Experimental validation of transposable element insertions using the Polymerase Chain Reaction (PCR)

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Authors

Miriam Merenciano, Marta Coronado-Zamora, Josefa Gonzalez

Abstract

Transposable elements (TEs), also known as transposons, are repetitive DNA sequences, present
in virtually all organisms, that can move from one genomic position to another. TEs can be a
source of mutations with important consequences for organisms. Despite their interest, its
repetitive nature has made their study very challenging. However, the emergence of new
sequencing technologies that allow obtaining long-read sequences, has improved the in silico de
novo detection and annotation of TEs. The de novo annotation of TEs has already been performed
in several organisms including the fruit fly Drosophila melanogaster. Yet, experimental validation
can be used to confirm the presence of TEs in specific D. melanogaster natural populations. Here,
we present a step-by-step protocol to experimentally validate by polymerase chain reaction (PCR)
the presence and/or absence of TEs in natural populations of D. melanogaster. This detailed
protocol has been implemented in the participant high schools of the Citizen Fly Lab activity that
is part of the international citizen science project Melanogaster: Catch the Fly!
(https://melanogaster.eu). Specifically, the students collaborate with the scientists of the
European Drosophila Population Genomics Consortium (DrosEU) in the experimental validation
of new genetic variants, previously identified using bioinformatic techniques.

DOI

https://doi.org/10.32942/osf.io/g5xhz

Subjects

Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences

Keywords

Dates

Published: 2022-07-30 21:06

License

CC-By Attribution-NonCommercial-NoDerivatives 4.0 International

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