Comparative cytogenomics enhanced with bioinformatic tools provides further insights into genome evolution of birds and other amniotes

Recent generation of multiple avian genome sequences enables further comparative analysis of their karyotypes, genome structure, and evolutionary changes. Using FISH and bioinformatic tools (e.g., Evolution Highway browser), we explore genome alignment for the sequenced birds, reptiles and mammals to infer ancestral genome organisation based on the information about their homologous synteny blocks and evolutionary breakpoints (EBRs). In EBRs shared between the birds, boa and opossum, we found over 6,000 human-chicken orthologous genes and examined their gene ontology (GO) categories. Four significant gene clusters were identified that embraced GO terms for phosphorylation (important for turning enzymes on and off and other metabolic pathways), and protein transport and maintenance at specific cell location. They were also enriched with genes of key cellular components (e.g. membranes, endoplasmic reticulum, Golgi membrane). Since chromosomal rearrangements occurred in EBRs may lead to new gene variants and, therefore, function changes, we suggest that the observed EBR enrichment could play a crucial part in evolution of metabolic networks and rates in higher vertebrates, including birds, adapted to various environments. We also developed a pipeline for analyzing cross-species FISH data including tools for semi-automated hybridization signal and FLpter identification, and comparative cytogenetic map construction.