The mitochondrial genome ofIsognomon nucleusand mitogenomics of pteriomorphia (Bivalvia: Autobranchia)

Due to the paucity of morphological characters and extensive convergent evolution, bivalve classification is a challenging, two-centuries-old problem (Giribet & Wheeler, 2005; Bieler et al., 2014; Lemer et al., 2016; Giribet & Edgecombe, 2020). Consequently, it is not surprising that morphology-based phylogenies conflict with sequence-based phylogenies (Giribet & Wheeler, 2005; Tëmkin, 2010; Bieler et al., 2014; Lemer et al., 2016; Giribet & Edgecombe, 2020). Pearl oysters (superfamily Pterioidea) make critical contributions to shellfisheries and pearl harvesting. Despite extensive study, their systematic placement and relationships with other taxa within the subclass Pteriomorphia remain disputed (Steiner & Hammer, 2000; Giribet & Distel, 2003; Matsumoto, 2003; Tëmkin, 2006, 2010). Previously, a phylogeny of pearl oysters was estimated using four genetic markers (three nuclear and one mitochondrial) in combination with morphological characters (Tëmkin, 2010). Despite the high taxonomic coverage of Pterioidea species (c. >80%), these four genes may not accurately capture deep divergences, some of which are more than 470 Myr old (Tëmkin, 2010). Resolving deep relationships may require phylogenomic approaches, which are starting to be applied to bivalves and other molluscs (Kocot et al., 2011; González et al., 2015; Lemer et al., 2016; Lemer, Bieler & Giribet, 2019). Nevertheless, despite decreasing sequencing costs, obtaining transcriptome and genome data still requires considerable resources, and assembling high-quality mollusc genomes is hindered by the difficulty in isolating long DNA fragments (due to the presence of polysaccharides), high heterozygosity and abundant long repeats (Sigwart et al., 2021).