Interdisciplinary Centre of Marine and Environmental Research

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Publications

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

Trophic niche overlap between native freshwater mussels (Order: Unionida) and the invasive Corbicula fluminea

Publication . Modesto, Vanessa; Dias, Ester; Ilarri, Martina; Lopes-Lima, Manuel; Teixeira, Amílcar; Varandas, Simone; Castro, Paulo S.; Antunes, Carlos; Sousa, Ronaldo

Freshwater mussels (Order Unionida) are highly threatened. Interspecific competition for food sources with invasive alien species is considered to be one of the factors responsible for their decline because successful invaders are expected to have wider trophic niches and more flexible feeding strategies than their native counterparts. In this study, carbon (δ13C: 13C/12C) and nitrogen (δ15N: 15N/14N) stable isotopes were used to investigate the trophic niche overlap between the native freshwater mussel species, Anodonta anatina, Potomida littoralis, and Unio delphinus, and the invasive bivalve Corbicula fluminea living in sympatry in the Tua basin (south-west Europe). The species presenting the widest trophic niches were C. fluminea and A. anatina, which indicate that they have broader diets than U. delphinus and P. littoralis. Nonetheless, all the species assimilated microphytobenthos, sediment organic matter, and detritus derived from vascular plants, although with interspecific variability in the assimilated proportions of each source. The trophic niche of the invasive species overlapped with the trophic niche of all the native species, with the extent varying between sites and according to the species. From the three native species analysed, Potomida littoralis may be at a higher risk for competition for food with C. fluminea in the Tua basin, if food sources become limited, because this native mussel presented the narrowest trophic niche across sites and the highest probability of overlapping with the trophic niche of C. fluminea. Given the global widespread distribution of C. fluminea, the implementation of management measures devoted to the control or even eradication of this invasive alien species should be a conservation priority given its potential for competition with highly threatened native freshwater mussels.

2021Journal article

Open access

The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

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

Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species’ unique biological and evolutionary features, helping promote its conservation.

2023Journal article

Open access

The profession of research management and administration in Portugal

Publication . Barbosa, Cláudia; Borrego, Filipa; Costa, Teresa; Ferreira, Ana S.; Martins, Madalena; Moreira, Susana; Santos, José M.R.C.A.; Silva, José Avelino

This chapter addresses the profession of research management and administration (RMA) in Portugal. It starts with a brief outline of the national research and innovation (R&I) ecosystem that contextualises the development of the profession. The RMA community is characterised and the expectations for the future of the RMA profession are summarised using data collected through a national online survey. It is posited that RMA in Portugal is an emergent career having developed key traits of a profession, namely common interests and practices, a concern with deepening specialised knowledge and skills, the existence of an organised network of practitioners, the offer of academic qualifications and training in the area, and the integration in international RMA communities of practice. Nevertheless, future developments in the European Research Area (ERA) are identified as a critical milestone that will influence the development and formal legislative institutionalisation of the RMA profession in Portugal.

2023Book part

Open access

Floating islands, a nature-based solution for the ecological integrity promotion in rivers? - The case of Fervença river (NE Portugal)

Publication . Geraldes, Ana Maria; Calheiros-Nogueira, Bruno; Calheiros, Cristina

Despite the existence of the Water Framework Directive (Directive 2000/60 / EC of 23 October, modified in 2019) and a set of “satellite legislation” advocating that water quality depends not only on the good physical-chemical state, but also on the good ecological status of freshwater ecosystems, these continue to be subjected of accelerated ecological degradation. Indeed, freshwater ecosystems are considered to be the most threatened ecosystems on the planet (Dudgeon et al., 2006). Urban rivers and streams are crucial to cities, because they provide environmental services that are essential to maintaining urban environmental quality (Hua & Chen, 2019). Nevertheless, many of the so called “urban river rehabilitation actions”, carried out either the past, either recently, promoted the regularization of the riverbeds and the riverbanks leading to riparian wood degradation and consequently to the entire riverine structure collapse.

2020Conference object

Open access