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O presente artigo de trabalho de conclusão de curso tem como objetivo apresentar soluções para o gestor e colaboradores de uma empresa distribuidora de descartáveis, localizada na região da Vila Guarani, na Zona Sul de São Paulo. As soluções foram obtidas a partir de estudos utilizando a metodologia 5S e ferramentas como o Diagrama de Ishikawa, Matriz G.U.T e o método de Pareto. O intuito com a aplicação das soluções encontradas é transformar o ambiente de trabalho, adequando-o às normas de trabalho existentes, proporcionando mais segurança e conforto para os colaboradores., Case study: Management tools applied in a disposables company to obtain improvements.

Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species, with a dispersed geographic distribution across the world’s freshwater ecosystems. Despite their fundamental ecological importance, they are highly threatened, being the faunal group with the highest records of wild extinctions. To date, only five freshwater mussel species have had their whole genome sequenced, of which only two are from European species. Here, we present the first genome assembly of the painter’s mussel, Unio pictorum (Linnaeus, 1758), the type species representative of the order and the most widespread species of the genus in Europe. We used long-read PacBio HiFi sequencing reads to produce a highly contiguous assembly that will pave the way for the study of European freshwater mussels in the Genome Era.

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly ofMargaritifera margaritifera(Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. Theab initiogene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species’ unique biological and evolutionary features that ultimately will help to promote its conservation.

The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast, and easily applied strategy for phylogenetic inference of non-model organisms. However, many existing pipelines used to create phylogenomic datasets from target capture data are incapable of incorporating whole genome sequencing data into their workflows. Here, we develop a highly efficient pipeline for capturing and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline allows capturing targeted loci accurately and efficiently, and given its unbiased nature, can easily be expanded to be used with any other target capture probe set. We demonstrate the utility of our approach by incorporating whole genome sequencing data into a recently developed target capture probe set to reconstruct the evolutionary history of the freshwater mussel family Margaritiferidae, reconstructing supraspecific relationships outside the Unionidae family, providing the first comprehensive multi-loci phylogeny of the Margaritiferidae. We also provide a catalogue of well-curated functional annotations of the targeted regions for the target capture probe set, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.

In this study, we present an announcement of Novaya Zemlya Collared Lemming Dicrostonyx torquatus ungulatus (von Baer, 1841) complete mitogenome. This rodent was described historically as an Arctic Collared Lemming subspecies endemic to Novaya Zemlya (Arctic Russia) but its taxonomic status was unclear due to the lack of available molecular data. Based on a comprehensive mitogenomic phylogeny of the Arctic Collared Lemming, we show that this insular population shares a highly divergent mtDNA sequence (total length 16,341 bp). Hence, it should be considered a valid subspecies of the Arctic Collared Lemming. Our findings support the hypothesis that the Novaya Zemlya Archipelago had served as a cryptic polar refugium for cold-tolerant terrestrial and freshwater taxa since the mid-Pleistocene or even earlier.

The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems. In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms. Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species., This research was partially supported by the ERA-NET BlueBio COFUND Project SIDESTREAM [Grant ID 68], co-funded through national funds provided by FCT [BLUEBIO/0005/2019]; Agencia Estatal de Investigación [PCI2020-111960], NRC – Norwegian Research Council [#311701]. A.G.S. was funded by the Portuguese Foundation for Science and Technology (FCT) under the Grant [SFRH/BD/137935/2018]. Additional strategic funding was provided by FCT [UIDP/04423/2020].

The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with Pacbio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3 % of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus Scomber.

