Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

Abstract

It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intrachromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intrachromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250 kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one-third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.

Figure 1

Example alignment between chicken chromosome 9 and orthologous turkey chromosome 11. (a) Shows the raw Genalyzer output and (b) shows the same after grouping into synteny blocks. Only synteny blocks ⩾250 kb are plotted.

Figure 2

Side-by-side alignments between chicken chromosome 9, turkey chromosome 11 and zebra finch chromosome 9. Colored arrows show the division of the chromosomes into segments, oriented with respect to turkey.

Figure 3

Example of a potential series of inversions from a Neoaves common ancestor leading to the organization seen in chicken chromosome 9, turkey chromosome 11 and zebra finch chromosome 9. Inverted segments are indicated with dotted arrows. Note that in this figure, segment order is presented with respect to the hypothetical Neoaves common ancestor. Note also that rearrangements shown in the path to zebra finch could have occurred in either the path from the avian common ancestor to zebra finch or from the avian common ancestor to the chicken–turkey ancestor, depending on the true ancestral organization.