Data to: First report on presence of mitochondrial introns in freshwater sponges, and pseudogenic evidence of their loss

Citation: Zhao, Zhen and Ma, Junye and Yang, Qun and Wörheide, Gert and Erpenbeck, Dirk: Data to: First report on presence of mitochondrial introns in freshwater sponges, and pseudogenic evidence of their loss. 15. October 2025. Open Data LMU. 10.5282/ubm/data.699

Abstract

Mitochondrial introns have a patchy distribution in sponges lineages. Here, we report on the finding of a group-II-intron in Eunapius rarus (Demospongiae, Spongillidae), which constitutes the first report of a mitochondrial intron in freshwater sponges. Group-II-introns are self-splicing ribozymes, and are particularly rare among sponge mitochondrial genomes. The intron contains complete open reading frames (ORFs), including typical intron-encoded proteins (IEPs). Phylogenetic analysis reveals that the intron is more closely related to those found in brown algae, and distant from other sponge group-II-introns, indicating an acquisition of this intron independent from other sponges. Remarkably, the congeneric E. fragilis does not possess this intron in their mitochondrial genome. However we found pseudogenic copies of the E. rarus group-II-intron in the nuclear genome of E. fragilis, which indicates patterns of group-II-intron presence and their pseudogene transposition into the nuclear genomes in sponges for the first time. Our results show that a group-II-intron must have been present in the last common ancestor of both Eunapius mt genomes, and subsequently lost in E. fragilis, rather than independent acquisition. Consequently, our findings provide an explanation for the patchy distribution of introns in sponges as a result of frequent losses, besides multiple acquisitions.

Uncontrolled Keywords

group-II-intron, mitochondrial intron, Porifera, freshwater sponges, Numt, Eunapius

• Item Type: Data
• Contact Person: Erpenbeck, Dirk
• E-Mail of Contact: erpenbeck at lmu.de
• Subjects: Biology
• Dewey Decimal Classification: 500 Natural sciences and mathematics; 500 Natural sciences and mathematics > 550 Earth sciences; 500 Natural sciences and mathematics > 590 Zoological sciences