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The gill transcriptome of threatened European freshwater mussels

Publication . Gomes-dos-Santos, André; Machado, André M.; Castro, L. Filipe C.; Prié, Vincent; Teixeira, Amílcar; Lopes-Lima, Manuel; Froufe, Elsa

Genomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with high conservation concern: Margaritifera margaritifera, Unio crassus, Unio pictorum, Unio mancus and Unio delphinus. The final assemblies, with N50 values ranging from 1069–1895 bp and total BUSCO scores above 90% (Eukaryote and Metazoan databases), were structurally and functionally annotated, and made available. The transcriptomes here produced represent a valuable resource for future studies on these species’ biology and ultimately guide their conservation.

2022Journal article

Open access

Diversity, biogeography, evolutionary relationships, and conservation of Eastern Mediterranean freshwater mussels (Bivalvia: Unionidae)

Publication . Lopes-Lima, Manuel; Gürlek, Mustafa Emre; Kebapçi, Ümit; Şereflişan, Hülya; Yanık, Telat; Mirzajani, Alireza; Neubert, Eike; Prié, Vincent; Teixeira, Amílcar; Gomes-dos-Santos, André; Barros-García, David; Bolotov, Ivan N.; Kondakov, Alexander V.; Vikhrev, Ilya V.; Tomilova, Alena A.; Özcan, Tahir; Altun, Ayhan; Gonçalves, Duarte V.; Bogan, Arthur E.; Froufe, Elsa

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.

2021Journal article

Open access

The crown pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Publication . Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M.; Ramos, António Marcos; Usié, Ana; Bolotov, Ivan N.; Vikhrev, Ilya V.; Breton, Sophie; Castro, L. Filipe C.; Fonseca, Rute R. da; Geist, Juergen; Österling, Martin E.; Prié, Vincent; Teixeira, Amílcar; Gan, Han Ming; Simakov, Oleg; Froufe, Elsa

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.

2021Journal article

Open access