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Retrotransposons are mobile genetic elements which transpose via an RNA intermediate. Because the transposition of retrotransposons causes insertional mutagenesis in a genome, the activation of retrotransposons has been used for basic and applied genome studies in plant biology. Some retrotransposons were shown to be transcriptionally activated by biotic and abiotic stress factors, such as UV light, ozone, pathogens, wounding, and drought. A pulsed streamerlike discharge in water is known to generate physical phenomena, such as high electric fields, UV, ozone, other chemically active species, and shock waves. In this paper, an underwater pulsed discharge treatment was used as a new tool for the activation of retrotransposons in a Porphyra yezoensis genome. The results of reverse-transcription polymerase chain reaction for the discharge treatment of P. yezoensis showed that a copia-like retrotransposon, called PyRE1G1, was transcriptionally activated by the underwater pulsed discharge without cell damage. The effects of pulse parameters on the mRNA accumulation of PyRE1G1 showed that a certain charging voltage and larger applied pulse numbers gave sufficient results for the transcriptional activation of PyRE1G1. The maximum activation of the PyRE1G1 expression was induced 1 h after the discharge treatment.