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© 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. The complete mitogenomes of one (M-)ale (North America), one Hermaphroditic (Europe), and two (F-)emale (North America and Europe) individuals of the freshwater pearl mussel Margaritifera margaritifera were sequenced. The M-type and F-type (Female and Hermaphroditic) mitogenomes have 17,421 and 16,122 nucleotides, respectively. All with the same content: 13 protein-coding genes, 22 transfer RNA, two ribosomal RNA genes, and one sex-related ORF. The M-type is highly divergent (37.6% uncorrected p-distance) from the F-type mitogenomes. North American and European F-type mitogenomes exhibit low genetic divergence (68 nt substitutions), and the Female and Hermaphroditic European mitogenomes are almost identical, and matching sex-related ORFs.

The unionid family Margaritiferidae, comprising 12 extant species, is widely distributed across the northern hemisphere in North America, Europe and Asia (Bolotov et al., 2016). Most species in this family have dramatically declined over the last century, with nine of the 12 species assessed as threatened in the most recent IUCN Red List (IUCN, 2016). Among these is the Moroccan pearl mussel Margaritifera marocana (Pallary, 1918), considered one of the 100 most threatened species on the planet (Baillie & Butcher, 2012). This species is now restricted to two small streams in the Oum Er Rbia and Sebou basins and conservation measures are urgently needed (Sousa et al., 2016). Beyond the conservation concern, Unionida are also biologically interesting. They present an unusual mechanism of mitochondrial inheritance called doubly uniparental inheritance (DUI), in which all individuals have the typical maternally transmitted mtDNA (F-type), but the males possess in their germ cells a paternally inherited mtDNA instead (M-type) (Zouros et al., 1994; Breton et al., 2009). So far, DUI has been observed in over 100 species from four bivalve orders (Gusman, Azuelos & Breton, 2017), including three families within Unionida, i.e. Unionidae, Hyriidae and Margaritiferidae (Walker et al., 2006). However, to date, no whole M-type mitogenome has been published for any species belonging to the last two of these families.