Abstract
Background: Animal cytogenetics evolved from a primarily descriptive science into an analytical discipline that addresses the complex mechanisms underlying genome architecture and evolution. The genetic study of avian lineages has historically been uniquely challenging due to their peculiar karyotypes, which combine extensive syntenic conservation of a few macrochromosomes with the presence of dozens of microchromosomes and an unusually low rate of interchromosomal change. Today, the integration of classical cytogenetics and advanced molecular approaches is driving the field of chromosomics, which effectively bridges the gap between cytogenetic data and sequence-based physical maps. Results: Using long-read sequencing technologies in conjunction with high-throughput chromosome conformation capture (Hi-C) and physical analysis methods enable the assembly of complex avian genomes with chromosome-level resolution. These modern approaches reveal hidden structural variants and explain the complex evolutionary dynamics of the repeatome, including transposable elements and satellite DNA. Furthermore, comparative genomic analyses demonstrate the Z and W sex chromosomes' complex, independent evolutionary trajectories, which are characterized by structural instability and recurrent reorganizations. Next-generation sequencing methodologies have also revealed the plasticity and dynamic nature of germline-restricted chromosomes in passerines. Meanwhile, oligonucleotide-based fluorescence in situ hybridization has emerged as a critical tool for physically validating these complex genome assemblies. Conclusions: Avian chromosome evolution cannot be fully understood through sequence data or cytogenetic observations alone. The future of avian cytogenomics requires connecting physical chromosome structure, DNA sequence, and three-dimensional nuclear organization in order to develop a mechanistic understanding of lineage diversification.

Key words: Chromosomics; Avian cytogenomics; Chromosome architecture; Chromosome evolution; Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH); Genomic anchoring; Physical mapping; Germline-restricted chromosomes (GCOs).