Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Gomes-Dos-Santos A

PROVIDER: S-EPMC10189783 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel <i>Margaritifera margaritifera</i> (Linnaeus, 1758).

Gomes-Dos-Santos André A Lopes-Lima Manuel M Machado André M AM Forest Thomas T Achaz Guillaume G Teixeira Amílcar A Prié Vincent V C Castro L Filipe LF Froufe Elsa E

GigaByte (Hong Kong, China) 20230515

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 <i>Margaritifera margaritifera</i> (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened specie ...[more]

PMID: 37207176

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Project description:The Freshwater Pearl Mussel (Margaritifera margaritifera) is an endangered organism across its entire range. It has a complex life cycle and stringent habitat requirements and is therefore an indicator species for the general ecosystem health of host rivers. Whereas historical intensive pearl fishing contributed to population declines, excess nutrient and sediment loss associated with current land use pressures in host river catchments, including modern intensive farming practices, are now highlighted as primary contributory factors. Accordingly, this study investigated the sources and dynamics of fine-grained sediment sampled in the mussel beds of the River Torridge, SW England. Sediment source fingerprinting using a combination of colorimetric and radiometric tracers to construct different composite signatures revealed the importance of roads both as a sediment source and delivery pathway for fine-grained sediment mobilised from fields predominantly supporting lowland livestock farming. Grassland fields with evidence of soil poaching were highlighted as important sediment sources, but equally, riparian woodland was also identified as important, especially during the latter stages of consecutive runoff events when its rainfall buffering capacity was exceeded. Bed sediment storage levels (median up to 393 g m-2) were found to be low (41st percentile) compared to typical values reported by a recent strategic scale survey across England and Wales, whereas elevated turbidity peaks were shown to be long duration (days) in conjunction with consecutive days of rainfall and corresponding runoff events. Hysteresis patterns varied but were generally clockwise during the largest runoff events associated with consecutive rain days; again, suggesting mobilisation of sediment from proximal woodland sources following exceedance of rainfall buffering capacity. In combination, the data assembled by this study provides a basis for planning sediment control measures for protecting the Freshwater Pearl Mussel (FPM) beds from excessive fine-grained sediment inputs associated with the intensive use of primarily grazing land.

Dataset Information

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

Publications

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel <i>Margaritifera margaritifera</i> (Linnaeus, 1758).

Similar Datasets

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