broader characterization of their genomic distribution is not yet available. In this study, we examined the distribution of TAGs in the Arabidopsis thaliana genome and examined TAG density with relation to recombination rates. Recombination rates along A. thaliana chromosomes were estimated by comparing a genetic map with the genome sequence. Average recombination rates in A. thaliana are high, and rates vary more than threefold among chromosomal regions. Comparisons between TAG density and recombination indicate a positive correlation on chromosomes 1, 2, and 3. Moreover, there is a consistent centromeric effect. Relative to single-copy genes, TAGs are proportionally less frequent in centromeres than on chromosomal arms. We also examined several factors that have been proposed to affect the sequence evolution of TAG members. Sequence divergence is related to the number of members in the TAG, but genomic location has no obvious effect on TAG sequence divergence, nor does the presence of unrelated genes within a TAG. Overall, the distribution of TAGs in the genome is not consistent with theoretical models predicting the accumulation of repeats in regions of low recombination but may be consistent with stabilizing selection models of TAG evolution.

Figure 1

Genetic and physical maps of all chromosomes and the distribution of TAGs with respect to the maps. For each chromosome, circles represent the genetic and physical position of markers, the histogram represents the number of TAG genes in the region, and the bar represents the centromeric region.

Figure 2

Recombination rates estimated by the global and local approaches. + represents global rate estimates by a fifth-order polynomial; circles represent local estimates. The bar represents the centromeric region and estimate recombination rates in this region.

Figure 3

The number of TAGs as a function of spacers and E-values. The numbers represent the chromosomes. For each chromosome, red numbers represent TAGs identified with an E-value 10^-10, blue numbers represent TAGs identified with an E-value of 10^-20, and black numbers represent TAGs identified with an E-value of 10^-30.

Figure 4

The distribution of the number of genes in a TAG for the data set with E-value 10^-30 and no spacer.

Figure 5

The physical distribution of TAGs along each chromosome. For each chromosome, the vertical line represents the physical location of TAGs, the horizontal line represents the chromosome itself, and the open box represents the centromere.