Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

Abstract

Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.

Figure 1.

Comparative analysis of marker order on chicken chromosome 4 (GGA4) and its zebra finch orthologs, TGU4 and TGU4A. The central part of the figure was created by aligning whole-chromosome sequences using the program GenAlyzer (Choudhuri et al. 2004). Line color between chromosome bars indicates the lengths of sequences exhibiting 100% sequence identity (between 100 and 900 bp). The rearrangements suggested by this analysis were verified using fluorescent in situ hybridization (FISH). Numbers indicate the positions of chicken and zebra finch bacterial artificial chromosome (BAC) clones with orthologous sequence content in the genome sequences of both species. Yellow dots illustrate the physical position as determined by FISH.

Figure 2.

Analysis of conserved synteny in chicken (Griffin et al. 2008) and zebra finch (TGU) microchromosomes by dual color fluorescent in situ hybridization (FISH) using chicken and zebra finch bacterial artificial chromosome (BAC) clones with orthologous sequence content. (A) Chicken BACs WAG-20E08 (red) and WAG-21I18 (green) on GGA24. (B) The corresponding zebra finch BACs TGAC-82A15 (red) and TGAC-321M03 on TGU24.

Figure 3.

Box-whisker plot representing the recombination rates in 118 1-Mb windows in regions with chromosomal breakpoints (mean ± SD = 2.13 ± 3.03 cM/Mb) and in 643 1-Mb windows without chromosomal breakpoints (1.14 ± 1.95 cM/Mb). The observed difference between the two is statistically significant (Wilcoxon's rank sum test, W = 6376, P = 0.0000183).

Figure 4.

An illustration of the randomization test. The histogram shows the distribution of the difference in median recombination rate between 17 windows drawn at random from the entire sample and the remaining windows. The thick vertical line represents the observed difference in median recombination rate between the 17 windows that contain CNVRs (median = 0.74 cM/Mb) and the remaining 741 windows (median = 0.23 cM/Mb).