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Title: Characterization and Diversity of Novel PIF/Harbinger DNA Transposons in Brassica Genomes
Authors: Nouroz, Faisal
Noreen, Shumaila
Heslop-Harrison, J. S. (Pat)
First Published: 19-Feb-2016
Publisher: Pakistan Botanical Society
Citation: Pakistan Journal of Botany, 2016, 48 (1), pp. 167-178
Abstract: Among DNA transposons, PIF/Harbinger is most recently identified superfamily characterized by 3 bp target site duplications (TSDs), flanked by 14-45 bp terminal inverted repeats (TIRs) and displaying DDD or DDE domain displaying transposase. Their autonomous elements contain two open reading frames, ORF1 and ORF2 encoding superfamily specific transposase and DNA-binding domain. Harbinger DNA transposons are recently identified in few plants. In present study, computational and molecular approaches were used for the identification of 8 Harbinger transposons, of which only 2 were complete with putative transposase, while rest 6 lack transposase and are considered as defective or non-autonomous elements. They ranged in size from 0.5-4 kb with 3 bp TSDs, 15-42 bp TIRs and internal AT rich regions. The PCR amplification of Brassica Harbinger transposase revealed diversity and ancient nature of these elements. The amplification polymorphism of some non-autonomous Harbingers showed species specific distribution. Phylogenetic analyses of transposase clustered them into two clades (monocot and dicot) and five sub-clades. The Brassica, Arabidopsis and Malus transposase clustered into genera specific sub-clades; although a lot of homology in transposase was observed. The multiple sequence alignment of Brassica and related transposase showed homology in five conserved blocks. The DD₃₅E triad and sequences showed similarity to already known Pong-like or Arabidopsis ATISI12 Harbinger transposase in contrast to other transposase having DD₄₇E or DD₄₈E motifs. The present study will be helpful in the characterization of Harbingers, their structural diversity in related genera and Harbinger based molecular markers for varietal/lines identifications.
ISSN: 0556-3321
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © 2016, Pakistan Botanical Society. Archived with permission of the publisher.
Appears in Collections:Published Articles, Dept. of Genetics

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