Novel tools for characterising inter- and intra-chromosomal rearrangements in avian microchromosomes

Avian genome organization is characterized, in part, by a set of microchromosomes that are unusually small in size and unusually large in number. Although occupying about a quarter of the genome, they contain around half the genes and three quarters of the chromosome count. Nonetheless, they continue to belie analysis by cytogenetic means. Chromosomal rearrangements play a key role in genome evolution, fertility and genetic disease and, thus, tools for the microchromosomes are essential to analyze such phenomena in birds. Here we report the development of chicken microchromosomal paint pools, generation of pairs of specific microchromosome BAC clones in chicken, and tools for in-silico genomic comparison of microchromosomes. We demonstrate the application of these tools cross-species, which can, in principle, be used in combination to generate a clear picture of microchromosomal rearrangements for numerous avian species. With increasing numbers of avian genome sequences being generated, tools such as these will find great utility in assembling genomes de-novo and asking fundamental questions about genome evolution from a chromosome perspective.