Demosponge (Porifera) mitogenomes reflect latitudinal structuration, reveal intraspecific architecture variation, and confirm mitochondrial intron splicing

Abstract Background Mitochondrial markers have historically been underused in demosponge genetic studies due to their low intra- and interspecific variability. Consequently, demosponge complete mitogenomes remain largely unexplored, even though they provide maternally inherited information that complements nuclear markers. Here, we assembled the mitochondrial genomes of 28 specimens of the ground-forming demosponge Phakellia ventilabrum across its North Atlantic distribution range to characterize them and evaluate their performance compared to already published results using restriction-site-associated DNA sequencing (RADseq) data. Results Our assemblies revealed two region-specific mitogenomes with divergent architectures and differential copy numbers. Moreover, we identified two mitochondrial introns: one in the 16S gene and another in the cox1 gene. The cox1 intron could be assigned to a group II intron, whereas the 16S intron could not be confidently assigned either to group I or group II introns. Nevertheless, BLAST results suggested horizontal gene transfer events from yeasts in both cases. The integration of RNA-seq data showed that intronic expression was significantly lower than that of exons in both the 16S and cox1 genes, confirming intron boundaries and providing strong evidence for intron splicing functionality. The genetic differentiation pattern recovered with mitochondrial markers is consistent with previous nuclear data, suggesting a differentiation between southern and northern localities. We further revealed two sympatric mitogenomic lineages in the north. Significantly, nad2 mirrored the same lineages recovered using complete mitogenomes. Conclusions This study demonstrates the value of mitogenomes for the robust evaluation of lineage differentiation in demosponges and provides new approaches for research on mitochondrial intron acquisition.