Cycle-Structure Generating Functions for Special Breakpoint Graphs

Abstract

Breakpoint graphs originate in comparative genomics, where their alternating cycles encode relationships between genomes. We study a constrained class of three-colored breakpoint graphs associated with permutations and develop cycle-refined generating functions for two extremal families. These families have a natural topological interpretation: their canonical surfaces are, respectively, the sphere and the projective plane. The spherical family is characterized by noncrossing configurations, while the projective-plane family admits a different decomposition involving a distinguished family of M\"obius ladders. The resulting generating-function equations retain the full cycle structure but nevertheless admit substantial reductions. This leads to explicit Catalan-weighted evaluations, polynomiality results for refined cycle statistics, and a connection between a natural diagonal specialization and noncrossing trees. The two topological families exhibit markedly different combinatorial mechanisms, providing complementary examples of how local transformations of breakpoint graphs can control refined permutation enumerations. As a further application, the same Catalan-weighted sums arise in asymptotic unitary-Weingarten expansions for entanglement of random Gaussian states in linear optics. The combinatorial results determine the leading and constant-order moment polynomials entering the R\'enyi entropy expansion, with the projective-plane contribution giving the finite-size constant correction.