Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model singlecelled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires significance in mRNA translation, design of transgenic and new gene discovery. Results:

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... he codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A-and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are influenced by both mutational pressure and natural selection, neutrality plot analysis showed that those two factors play major roles. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the first attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base