Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes

Prokaryotic and Eukaryotic Horizontal Transfer of Sailor (DD82E), a New Superfamily of IS630-Tc1-Mariner DNA Transposons

“…Then, these transposase sequences were used as a query to search the genomes deposited in the National Center for Biotechnology Information (NCBI) genome project database (https://blast.ncbi.nlm.nih.gov/Blast, accessed on 25 October 2020) using TBLASTN with an E-value of 1e-100. Subsequently, the best hits were extracted with 2-kb flanking sequences, since most ITm families contain TIRs (including untranslated region) less than 2 kb as previous studies reported, such as DD35E/TR [20], DD36E/IC [21], DD38E/IT [22], DD37D/maT [23], DD39D/GT [23]. The presence of TIRs and TSDs was manually screened in the resulting sequences, to identify potential DNA transposons.…”

“…Variants are possible when TEs are immobilized and cannot proceed to the amplification stage or are weakly amplified and degrade relatively quickly. In addition, TE "resurrection" options are possible: horizontal transfer or intragenomic life-cycle restart [23,44]. Moreover, it is also possible to avoid "death" via the transition from the "wild" to "domestication" state, i.e., co-optation of the TE gene by the host genome [10,45].…”

“…The second half contains the DDE/D domain, which possesses the catalytic activity required for the excision and insertion of the TE. The GRPR-like motif is located between the two HTH motifs of the paired domain and is supposed to mediate the binding of the paired domain to the target site duplication (TSD), the TA dinucleotide [19], which has been identified in most Tc1/mariner superfamilies, such as DD35E/TR [20], DD36E/IC [21], DD38E/IT [22], DD37D/maT [23], DD39D/GT [23] and DD41D/VS [24]. The classification of ITm transposons is reliably associated with the length of the peptide chain between the second "D" and the third "E/D" amino acid residues (aa) of the catalytic domain, the so-called DDE/D signature.…”

“…The classification of ITm transposons is reliably associated with the length of the peptide chain between the second "D" and the third "E/D" amino acid residues (aa) of the catalytic domain, the so-called DDE/D signature. Nine families are classically considered, and most of their phylogenetic relationships have been updated and are well defined: DD34E/Tc1 [25], DD34D/mariner [26], DD37D/maT [23], DD39D/GT [23], DD41D/VS [24], DD35E/TR [20], DD36E/IC [21], DD37E/TRT [27] and DD38E/IT [22]. However, until recently, studies have shown that many groups of ITm transposons carry the same DDE/D signatures but have different phylogenetic origins [28][29][30].…”

Diversity and Evolution of pogo and Tc1/mariner Transposons in the Apoidea Genomes

“…Based on the phylogeny of the DDE-conserved catalytic motif, Tc1/mariner is classified into DD34E/ Tc1 [ 34 , 35 , 36 , 37 , 38 ], DD34D/ mariner [ 39 , 40 , 41 , 42 ], DD35E/ TR [ 43 ], DD36E/ IC [ 29 ], DD37D/ maT [ 44 , 45 ], DD37E/ TRT [ 46 ], DD39D/ GT [ 31 ], and DD41D/ VS [ 30 ]. The pogo transposon was first found in flies [ 47 ], then more pogo -like elements were detected, such as Tigger [ 48 ] was found in the human genome; Fot , Tan1 , Pot1 , Pot2 , Flipper, and Aft1 -transposons were found in the genome of fungi [ 49 , 50 , 51 , 52 , 53 , 54 ]; Lemi1 was found in the genome of plants [ 55 ]; and pogo -like elements were found in the teleost genome [ 56 ].…”