3.4 Intergenic Spacers and Overlapping Sequences
Fig.3 Secondary structures of 22 tRNAs encoded by the Thitarodes sp.mt genome
The tRNAs are labeled with the abbreviations for their corresponding amino acids.
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Fig.4 Alignment of the spacer regions between trnS2 and nad1(Fig.4A)and between trnW and trnC(Fig.4B)of Hepialidae insects
Spacer 1 of the Thitarodes sp.mt genome was observed to contain the conserved motif TATACTA(Fig.4A).However，the sequence of this corresponding conserved motif is ATACTAA in other sequenced lepidopteran mt genomes(Cameron and Whiting，
In addition to the AT-rich region，this moth mt genome contains a total of 49bp intergenic regions，distributed in 14 regions.The length of this intergenic spacer ranges from 1bp to 15bp，with the longest intergenic region，Spacer 1，located between trnS2 and nad1and containing the high AT content of 93.33%(Fig.4A).This differs from the mt genomes of other Lepidoptera，in which the longest intergenic spacer is typically located between trnQ and nad2(Dai et al.，2015；He et al.，2015；Liu et al.，2016；Park et al.，2016).There is no intergenic spacer between trnM and nad2 in Hepialidae.2008；Salvato et al.，2008；Wang et al.，2016)，while it is TATACTA in all sequenced Hepialidae to date，except in T.pui(CATACTA).This motif is also observed in variable in other Lepidoptera，being ATACTAT in Corcyra cephalonica(Wu et al.，2012)and ATCATAT in Sesamia inferens(unpublished，NC_015835).This motif has been suggested to be a possible binding site of the transcription termination peptide(mt TERM protein)(Taanman，1999；Roberti et al.，2003).It is located just downstream of the cob gene in the heavy strand of the mt genome and might serve to stop the transcription of cob.In addition to this transcriptional stop function，this binding site might also control the overlapping of a large number of transcripts generated by the peculiar transcription mechanism operating in this organism(Roberti et al.，2003).
The mt genome overlaps by 18bp in 5 locations，with the longest overlap being 8bp in length between trnW and trnC(Table 1).Among these overlapped sequences，most were conserved in the number of overlapped nucleotides，with the exception of those sequences that overlapped between nad4 and nad4L.The 8bp overlapping sequence between trnW and trnC is conserved as AARYYTTA in the lepidopteran mt genomes(Fig.4B).