title: Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization.
abstract: There is a growing interest in copy number variation (CNV) and the recognition of its importance in phenotype, disease, adaptation and speciation. CNV data is usually ascertained by array-CGH within-species, but similar inter-species comparisons have also been made in primates, mice and domestic mammals. Here, we conducted a broad appraisal of putative cross-species CNVs in birds, 16 species in all, using the standard array-CGH approach. Using a chicken oligonucleotide microarray, we detected 790 apparent CNVs within 135 unique regions and developed a bioinformatic tool 'CNV Analyser' for analysing and visualising cross-species data sets. We successfully addressed four hypotheses as follows: (a) Cross-species CNVs (compared to chicken) are, as suggested from preliminary evidence, smaller and fewer in number than in mammals; this 'dogma' was rejected in the light of the new evidence. (b) CNVs in birds are likely to have a functional effect through an association with genes; a large proportion of detected regions (70 %) were indeed associated with genes (suggesting functional significance), however, not necessarily more so than in mammals. (c) There are more CNVs in birds with more rearranged karyotypes; this hypothesis was rejected. Indeed, Falco species contained fewer than most with relatively standard (chicken-like) karyotypes. (d) There are more CNVs per megabase on micro-chromosomes than macrochromosomes; this hypothesis was accepted. Indeed, in species with rearranged karyotypes characterised by chromosomal fusions, the fused former microchromosomes still 'behaved' as though they were their microchromosomal ancestors. Gene ontology analysis of CNVRs revealed enrichment in immune response and antigen presentation genes and five CNVRs were perfectly correlated with the unique loss of sexual dichromatism in one Galliformes species.
authors.affiliation: School of Biosciences, University of Kent, Canterbury, UK, CT2 7NJ.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Skinner
authors.forename: Abdullah
authors.initials: A
authors.lastname: Al Mutery
authors.forename: Deborah
authors.initials: D
authors.lastname: Smith
authors.forename: Martin
authors.initials: M
authors.lastname: Völker
authors.forename: Nilofour
authors.initials: N
authors.lastname: Hojjat
authors.forename: Sannaa
authors.initials: S
authors.lastname: Raja
authors.forename: Steven
authors.initials: S
authors.lastname: Trim
authors.forename: Peter
authors.initials: P
authors.lastname: Houde
authors.forename: William J
authors.initials: WJ
authors.lastname: Boecklen
authors.forename: Darren K
authors.initials: DK
authors.lastname: Griffin
mesh_terms: D000818:Animals; D001717:Birds / Q000235:genetics*; D055028:Comparative Genomic Hybridization / Q000379:methods* / Q000662:veterinary*; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D019143:Evolution, Molecular; D063990:Gene Ontology; D017404:In Situ Hybridization, Fluorescence; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D060888:Real-Time Polymerase Chain Reaction; D013045:Species Specificity