Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis

Abstract

BackgroundThe availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu.ResultsWe provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey.ConclusionOur results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies.

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

“…Although the chromosomal rearrangement between GGA3 and CCO3 we identified should be considered as a pericentric inversion, an independent event, namely centromere repositioning to a different genetic location, must have driven the change of chromosome morphology. De novo centromere formation has been earlier proposed for chromosome 4 in red-legged partridge (Kasai et al 2003) and chromosome Z in Pekin duck as compare with chicken orthologs (Skinner et al 2009). The centromere repositioning during karyotype evolution, the so-called evolutionary new centromere (ENC) formation, is rather a common phenomenon.…”

“…The centromere repositioning during karyotype evolution, the so-called evolutionary new centromere (ENC) formation, is rather a common phenomenon. It has been repeatedly described in different taxonomic groups as diverged as mammals, birds, and plants (Kasai et al 2003;Nagaki et al 2004;O'Neill et al 2004;Galkina et al 2006;Han et al 2009;Skinner et al 2009;Rocchi et al 2012). Though mechanisms of ENC formation are obscure, an attractive hypothesis implies the following events: old centromere inactivation and neocentromere formation in a new euchromatic locus, with fixation of these first steps in population.…”

Gene Duplication of endothelin 3 Is Closely Correlated with the Hyperpigmentation of the Internal Organs (Fibromelanosis) in Silky Chickens

“…Furthermore, recent studies have found CNVs related to various human diseases (Wain et al 2009;Zhang et al 2009;Stankiewicz and Lupski 2010). CNVs are also observed in Aves both in inter-and intraspecies (Griffin et al 2008;Skinner et al 2009;Völker et al 2010;Wang et al 2010). In addition, an association between CNVs and Figure 3 Genetic (left) and physical (right) maps of Fm on chicken chromosome 20.…”

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

“…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.…”