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Complete mitogenome sequence and phylogenetic analysis of the Atlantic Mudskipper
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(Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes: Gobiidae)
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Olosula Sokefun1, Han Ming Gan2, Min Pau Tan3*
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Terengganu, Malaysia
Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus,
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*Corresponding author: mptan@umt.edu.my
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Abstract
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The complete mitochondrial genome of the Atlantic mudskipper (Periophthalmus barbarus) was
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determined in this study. The circular genome was 16,502 bp long and consisted of 13 protein-
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coding genes, two rRNA genes, 22 tRNA genes and one control region. The final partitioned
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nucleotide alignment consists of xx bp and showed kinship between Periophthalmus and xxx with
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high bootstrap support. The complete mitogenome sequence of P. barbarus would be useful for
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further studies on molecular phylogenetic relationship and population genetics of the subfamily
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Oxudercinae.
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Keywords: Mudskipper, mitochondrial genome, fish, Periophthalmus barbarus
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The Atlantic Mudskipper (Periophthalmus barbarus) (Family: Gobiidae, Subfamily:
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Oxudercinae) is an amphibious and euryhaline fish that occurs along the tropical Atlantic coasts
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of Africa including most offshore islands. It is small-sized, but important as indicator for
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environmental pollution especially at the mudflat ecosystem. Recent study aims at exploring its
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complete mitochondrial genome (the seventh representative from the 19 species of genus
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Periophthalmus described to date) and the phylogenetic relationship of the mudskippers from
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subfamily Oxudercinae inferring from the complete mitochondrial genomes. The sample was
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collected from Port Harcourt, Nigeria (geographical coordinate) and the specimen was deposited
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at xxx (Olusola Sokefun, osokefun@gmail.com) under voucher specimen xxx. Approximately 50
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mg of the ethanol-preserved fin sample were treated with 1 uL of RNAse (10 mg/mL) for 30
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minutes at room temperature followed by purification using bead-bead approach (Oberacker et al.
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2019). The purified DNA was measured using Denovix high sensitivity kit giving a concentration
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of 54.2 ng/uL. Approximately 100 ng of DNA was fragmented to 350 bp using a Bioruptor
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followed by NEB Ultra II library preparation (NEB, Ipswich, MA) according to the manufacturer’s
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instructions. Sequencing was performed on an Illumina NovaSEQ6000 (Illumina, San Diego, CA)
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using a run configuration of 2 x 150 bp to generate approximately 1 gb of data. Raw reads were
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trimmed with fastp v0.21 (Chen et al. 2018) to remove low-quality bases and Illumina adapter
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sequences. The trimmed reads were subsequently used for de novo assembly in MegaHIT (default
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setting) (Li et al. 2015). The mitochondrial-derived contig was identified and circularized with
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MitoZ (Meng et al. 2019). Orientation and annotation of the circular contig was performed with
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MitoAnnotator (http://mitofish.aori.u-tokyo.ac.jp/annotation/input.html) (Iwasaki et al. 2013).
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The final partitioned nucleotide alignment consists of 16,502 bp long and supports the
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monophyly of the genus Periophthalmus.
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Figure 1 Maximum likelihood inference of the goby phylogeny based on whole mitogenome. The
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final alignment consists of xx sites. The log-likelihood of consensus tree is -xx. Node values
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represent ultrafast bootstrap support values based on 1,000 bootstraps. Branch lengths correspond
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to the mean number of nucleotide substitutions per site.
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Acknowledgements
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We thank
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Disclosure statement
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The authors report no conflict of interest and are responsible for the content and writing of the
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manuscript.
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Data availability statement
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The data that support the findings of this study are openly available at the US National Center for
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Biotechnology Information (NCBI database) at https://www.ncbi.nlm.nih.gov/. The GenBank
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accession number is xxx.
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Funding
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This work was supported by the xxx.
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