Identification and evolutionary genomics of novel LTR retrotransposons in Brassica

Brassica Copia retrotransposon motifs. Nouroz et al. 2015
Brassica Copia retrotransposon motifs. Nouroz et al. 2015

315. Nouroz F, Noreen S, Heslop-Harrison JS. 2015. Identification and evolutionary genomics of Novel LTR retrotransposons in Brassica. Turkish Journal of Biology 39: 740-757 DOI: 10.3906/biy-1501-77

Link to manuscript PDF download at publisher site

Retrotransposons (REs) are the most abundant and diverse elements identified from eukaryotic genomes. Using computational and molecular methods, 262 intact LTR retrotransposons were identified from Brassica genomes by dot plot analysis and data mining. The Copia superfamily was dominant (206 elements) over Gypsy (56) with estimated intact copies of ~1596 Copia and 540 Gypsy and ~7540 Copia and 780 Gypsy from Brassica rapa and Brassica oleracea whole genome respectively. Canonical Copia and Gypsy gag-pol polyprotein organizations were observed in most elements with few displaying 1-3 additional or internally deleted domains. The PBS and PPT motifs were identified with tRNA complementary to tRNAMet, or rarely other tRNA types. PCR amplification of RT regions revealed their abundance and distribution among A, B and C-genome Brassicas indicating their origin from a common ancestor. The evolutionary relationship of Brassica REs resolved them into superfamily (Copia/Gypsy) specific lineages. The phylogenetic analysis of 130 Brassica Copia clustered them into 2 clades, 10 sub-clades of 18 families, while Gypsy elements clustered into 2 clades. The results enabled the identification and understanding of the structure and nature of full length REs and their derivatives in Brassica. The markers derived here will be useful for examining chromosome and genome evolution in Brassica.

Key words: LTR retrotransposons, Brassica, Copia, Gypsy, evolutionary relationship, RTAP markers

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