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

  1. André Gomes-dos-Santos
  2. Manuel Lopes-Lima
  3. André M. Machado
  4. Thomas Forest
  5. Guillaume Achaz
  6. Amílcar Teixeira
  7. Vincent Prié
  8. L. Filipe C. Castro
  9. Elsa Froufe

  • Curated by GigaByte

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    Editor’s Assessment

    Like other mollusc species, the freshwater pearl mussel (Margaritifera margaritifera) has a challenging genome to assemble owing to the large size of their genomes, heterozygosity, and repetitive sequence. The first published M. margaritifera genome was highly fragmented, but here an improved reference genome assembly was generated using PacBio CLR long reads to reduce fragmentation levels, missing and truncated genes, and chimerically assembled regions. The number of gene models predicted is a bit higher compared than other molluscan genomes, but after clarification and double checking these seem in line with some Mollusca and Bivalvia with similar and higher numbers of gene predictions. This new genome represents a new resource to start exploring the many biological, ecological, and evolutionary features of this threatened and commercially important group of organisms.

    This assessment refers to version 1 of this preprint.

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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.

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  1. GigaByte

    Editor’s Assessment

    Like other mollusc species, the freshwater pearl mussel (Margaritifera margaritifera) has a challenging genome to assemble owing to the large size of their genomes, heterozygosity, and repetitive sequence. The first published M. margaritifera genome was highly fragmented, but here an improved reference genome assembly was generated using PacBio CLR long reads to reduce fragmentation levels, missing and truncated genes, and chimerically assembled regions. The number of gene models predicted is a bit higher compared than other molluscan genomes, but after clarification and double checking these seem in line with some Mollusca and Bivalvia with similar and higher numbers of gene predictions. This new genome represents a new resource to start exploring the many biological, ecological, and evolutionary features of this threatened and commercially important group of organisms.

    This assessment refers to version 1 of this preprint.

  2. GigaByte

    Abstract

    This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.81), and has published the reviews under the same license. These are as follows.

    **Reviewer 1. Jin Sun **

    Gomes-dos-Santos et al., have upgraded the freshwater mussel Margaritifera margaritifera genome with the usage of long-read sequencing. Overall, this version has been dramatically improved compared to the former one, with the increased N50 value and BUSCO score and decreased No. of contigs. Considering the important economic value of M. margaritifera and the high quality of assembly, I must congratulate the authors on this. However, in contrast to the high-quality assembly, I am a bit aware of the genome annotation part. To me, the number of gene models predicted is a bit higher compared with other molluscan genomes. This can also be reflected by the low proportion of gene models that can be annotated by Swissprot or GO etc. I suspect that the high number of gene models could be the consequence that only the ab initio evidence was applied in the current study. More sophisticated ways, such as EVM or maker, shall be used to see whether the number of gene models can be reduced without sacrificing the BUSCO scores on the gene models.

    Line 76, The official name shall be “Oxford Nanopore Technology (ONT)”.

    Fig. 1, it is interesting to see the wide distribution of M. margaritifera. I am a bit interested to know whether there are any genetic differentiations between the European population and the North American population.

    **Reviewer 2. Rebekah L. Rogers **

    Is there sufficient detail in the methods and data-processing steps to allow reproduction?

    Y. All methods seem standard and high quality for a genome release.

    If the authors could add a table comparing with other Unio genomes, that might be helpful. Gene numbers, BUSCO scores, N50s, and other relevant stats. It will help readers see the value of this more contiguous genome -V. ellipsiforma (Renaut et al.) -M nervosa -P. streckersonii

  3. Version published to 10.46471/gigabyte.81
  4. Version published to 10.1101/2023.02.11.528107v1 on bioRxiv