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In this paper, we study the structure of the differential operator algebra and its associated eigenvalue algebra for matrix-valued orthogonal polynomials. While is isomorphic to , its simpler framework allows us to efficiently derive strong results about and its center . We analyze the behavior of the center under Darboux transformations, establishing explicit relationships between the centers of Darboux-equivalent weights. These results are illustrated through the study of both reducible and irreducible matrix weights, including a detailed analysis of an irreducible Jacobi-type weight.

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