Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification
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Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.
KeywordsTransposable element Retrotransposon Consensus sequence Polymerase chain reaction Trifolium Clover Sanger sequencing
KEB, SM, TS, VD, and RMS were supported by Loyola University undergraduate research fellowships. We thank Emily Welebob and Stephanie Vargas for their experimental contributions, Stefan Kanzok for qPCR guidance, and Haley Luebke for helpful suggestions.
Compliance with ethical standards
Conflict of interest
The authors declare that there is no conflict of interest.
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