South-western Australia is isolated from other forested regions of Australia by desert and bounded on southern and western sides by the Southern and Indian Oceans, respectively, with Westralunio carteri (Iredale, 1934) as the sole endemic freshwater mussel. Its conservation status is vulnerable. This species has a history of nomenclatural change and its systematic placement and population genetic history are largely unknown. We sampled 46 individuals from 13 sites across W. carteri’s distribution and sequenced two mitochondrial genes (16S rDNA and cytochrome c oxidase subunit I) and one nuclear gene (28S rDNA). The mitochondrial haplotype networks and COI phylogenies revealed three evolutionarily significant units (ESUs): “W. carteri” I including the west coast populations, “W. carteri” II from the south and south-eastern range, and “W. carteri” III only occurring in the south-western tip of Australia. Four species delimitation methods identified two molecular operational taxonomic units supporting two distinct species (“W. carteri” I and “W. carteri” II + III). Phylogeographic patterns revealed herein confirm the historical separation of Western and Southern paleo-basins, also highlighting the isolation of the south-western extremity of the region. This underlines the need for taxonomic revision and will require a re-evaluation of W. carteri’s conservation status.

Mollusca is the second most species-rich phylum within the metazoans, displaying critical economic, ecological and scientific importance. Yet, they are still largely underrepresented with respect to genomic resources. The emergence of next-generation sequencing technologies has revolutionized deep-scale genomic characterization of non-model organisms, and molluscs are slowly entering this transformative era. Here, we provide a historical contextualization of the Genome Revolution in molluscs with a tour de force revision of key research trends observed over the past decade. Omic approaches such as RAD-seq, transcriptome, mitogenome and whole-genome sequencing represent the most significant resources produced for this phylum. Importantly, the molecular mechanisms underscoring multiple biological novelties and adaptations observed in molluscs are starting to be unravelled. In contrast, compared to other metazoan lineages the genomic resources currently available for this lineage still lag far behind. We put forward that to fully grasp the evolutionary and adaptive roads of this tantalizing group of organisms crucially depends on the full embracement of high-throughput sequencing (HTS) technologies in the near future.

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation. A.G.-d.-S. was funded by the Portuguese Foundation for Science and Technology (FCT) under the grants SFRH/BD/137935/2018, EF (CEECIND/00627/2017) and MLL (2020.03608.CEECIND). This research was developed under ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project No. NORTE-01-0145-FEDER- 030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020. Authors’ interaction and writing of the article was promoted and facilitated by the COST Action CA18239: CONFREMU—Conservation of freshwater mussels: a pan- European approach. info:eu-repo/semantics/publishedVersion

Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddoni sp. nov. and Leguminaia anatolica sp. nov. Six additional taxa, Unio delicatus stat. rev., Unio eucirrus stat. rev., Unio hueti stat. rev., Unio sesirmensis stat. rev., Unio terminalis stat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensis stat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt and Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities. We thank John Pfeiffer and David Zanatta for their helpful comments and suggestions to improve the quality of the manuscript, Jamie Smith for the help with the shell images and Cindy Bogan for reviewing and formatting several versions of the manuscript and supplementary appendix. We also like to thank the following people for their assistance with the identification and/or access to specimens or images of museumtype lots. Adam Baldinger, Museum of Comparative Zoology, Harvard University, Paul Callomon, Academy of Natural Sciences of Drexel University, Philadelphia, John Pfeiffer Smithsonian Institution, Washington D.C., Karl-Otto Nagel, Senckenberg Museum, Frankfurt, Maxim Vinarski, Saint Petersburg State University, Russia, and Harriot Wood, National Museum of Wales, Cardiff. This work was supported by a Conchological Society of Great Britain & Ireland Grant Award to MLL entitled “Conservation and Phylogeography of the Eastern Mediterranean Naiads (Bivalvia: Unionoida), the European Union’s Horizon 2020 research and innovation programme - BIOPOLIS, grant agreement no. 857251, and the project ConBiomics: the missing approach for the Conservation of Freshwater Bivalves Project No. NORTE-01-0145- FEDER-030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT - Fundação para a Ciência e a Tecnologia, through national funds, the strategic funding UIDB/04423/2020 and UIDP/04423/2020 provided by FCT. FCT also supported MLL (2020.03608.CEECIND), EF (CEECIND/00627/2017), and AGS (SFRH/BD/137935/2018). The Ministry of Science and Higher Education of the Russian Federation supported INB (project 0793-2020- 0005) and AAT (project AAAA-A18-118012390161-9). The Russian Science Foundation funded INB (project No. 21-17-00126), IVV (project 19-14-00066). The Russian Foundation for Basic Research supported AVK (project 18-44-292001). Interactions of authors and writing of the paper were promoted and facilitated by the COST Action CA18239: CONFREMU - Conservation of freshwater mussels: a pan-European approach. info:eu-repo/semantics/publishedVersion

Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini. FCT: PTDC/ART-DAQ/29537/2017/ FEDER: POCI-01-0145-FEDER-029537/ PT2020 COMPETE 2020 – FCT: UIDB/04423/2020, UIDP/04423/2020 / SFRH/BD/137935/2018/ SFRH/BD/147493/2019 PTDC/ASP-PES/28053/2017 info:eu-repo/semantics/publishedVersion

Graylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.

Cartilaginous fish are fascinating taxa, present in the folklore and art of many different cultures. Moreover, they display several unique anatomical, physiological, molecular, and behavioral characteristics making them extremely interesting from a biological perspective. Nevertheless, some crucial knowledge gaps remain, including phylogenetic relationships among extant species. Here, we produced the complete mitogenome sequence of the large-eyed rabbitfish, Hydrolagus mirabilis (Chimaeriformes). The complete mitogenome is 19,435 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA, and two ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions including 12 Holocephalan and three outgroup Elasmobranch mitogenomes place the H. mirabilis within the family Chimaeridae but revealed paraphyletic Hydrolagus and Chimaera, in line with a previous study, highlighting the importance for collecting additional molecular data to improve phylogenetic reconstruction in this group of vertebrates.

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2,4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a ‘textbook description’. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed ‘doubly uniparental inheritance’. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

Nuclear receptors (NRs) are key transcription factors that originated in the common ancestor of metazoans. The vast majority of NRs are triggered by binding to either endogenous (e.g. retinoic acid) or exogenous (e.g. xenobiotics) ligands, and their evolution and expansion is tightly linked to the function of endocrine systems. Importantly, they represent classic targets of physiological exploitation by endocrine disrupting chemicals. The NR gene repertoire in different lineages has been shaped by gene loss, duplication and mutation, denoting a dynamic evolutionary route. As the earliest diverging class of gnathostomes (jawed vertebrates), cartilaginous fishes offer an exceptional opportunity to address the early diversification of NR gene families and the evolution of the endocrine system in jawed vertebrates. Here we provide an exhaustive analysis into the NR gene composition in five elasmobranch (sharks and rays) and two holocephalan (chimaeras) species. For this purpose, we generated also a low coverage draft genome assembly of the chimaera small-eyed rabbitfish, Hydrolagus affinis. We show that cartilaginous fish retain an archetypal NR gene repertoire, similar to that of mammals and coincident with the two rounds of whole genome duplication that occurred in the gnathostome ancestor. Furthermore, novel gene members of the non-canonical NR0B receptors were found in the genomes of this lineage. Our findings provide an essential view into the early diversification of NRs in gnathostomes, paving the way for functional studies.

The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs)., This research was developed under ConBiomics: the missing approach for the Conservation of Freshwater Bivalves Project No. NORTE-01-0145-FEDER-030286, co-financed by COMPETE 2020, Portugal 2020, and the European Union through the ERDF, and by the Portuguese Foundation for Science and Technology (FCT) through national funds, and Strategic Funding UIDB/04423/2020 and UIDP/04423/2020. FCT also supported A.G.S. (SFRH/BD/137935/2018) and S.V. (UID/AGR/04033/2019). A.Z.was supported by an Anne McLaren Research Fellowship from the University of Nottingham. I.N.B. was supported by the Ministry of Science and Higher Education of Russia (Project No. AAAA-A18-118012390161-9 and Project No. FSRU 2020-0007) and the Russian Scientific Fund (Project No. 19-04-00066).

