The male and female complete mitochondrial genomes of the threatened freshwater pearl mussel <i>Margaritifera margaritifera</i> (Linnaeus, 1758) (Bivalvia: Margaritiferidae)

Gomes‐dos‐Santos, André; Froufe, Elsa; Amaro, Rafaela; Ondina, Paz; Breton, Sophie; Guerra, Davide; Aldridge, David C.; Bolotov, Ivan N.; Vikhrev, Ilya V.; Gan, Han Ming; Gonçãlves, Duarte V.; Bogan, Arthur E.; Sousa, Ronaldo; Stewart, Donald T.; Teixeira, Amílcar; Varandas, Simone; Zanatta, David T.; Lopes‐Lima, Manuel

doi:10.1080/23802359.2019.1598794

Cited by 10 publications

(4 citation statements)

References 22 publications

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“…The disagreeing results between nuclear markers and the F‐type mtDNA here reported suggest a divergent evolutionary history and given the notably low Margaritiferidae mitochondrial evolutionary rates (Bolotov et al, 2016), it is unlikely a result of nucleotide substitution saturation. On the other hand, the M‐type phylogeny provided by Gomes‐dos‐Santos et al (2019) groups Cumberlandia and Pseudunio as sister clades, a relationship congruent with our AHE dataset. The split between the F and M type Unionida mitochondrial lineages can be traced back to the origin of the order, thus reflecting two independently evolving and phylogenetic informative units (Guerra et al, 2019).…”

Section: Discussionsupporting

confidence: 89%

“…The results of the AHE phylogeny agree with the published works based on combined mitochondrial and nuclear markers (Araujo et al, 2017;Huff et al, 2004;Lopes-Lima et al, 2018). On the other hand, the mitogenome phylogeny is congruent with other mitochondrial makers-based studies (Araujo et al, 2009;Gomes-dos-Santos et al, 2019;Inoue et al, 2014). These expected differences do not contradict the inferred relationships within genera, which have high support among both phylogenies (Figures 1a,b).…”

Section: Phylogenetic Analysessupporting

confidence: 89%

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A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

Gomes‐dos‐Santos

Froufe

Pfeiffer

et al. 2023

Molecular Ecology Resources

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The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost‐effective, fast and easily applied strategy for phylogenetic inference of non‐model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re‐sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high‐coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well‐curated functional annotations of these previously uncharacterized freshwater mussel‐specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.

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Section: Discussionsupporting

confidence: 89%

Section: Phylogenetic Analysessupporting

confidence: 89%

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

Gomes‐dos‐Santos

Froufe

Pfeiffer

et al. 2023

Molecular Ecology Resources

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“…The whole mitochondrial genome obtained with MitoBim is 16,124bp long and its gene content is the expected for Margaritiferidae female type mitogenomes 64 with 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA.…”

Section: Resultsmentioning

confidence: 84%

The Crown Pearl: a draft genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)

et al. 2021

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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.

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“…Despite the cultural significance and poor conservation status of the freshwater pearl mussel, the availability of genomic resources to study this species is still limited [13, [18][19][20][21][22]. Also, almost nothing is known about the molecular mechanism governing the regulation and functioning of its many relevant biological features.…”

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confidence: 99%

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

et al. 2023

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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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The male and female complete mitochondrial genomes of the threatened freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) (Bivalvia: Margaritiferidae)

Cited by 10 publications

References 22 publications

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

The Crown Pearl: a draft genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)

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

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