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Abstract

Recently, the genome of the ctenophore Mnemiopsis leidyi was resequenced to its full potential (i.e., gapless, telomere-to-telomere). Compared to the existing reference genome, the newer assembly contains over 50 megabase pairs (Mb) of additional genome. The new assembly covers most, if not all, repeat regions and opens the possibility to re-annotate and evaluate unique new elements in the genome. In this study, a comprehensive pipeline from repeat annotation and masking to gene prediction evaluation was created with strong reference to best practices observed in the literature. The resulting reannotation contains 15,545 gene models, 1003 less than the previous annotation. However, all completeness metrics used to evaluate the reannotation increased not only relative to the previous annotation, but also relative to the other existing ctenophore annotations. In addition, the repeat landscape of ctenophores was assessed by capturing the age and bursts of expansion of TEs. Notable differences between the genomes of the analyzed lobates and cydippids are observed, suggesting potential mechanisms that ultimately led to the diversification of these ctenophore lineages. Furthermore, annotation of rRNA gene copies shows that highly complex regions, which can be problematic for genome assembly, have been correctly captured and resolved. Lastly, synteny studies were performed, placing M. leidyi within the range of such analyses for the first time. They show consistency with previous studies in the literature that define ctenophores as the sister group to all other animals. This re-annotation effort provides a stepping stone towards a better understanding of the biology of this species and offers a reliable reference for future in silico or experimental studies.