The IUCN Red List assessments are essentially based on population trends and range, namely Area of Occupancy (AOO) and Extent of Occupancy (EOO). Range estimations are based on fixed grids, but this is likely inappropriate for species living in river networks. Furthermore, AOO and EOO are measured using the whole hydrographic network, therefore disregarding temporary sections, which is particularly problematic in arid and semi-arid regions. Here we mapped the permanent hydrographic network of Morocco using satellite imagery, complemented with field surveys to collect samples for molecular analyses of the five freshwater mussel species present and assess their distribution. The phylogeographic patterns are described for each species and used to identify priority areas and evolutionary significant units for conservation. Permanent hydrographic river sections represent only 18.3% of the whole hydrographic network. A north-to-south gradient of genetic diversity, species richness and distribution range was found, being coherent with water availability and river intermittence. Isolated evolutionary units were detected in southern basins that should also receive particular attention in conservation planning. We propose the mean river width multiplied by the extent of the river network as the best and the most adequate way to estimate both EOO and AOO. Given the worldwide degradation of freshwater systems and biodiversity, an accurate (re)assessment of species conservation status supported with maps of intermittent water bodies will be essential for prioritizing and guiding conservation actions and management plans, especially in arid and semi-arid regions., This work was partially supported by the Portuguese Foundation for Science and Technology (FCT) under grant SFRH/BD/115728/2016 (MLL) and grant SFRH/BD/137935/2018 (AGS). This research was developed under ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project N° NORTE-01-0145-FEDER-030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds. This study was additionally conducted within the scope of project “Biodiversity and conservation of the critically endangered freshwater mussels in Morocco: ecogeographic, genetic and physiological information”, funded by Mohamed bin Zayed Species Conservation Fund (Reference 15256799) and project “Breeding the most endangered bivalve on Earth: Margaritifera marocana”, funded by IUCN SOS save our species fund (Reference 2015B-015). Official capture and sampling licenses were issued by the Université Cadi Ayyad (Faculté des Sciences, Semlalia, Marrakech, Maroc).

Freshwater mussels are a critically imperiled group of mollusks that play key ecological roles and provide important services to humans. The Ambleminae is the only subfamily of these mussels, endemic to North America. Complete mitogenomes have only been sequenced for two of five tribes of the subfamily. Pleurobema oviforme, Amblema plicata, and Popenaias popeii each belong to tribes Pleurobemini, Amblemini, and Popenaidini, respectively, and have not had published mitogenomes. Thus, this study aims to present the complete mitogenomes for these species, to provide a phylogeny of the Ambleminae and confirm the gene arrangements with representation from each of its tribes. The newly sequenced mitogenomes range from 15,852 to 15,993 nucleotides, are composed of 13 PCGs, 22 tRNAs, and two rRNAs and all share the same (UF1) gene order. This work was supported by Portuguese Foundation for Science and Technology (FCT) [grant number ConBioMics/BI-Lic/2019-037 (JTT), grant number SFRH/BD/137935/2018 (AGS)]; COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by Portuguese Foundation for Science and Technology (FCT) through national funds [UID/Multi/04423/2019] under project ConBiomics: the missing approach for the Conservation of Bivalves Project, and [project number NORTE-01- 0145-FEDER-030286]. Fieldwork in Texas was funded by the U.S. Fish and Wildlife Service, and Texas Parks and Wildlife Department (TPWD) as a Joint Traditional Section 6 Project 407348. info:eu-repo/semantics/publishedVersion

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., This work was supported by Portuguese Foundation for Science and Technology (FCT) [grant number SFRH/BD/115728/2016 (MLL), grant number SFRH/BD/137935/2018 (AGS)]; Russian Foundation for Basic Research [grant number 18-34-20033 (IVV)]; Dawson Fellowship at St. Catharine's College, Cambridge (DCA); Life Margal Ulla [number LIFE09 NAT/ES/000514 (RA and PO)]; COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by Portuguese Foundation for Science and Technology (FCT) through national funds [UID/Multi/04423/2019] under project ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project, and [project number NORTE-01-0145-FEDER-030286]; Federal Agency for Scientific Organizations under Grants [grant number 0409-2015-0143 (INB and IVV)]