Phylogenetic analysis, gene rearrangement and divergence time estimation of Patellogastropoda (Mollusca, Gastropoda) based on complete mitochondrial genomes.

Background: Patellogastropoda, or true limpets, is a major taxonomic group within the Gastropoda, Mollusca. The complete mitochondrial genomes have been widely used to study the phylogenetic relationships of Patellogastropoda. To further enhance the understanding of the phylogenetic relationships among families within this subclass, we obtained the complete mitochondrial genome sequences of five species using third-generation sequencing technology: Limalepeta lima, Lepeta kuragiensis, Lottia versicolor, Lottia instabilis, and Lottia tenuisculpta. We examined mitochondrial genome structure, nucleotide composition and skew, as well as amino acid content and codon usage. Additionally, we assessed selective pressures on protein-coding genes in Lepetidae and Lottiidae species, constructed a phylogenetic tree for Patellogastropoda, analyzed gene arrangement, and estimated the divergence times within Patellogastropoda.

Results: The mitochondrial genomes of these five species all encoded 38 genes. They exhibited a higher AT base content, and the protein-coding genes were under purifying selection. The Patellogastropoda was divided into two clades: Clade 1 included a part of the Lottioidea superfamily and the Patelloidea superfamily, whereas the Lottiidae family within the Lottioidea superfamily formed a separate clade (Clade 2). The mitochondrial genomes of the Patellogastropoda exhibited extensive gene rearrangements, particularly those in Lottiidae, which were the most complex. The Patellogastropoda lineage was estimated to have originated in the Paleozoic Permian era, with active differentiation occurring in the Mesozoic Cretaceous and the Cenozoic era.

Conclusions: Our research results contribute to a better understanding of the phylogenetic relationships within the Patellogastropoda, and reveal the extensive gene rearrangements, providing further insights into the evolution and genetics of gastropods.