Identification and evolutionary genomics of novel LTR retrotransposons in Brassica

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 genomes, respectively. Canonical Copia and Gypsy gag-pol polyprotein organizations were observed in most elements with a 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 a common ancestor. The evolutionary relationship of Brassica REs resolved them into superfamily-specific (Copia/Gypsy) lineages. The phylogenetic analysis of 130 Brassica Copia clustered them into 2 clades and 10 sub-clades of 18 families; Gypsy elements clustered into 2 clades. The results enabled 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.