Identification, characterization and diversification of non-autonomous hAT transposons and unknown insertions in Brassica

Abstract

Transposons, the mobile genetics elements played an important role in genome evolution and duplication. Several DNA transposons superfamilies are described in plants and animal genomes; CACTA, hAT, Mariner Mutator and Harbinger being the most diverse among plants. The hAT transposons are proliferating in many plant and animal species. The dot plot comparison, computational and molecular approaches were used for the characterization and diversification of non-autonomous hAT families in Brassica and 494 and 30 full length elements were collected with estimated copies of ~5052 and ~4110 from whole Brassica rapa and Brassica oleracea genomes respectively. The analysis of terminal inverted repeats (TIRs) of these hAT sequences classified them into 13 families on the basis of TIRs sequence similarities. The WebLogo of TIRs of hATs confirmed that few family based TIRs are highly conserved, while other showed variable nucleotide sequences. Transposons based sequence specific amplification polymorphism markers revealed the insertion preference of hATs in diverse Brassica genomes and found many elements as polymorphic across Brassica accessions. Some elements were A or C-genome specific, while most of them are present in Brassica diploids and allopolyploids revealing their presence before separation of A, B and C-Brassica genomes around 8 MYA. Several other unknown mobile insertions were identified with or without TIRs and TSDs of varied lengths, not common to known transposon superfamilies. The detailed study of these insertions revealed their distribution and mobile nature, which although less in numbers and small in sizes are playing a role in genome evolution.