The availability of an increasing number of animal genomes, mostly being of vertebrate and insect species, provides us an opportunity to employ comparative genomics approaches to study the evolution of gene arrangements. Genome architecture evolution through genome rearrangement events such as fission, fusion, inversion, translocation, and transposition leads to continual divergence from the ancestral architecture. In order to detect the conserved genomic regions across distant species, a large-scale ortholog-anchored multiple-species synteny delineation workflow is developed in this research. Moreover, the database that stores the resulted synteny information generated by the workflow is presented in this thesis, as well as the web interface which allows public queries for the synteny information. This thesis also elaborates the evolutionary constraints on gene arrangements revealed by various analyses on the arthropod and vertebrate synteny block data. Furthermore, a detailed case study of a remarkably stable TipE gene cluster in insects and examples of genome rearrangement studies for tobacco hawkmoth are addressed to demonstrate the use of synteny information in evolutionary studies. Applying the computational comparative approaches to investigate animal genomes, this research has successfully provided a promising tool and a comprehensive resource for the studies of conserved genomic regions, and helped to develop a better understanding of the forces shaping these genome architectures.