Fig. 3: The genomic structure and transposon-like signatures of M^V.

a Dotplot visualizations of Mdmd presence in inverse orientation on M^V-contig indicated by blue (forward) and orange (reverse) lines that represent longer stretches of sequence similarity. b Alignments between M^V-contig and non-M^V-contigs show M^V was inserted in a tandem repetitive region, indicated by the gap. c Self-alignment of M^V demonstrates that the main part of M^V is a palindrome with a non-palindromic spacer sequence of 3046 bp in the middle. Two blocks of tandem repeats exist on each end of M^V (indicated by red arrows). d Schematic drawing indicates the sequence contents of M^V and percentage identities between palindromic arms. The spacer sequence shows homology to a reverse transcriptase sequence and an ncRNA. The red blocks and the missing parts represent insertions/deletions. The small green blocks indicate the existence of 9 bp direct repeats at the M^V borders. e Single-copy BUSCOs in the M^V-contig mainly correspond to those on chromosome 2 R (Muller element C, chromosome V in the housefly) in Drosophila melanogaster. f The 9-bp direct repeats (TTTTAGGTT) are found with one copy in non-M^V-contigs at insertion sites, indicated by the red dashed-line box. In non-M^V-contigs, the upstream and downstream sequences of TTTTAGGTT match with the upstream and downstream sequence of M^V (indicated by the blue and orange shading). g Two examples of other genomic regions that contain the same tandem repeat blocks as M^V. The self-alignment figures demonstrate M^V-like palindromic structures in Contig1514 and Contig1321. Alignment between Contig1514 and Contig1321 shows sequence similarity only for the palindromic region but not for the palindrome flanking sequences. The TIRs in M^V are also found in Contig1514 and Contig1321 palindromes, and direct repeats with the same 9-bp length are flanking them.