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Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome
Ist Teil von
Genes & Genomics, 2018, 40(5), , pp.485-495
Ort / Verlag
Seoul: The Genetics Society of Korea
Erscheinungsjahr
2018
Quelle
MEDLINE
Beschreibungen/Notizen
TC1
/
Mariner
transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (
Bombyx mori
) has a large amount of
TC1
/
Mariner
elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670
TC1
/
Mariner
(
Bmmar
) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of
TC1
/
Mariner
were grouped into five subgroups:
Mariner, Tc1, maT
, DD40D and DD41D/E. Of these five subgroups,
maT
rather than
Mariner
possessed most members of
TC1
/
Mariner
(51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that
Bmmar15
(DD40D) formed a new basal subgroup of
TC1
/
Mariner
element in insects, which was referred to as
bmori
. Furthermore, we concluded that DD40D appeared to intermediate between
mariner
and
Tc1
. Finally, we estimated the insertion time for each copy of
TC1
/
Mariner
in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that
Bmmar1, Bmmar6
and
Bmmar9
had EST evidence and intact transposases. These implied that
TC1
/
Mariner
might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of
TC1
/
Mariner
in the insect genomes.