Transposable elements constitute a substantial fraction of host genomes. Ty3/gypsy retrotransposon, one group of LTR retrotransposons, is widespread in different species. By inversePCR and genome walking, a novel member of Ty3/gypsy retrotransposons was cloned from Chilo suppressalis. This new member of Ty3/gypsy retrotransposons was named CsuTy3 (GenBank accession No. KJ191261). The sequence is 4 934 bp in length and integrated into the “AACGT” target site duplications (TSDs) of the genome. There is a pair of noncompletely identical long terminal repeats (LTRs) in the CsuTy3 retrotransposon. The 5′LTR is 161 bp in length and the 3′LTR is 168 bp, sharing 935% similarities. A polypurine tract (PPT), 15 bp in length, is adjacent to the 3′LTR. There are three independent open reading frames (ORFs) in CsuTy3. The first ORF encodes a protein which is related to viral structural protein, termed GAG. The second encodes aspartic protease (AP). The third encodes a polyprotein including a reverse transcriptase (RT) which produces a cDNA copy of the transposon′s RNA, an RNase H (RH) which splits the DNARNA hybrid and an integrase (IN) which inserts the cDNA into the host′s genome. The southern hybridization indicated that there were many CsuTy3 copies in different C. suppressalis populations. Flanking PCR results showed that the CsuTy3 copy was inserted at the same locus in different populations. At this locus, all the individuals have the CsuTy3 copy insertion except some individuals from Deyang and Jiangjin populations. The CsuTy3 insertion ratio varied with field populations.
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