The centromere is a domain essential for chromosomal segregation in cell divisions. Understanding its structure and function is of the highest importance in biology, and also crucial from biomedical point of view. Functional centromeres are marked by centromere-specific histone H3-like proteins (CenH3). Centromere identity involves both genomic and epigenetic mechanisms, favoring rapid co-evolution and species specificity of CenH3 and associated DNA sequences without impairing the function. Complexity and variations make perception of centromere genomics still fragmental and worked out only in a few most common plant and animal model systems. Among invertebrates, sequenced genomes of model organisms with diverse constitution of centromeric regions became recently available. Tribolium beetles have centromeres embedded deeply into the satellite DNA-rich pericentromeric heterochromatin, Meloidogyne root-knot nematodes have holocentric chromosomes, while the mollusk Crassostrea gigas lacks uniform distribution of satellite DNAs in centromeres. The main goal of this research proposal is to identify CenH3 and CenH3-associated DNA sequences as well as their non-functional genomic counterparts in order to explore genomics of differently organized centromeres. In addition, organizational and evolutional aspects of CenH3 and centromeric DNA sequences will be addressed. The research strategy will combine CenH3 identification, chromatin immunoprecipitation (ChIP)-based assays using anti-CenH3 antibodies, fluorescence in situ hybridization (FISH), immunofluorescence in situ localization (IF) and the bioinformatics pipeline. Such integrative approach will help filling the gaps in functionally essential regions of sequenced genomes and will forward our understanding of the synergy and coevolution between DNA sequences and protein components in the centromeres.