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Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family

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Abstract

Background

Freshwater mussels play a key role in ecology and are often considered as ecological indicators. Conversely, these molluscs are one of the most threatened groups due to several anthropogenic factors. Knowledge of phylogenetic diversity would assist in formulating effective management and conservation measures. Lamellidens marginalis is one of the most widely used freshwater mussel for pearl production in India. The genomic resources for investigating its evolutionary relationship within the Unionidae family are lacking.

Methods and Results

In this study, the f-type mitochondrial genome of L. marginalis was sequenced using the Illumina sequencing platform. The length of the mitochondrial genome was 15,732 bp consisting of 23 tRNAs, 2 rRNAs and 13 protein coding genes. The arrangement of genes was UF1 type and gene overlap was observed between trnG and nad1. Comparative analysis with other Unionidae species showed a high divergence rate in nad6 followed by nad2 atp8 and nad5. The phylogenetic tree supported monophyly of the Unioninae subfamily and L. marginalis (Parreysiinae) formed a sister branch to this subfamily. The divergence time of the Parreysiinae from its most recent common ancestor (MRCA) was placed in the Mesozoic era.

Conclusion

This information will be useful for the understanding the evolutionary pattern of the species of Parreysiinae subfamily.

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Acknowledgements

The first author acknowledges the Director, ICAR-Central Institute of Fisheries Education for providing the necessary facilities for conducting the research. The second and third author acknowledges the Indian Council of Agricultural Research for providing the fellowship during the research period. The authors thanks editor and anonymous reviewers for their suggestions to improve the manuscript quality.

Funding

The research was funded by the Department of Biotechnology (Sanction No. BT/PR16977/NER/95/377/2015), Government of India.

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Authors and Affiliations

  1. Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Yari Road, Mumbai, 400061, India

    Annam Pavan-Kumar, Sonal Suman, A. Chaudhari & G. Krishna

  2. Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway

    Shubham Varshney

  3. Division of Fisheries, ICAC Complex for NEH Region, Tripura Centre, Lembucherra, India

    Rekha Das

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  1. Annam Pavan-Kumar
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Contributions

APK: Conceptualization, Methodology, Writing—Original Draft, Data Curation, Funding acquisition SV: Methodology, Data Curation, Writing—Original Draft SS: Methodology, Data Curation RD: Data Curation, Writing—Review & Editing AC: Supervision, Writing—Review & Editing GK: Supervision, Writing—Review & Editing.

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Correspondence to Annam Pavan-Kumar.

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Supplementary Information

Below is the link to the electronic supplementary material.

11033_2022_7857_MOESM1_ESM.docx

Details of the reported species used in this study along with GenBank accession numbers. Supplementary file1 (DOCX 24 kb)

11033_2022_7857_MOESM2_ESM.tif

Predicted amino acid transmembrane helix structure from putative f-orf. (The online software TMHMM-2.0 (https://services.healthtech.dtu.dk/service.php?TMHMM-2.0) is used to predict the transmembrane helix structure). Supplementary file2 (TIF 166 kb)

11033_2022_7857_MOESM3_ESM.tif

Predicted secondary structure of putative control region (The online software Mfold webserver [http://www.bioinfo.rpi.edu/applications/mfold] was used to predict the secondary structure). Supplementary file3 (TIF 173 kb)

11033_2022_7857_MOESM4_ESM.tif

Predicted secondary structure of mitochondrial 12S rRNA (The online software RNAfold webserver http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/ RNAfold.cgi) was used to predict the secondary structure). Supplementary file4 (TIF 114 kb)

11033_2022_7857_MOESM5_ESM.tif

Predicted secondary structure of mitochondrial 16S rRNA (The online software RNAfold webserver [http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi] was used to predict the secondary structure). Supplementary file5 (TIF 122 kb)

11033_2022_7857_MOESM6_ESM.tif

Time-calibrated phylogeny of the Unionidae based on the protein coding gene data set of mitochondrial genome. Supplementary file6 (TIF 210 kb)

11033_2022_7857_MOESM7_ESM.docx

Predicted mitochondrial tRNA structures of Lamellidens marginalis. (The online software “tRNAscan-SE” [http://lowelab.ucsc.edu/tRNAscan-SE/] and “ARWEN” (http://130.235.244.92/ARWEN/index.html) were used for predicting tRNA structures. Supplementary file7 (DOCX 1567 kb)

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Pavan-Kumar, A., Varshney, S., Suman, S. et al. Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family. Mol Biol Rep 49, 9593–9603 (2022). https://doi.org/10.1007/s11033-022-07857-5

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