Secondary Structure Diversity of the Mitochondrial Small-Subunit rRNA in Porifera

Animal mitochondrial rRNAs are commonly viewed as structurally reduced, yet sponge mt SSU rRNAs range from compact to highly expanded structures. Using nine conserved structural anchors, we compared 216 taxonomically resolved records from four classes and 22 orders, including 16 freshwater Spongillida and 200 marine sponges. Twelve homologous hypervariable substructures were coded as structural types, and their ordered combinations as composite types. We identified 38 structural types and 62 composite types across molecules ranging from 853 to 2,019 nt. Hexactinellida and freshwater Spongillida were each uniform for a distinct composite type but differed markedly in overall structure: hexactinellid mt SSU rRNAs were compact, whereas those of Spongillida were long and contained four to five candidate insertion regions. These results show that a conserved scaffold can accommodate extensive lineage-associated structural variation and provide a practical framework for comparing highly divergent mitochondrial rRNAs.