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Even though antigenic variation is employed among parasitic protozoa for host immune evasion,  Tetrahymena thermophila , a free-living ciliate, can also change its surface protein antigens. These cysteine-rich glycosylphosphatidylinositol (GPI)-linked surface proteins are encoded by a family of polymorphic  Ser  genes. Despite the availability of  T. thermophila  genome, a comprehensive analysis of the  Ser  family is limited by its high degree of polymorphism. In order to overcome this problem, a new approach was adopted by searching for  Ser  candidates with common motif sequences, namely length-specific repetitive cysteine pattern and GPI anchor site. The candidate genes were phylogenetically compared with the previously identified  Ser  genes and classified into subtypes.  Ser  candidates were often found to be located as tandem arrays of the same subtypes on several chromosomal scaffolds. Certain  Ser  candidates located in the same chromosomal arrays were transcriptionally expressed at specific  T. thermophila  developmental stages. These  Ser  candidates selected by the motif analysis approach can form the foundation for a systematic identification of the entire  Ser  gene family, which will contribute to the understanding of their function and the basis of  T. thermophila  antigenic variation.

Genome-Wide Prediction of the Polymorphic Ser Gene Family in Tetrahymena thermophila Based on Motif Analysis