Differential Activity of Genes with IS630/TC1/MARINER Transposon Fragments in the Genome of the Ctenophore Mnemiopsis leidyi

Abstract—Mobile genetic elements (MGEs) have a significant impact on genome structure and function being also a source of new genes. As a result of “molecular domestication,” genes encoded by MGEs become functional parts of the host genome. The IS630/Tc1/mariner (ITm) DNA transposon superfamily is one of the most widespread and diverse. To date, several genes are known to have resulted from the ITm transposon co-option. The aim of the present work was to search for the ctenophore Mnemiopsis leidyi genes with integrated fragments of ITm-transposons and subsequent analysis of their of expression levels. In the present work, the local alignment method (BLASTn) was used to search for the hypothetical chimeric genes. The analysis of differential gene activity was performed with the combined use of the Kallisto and Sleuth software. No cDNAs were found that would match the full coding sequence of any M. leidyi ITm transposase. However, 21 unique transcripts of hypothetical chimeric genes containing regions homologous to ITm transposons have been found. Transcriptional analysis showed that during early embryonic development, as well as in the crest and epithelium tissues of adult animals, most hypothetical chimeric genes are not expressed or are expressed at a low level. However, several loci showed differential activity levels during regeneration. The differential activity of some hypothetical chimeric genes during regeneration may indicate their possible “domestication” and involvement in molecular genetic processes in ctenophores.