Characterization, Comparative, and Phylogenetic Analyses of Retrotransposons in Diverse Plant Genomes

Abstract

Retrotransposons are transposable elements that use reverse transcriptase as an intermediate to copy and paste themselves into a genome via transcription. The presence of retrotransposons is ubiquitous in the genomes of eukaryotic organisms. This study analyzed the structures and determined the comparative distributions and relatedness of retrotransposons across diverse orders (34) and families (58) of kingdom Plantae. In silico analyses were conducted on 134 plant retrotransposon sequences using ClustalW, EMBOSS Transeq, Motif Finder, and MEGA X. So far, the analysis of these plant retrotransposons showed a significant genomic relationship among bryophytes and angiosperms (216), bryophytes and gymnosperms (75), pteridophytes and angiosperms (35), pteridophytes and gymnosperms (28), and gymnosperms and angiosperms (70). There were 13 homologous plant retrotransposons, 30 conserved domains, motifs (reverse transcriptase, integrase, and gag domains), and nine significant phylogenetic lineages identified. This study provided comprehensive information on the structures, motifs, domains, and phylogenetic relationships of retrotransposons across diverse orders and families of kingdom Plantae. The ubiquitousness of retrotransposons across diverse taxa makes it an excellent molecular marker to better understand the complexity and dynamics of plant genomes.