Browsing by Author "Castro, L. Filipe C."
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- 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, ElsaSince 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.
- Methyl-end desaturases determine the capability for de novo biosynthesis of polyunsaturated fatty acids in bivalvesPublication . Kabeya, Naoki; Ramos-Llorens, Marc; Nakano, Yo; Gomes-dos-Santos, André; Teixeira, Amilcar; Fujibayashi, Megumu; Haro, Juan G.; Navarro, Juan C.; Castro, L. Filipe C.; Haga, Yutaka; Monroig, ÓscarRecent studies have shown that many invertebrate species possess methyl-end desaturases (herein referred to as ‘ωx’), enabling biosynthesis of polyunsaturated fatty acids (PUFA). However, the phylogenetic distribution of these enzymes across the animal kingdom remains puzzling, possibly due to horizontal gene transfer (HGT) and/ or independent large-scale gene loss in certain invertebrate lineages. In molluscs, ωx genes have been identified in various cephalopods and gastropods but remain barely explored in bivalves. The increasing availability of genomic and transcriptomic resources enables a comprehensive exploration of the ωx gene repertoire in bivalves. To elucidate the distribution of ωx in bivalves, we conducted a broad homology search across existing genome and transcriptome assemblies, followed by functional characterisation of ωx in lineage representative species. Our results revealed no ωx-like sequences in any of the 65 Pteriomorphia species, suggesting gene loss in this clade. However, ωx-like sequences were found in Protobranchia, Palaeoheterodonta and Imparidentia. We analysed ωx from Solemya pusilla (Protobranchia), Lanceolaria oxyrhyncha and Margaritifera margaritifera (Palaeoheterodonta), and Ruditapes philippinarum and Tridacna crocea (Imparidentia). Except for M. margaritifera, which had two ωx genes, each species had a single ωx gene. Functional analysis showed Δ15Δ17Δ19 desaturase activity in the R. philippinarum and T. crocea ωx, while the L. oxyrhyncha ωx exhibited Δ15Δ17 activity but not Δ19. Both ωx from M. margaritifera showed no detectable activity in yeast. Interestingly, the S. pusilla ωx exhibited Δ12 desaturase activity. These findings highlight the diversity of ωx desaturation capabilities in bi- valves, with significant gene loss in Pteriomorphia
- PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793Publication . Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, M. André; Teixeira, Amílcar; Castro, L. Filipe C.; Froufe, ElsaMussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world freshwater ecosystems. They are highly threatened showing the highest record of extinction events within faunal taxa. Conservation is particularly concerning in species occurring in the Mediterranean biodiversity hotspot that are exposed to multiple anthropogenic threats, possibly acting in synergy. That is the case of the dolphin freshwater mussel Unio delphinus Spengler, 1793, endemic to the western Iberian Peninsula with recently strong population declines. To date, only four genome assemblies are available for the order Unionida and only one European species. We present the first genome assembly of Unio delphinus. We used the PacBio HiFi to generate a highly contiguous genome assembly. The assembly is 2.5 Gb long, possessing 1254 contigs with a contig N50 length of 10 Mbp. This is the most contiguous freshwater mussel genome assembly to date and is an essential resource for investigating the species' biology and evolutionary history that ultimately will help to support conservation strategies.
- 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, ElsaContiguous 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.
- The gill transcriptome of threatened European freshwater musselsPublication . Gomes-dos-Santos, André; Machado, André M.; Castro, L. Filipe C.; Prié, Vincent; Teixeira, Amílcar; Lopes-Lima, Manuel; Froufe, ElsaGenomic 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.