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.

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

“…The Z-chromosome assembly for turkey was not complete enough to align properly. The chicken-zebra finch alignments were already available from our previous study (Volker et al, 2010). Subsequently, to aid visualization, the GenAlyzer output matches (of 100+ base pairs) were combined into contiguous blocks using a custom script.…”

“…Between 2004 and 2010 the chicken genome was the only avian representative being completely characterized and karyotyped (Hillier et al, 2004;Masabanda et al, 2004), but this nevertheless has allowed cross-species chromosome painting to numerous other birds (reviewed in Griffin et al, 2007) and BAC mapping to build physical maps of a few others. These include turkey, duck and zebra finch Skinner et al, 2009a;Volker et al, 2010). From these studies, a number of key messages emerge: first, chicken chromosomes 1-3 and 5-10+Z are representative of the ancestral pattern.…”

“…Third, whole-chromosome blocks represent ancient conservation of synteny, with chromosomes 1-5+Z being present and intact in turtles (Matsuda et al, 2005) and chromosome 4 similarly intact in humans (Chowdhary and Raudsepp, 2000;Hillier et al, 2004). Finally, despite interchromosomal conservation, intrachromosomal changes are common; for example, 114 tentative rearrangements, both inversions and translocations were noted between chicken and zebra finch (Volker et al, 2010). The overall picture of avian genome organization is of a successful and conserved karyotypic pattern, with changes, when they occur, tending to recur much more than in mammals.…”

“…Recently we (Volker et al, 2010;Warren et al, 2010) generated comparative maps by aligning whole chromosomal sequences between chicken (Gallus gallus) and zebra finch (Taeniopygia guttata), and subsequently verifying rearrangements by fluorescence in situ hybridization (FISH). This showed an apparent combination of multiple inversions and translocations within chromosomes.…”

“…With the publication of the turkey (Meleagris gallopavo) genome (Dalloul et al, 2010), we can identify some lineage-specific rearrangements and provide evidence for regions of recurrent breakpoints. In this study therefore we have used whole-chromosomal sequence alignments among turkey, chicken and zebra finch, combined with our previously published physical maps Volker et al 2010) generated comparative genomic maps among the three avian species. Using zebra finch as an outgroup, we also tested the hypothesis that there are genomic regions within which breakpoints recur during avian evolution.…”