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Ciliates have developed a puzzling genomic organization. Genes are broken into many pieces in the micronucleus, separated by non-coding sequences, and sometimes also shuffled and inverted. During sexual reproduction, all pieces are precisely assembled in the orthodox order to yield the transcriptionally active macronuclear genes. We give in this paper a brief survey of the genome structure in stichotrichous ciliates and present two molecular models proposed for gene assembly. We then establish a set of invariants for gene assembly. We prove that in any model based on the paradigm of pointer-directed assembly, the set of molecules excised during the assembly of a given gene, the linearity of the assembled gene, and its IES context are all uniquely defined by the micronuclear structure of the gene and thus, are invariants of the gene assembly process.

Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia)