Abstract: 【Aim】 Ty3/gypsy is a retrotransposon that is widespread in many organisms. Aspartic protease (AP) gene is important for the retrotransposon transposition. Since the AP gene is difficult to be cloned based on degenerate primers because the members of AP family have low similarities, there are few researches about AP genes. 【Methods】 The AP gene in Ty3/gypsy retrotransposon was cloned from Chilo suppressalis (Walker) with PCR method, and its sequence characteristics and variations in the Chinese populations were analyzed. 【Results】 The AP gene has a single open reading frame (ORF) of 528 bp encoding a protease of 175 amino acids (GenBank accession no.: KF886014). The Conserved Domain Search analysis showed that there is a conserved Asp_protease_2 domain in this AP protein. Seventy copies of AP gene were cloned from 7 field populations. Multiple sequences alignment revealed that there are 46 single-base substitutions including 31 transitions and 15 transversions. Sixty-nine of 70 copies have intact ORF. The base changes of A→G (15) and T→C (11) occur more frequently than the others. 【Conclusion】 There is no significant relationship between the patterns of base substitutions and the distribution area of C. suppressalis. This study will be helpful to investigate the variation features of retrotransposon.

Key words: Chilo suppressalis, retrotransposon, Ty3/gypsy, aspartic protease (AP), gene cloning, sequence analysis