Genome skimming of Poecilosclerida (Porifera) reveals conserved and hyperrearranged mitochondrial genomes

Genome skimming is a cost-effective approach that efficiently recovers multi-copy genomic regions, making it particularly valuable for phylogenetic research and biodiversity assessments. In this study, we applied shallow shotgun metagenome sequencing to 15 poecilosclerid sponges, successfully assembling complete mitochondrial genomes for four species and full rDNA clusters for the majority of samples, despite considerable variation in the retrieval of genomic regions and exogenous, non-poriferan sequences. Phylogenetic reconstructions using both rDNA and mtDNA sequences uncovered extensive polyphyly within several key families, such as Coelosphaeridae and Mycalidae, underscoring significant systematic inconsistencies at generic, familial, and ordinal levels, and emphasizing the need for comprehensive taxonomic revision throughout Poecilosclerida to reflect natural groups. The mitogenomes obtained from Clathria ( Microciona ) sp. (18,725 bp), Desmapsamma anchorata (19,099 bp), Latrunculia biformis (19,630 bp), and Neopodospongia tupecomareni (19,983 bp) exhibited conserved architectural features typical of the order, alongside notable variations such as gene overlaps, non-canonical start codons, and an unusual fused nd3 :: nd4L gene. Our findings highlight the applicability of genome skimming for phylogenetics and metagenomic insights, though success can vary due to biological and methodological factors. This approach has proven to be a cost-effective and powerful tool for advancing sponge systematics, despite challenges in assembling hyperrearranged mitogenomes in certain lineages, paving the way for broader genomic surveys in non-model organisms.