Identification and characterization of mobile genetic elements LINEs from Brassica genome

• Published in: Gene 2017-09, Vol.627, p.94-105
• Main Authors: Nouroz, Faisal, Noreen, Shumaila, Khan, Muhammad Fiaz, Ahmed, Shehzad, Heslop-Harrison, J.S. Pat
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Brassica; Brassica - classification; Brassica - genetics; Data Mining; Diversity; Genome, Plant; LINEs; Long Interspersed Nucleotide Elements; Open Reading Frames; Phylogeny; Retrotransposons; Reverse transcriptase; RNA-Directed DNA Polymerase - chemistry; Sequence Alignment
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2017.06.015

Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to ‘R’ and ‘I’ type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II–V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars. •Transposable elements especially retrotransposons are major drivers of genome evolution including LINE related elements•Using computational and molecular methods, 30 intact and 4 non-autonomous LINEs were identified from Brassica genomes•Structural features, protein domain organizations, evolutionary dynamics and abundance of 4 novel LINE families were described in Brassica•The molecular analysis by PCR methods confirmed the presence and distribution of LINE families in various Brassica cultivars•The LINEs described and annotated here will be helpful to understand the LINEs landscape and evolution in Brassica and related genera Arabidopsis