{"paper_id":"194f2030-c178-442f-aaa3-a1d73504e2bc","body_text":"Mitogenome Announcement \n 1 \nThe first complete mitochondrial genome of the endangered 1 \nspotted eagle ray Aetobatus ocellatus 2 \n 3 \n 4 \n 5 \nAlan Marín1 6 \n 7 \n 8 \n 9 \n 10 \n 11 \n 12 \n 13 \n1Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad 14 \nNacional del Santa, Chimbote, Perú 15 \n 16 \n 17 \n 18 \n 19 \n 20 \n 21 \n 22 \n 23 \n 24 \n 25 \n 26 \n 27 \n 28 \nCONTACT: Alan Marín amarin@uns.edu.pe 29 \n 30 \n 31 \n 32 \n 33 \n 34 \n 35 \n 36 \n 37 \n 38 \n 39 \n 40 \n 41 \n 42 \n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 2 \nAbstract 43 \nThe complete mitochondrial genome of the endangered spotted eagle ray Aetobatus ocellatus 44 \nwas determined for the first time using Next Generation Sequencing (NGS) reads mined from 45 \nthe Sequence Read Archive (SRA) of the GenBank database (BioSample SAMN31811701, 46 \ncollection site: Bohol Island, Philippines ). The spotted eagle ray  mitogenome (GenBa nk 47 \naccession pending ) has 20,217  bp in length displaying a typical vertebrate mitogenome 48 \norganization (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region). 49 \nA phylogenetic analysis based on the nucleotide sequence information of 13  protein-coding 50 \ngenes from different related species confirmed the species status of A. ocellatus as an Indo -51 \nWest Pacific species , which was formerly described as A. narinari whose current accepted 52 \ndistribution is restricted to the Atlantic Ocean. 53 \n 54 \n 55 \n 56 \nKeywords: Aetobatidae, mitogenome, phylogenetics, Next Generation Sequencing 57 \n 58 \n 59 \n 60 \n 61 \n 62 \n 63 \n 64 \n 65 \n 66 \n 67 \n 68 \n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 3 \nEagle r ays of the genus Aetobatus (Myliobatiformes: Aetobatidae) suffer from strong 69 \noverfishing and slow recovery from overexploitation due to their low regeneration rate, slow 70 \ngrowth, and late maturity ( Yamaguchi et al.  2021), which has led to a continued population 71 \ndecline throughout their distribution ranges (Dulvy et al. 2021; Finucci et al. 2024) and  72 \nsubsequent categorization of all of its members as Endangered or Vulnerable within the IUCN 73 \nred list (IUCN  2024). The classification of Aetobatidae species is particularly susceptible to 74 \ntaxonomic confusion due to the interspecific overlap of their morphological features (White et 75 \nal. 2013) and during the last decade a number of taxonomic changes were introduced with the 76 \naid of genetic markers, including the resurrection of old synonyms  and description of new 77 \nspecies (White 2010; White and Moore 2013; White et al. 2013). 78 \nHerein, I report the first complete mitochondrial genome of the endangered spotted eagle ray 79 \nAetobatus ocellatus, which has only recently been resurrected as the valid name for the Indo -80 \nWest Pacific member of the narinari complex (White et al. 2010). The A. ocellatus sample was 81 \ncollected in Bohol Island, Philippines (BioSample: SAMN31811701) and sequenced by the 82 \nSmithsonian National Museum of Natural History  in their  “NOAA Genome Skimming of 83 \nMarine animals” project (BioProject accession: PRJNA720393). Paired-end FASTQ genomic 84 \nreads (2.2 Gbp within 14.6 million reads, Platform: Illumina NovaSeq 6000) were downloaded 85 \nfrom the  public GenBank SRA repository  (SRA accession: SRS15852991), trimmed with 86 \nBBDuk (14.5 million reads remained), and merged with BBMerge (4.1 million reads remained) 87 \nimplemented in Geneious Prime v. 2021.1.1 (Biomatters  Ltd., Auckland, New Zealand) . 88 \nUnmerged (22,239) and merged (16,553) reads were independently assembled against the only 89 \ncomplete available mitogenome reference sequence of Aetobatus prior to this study  (A.  90 \nflagellum, 20,201 bp, GenBank accession NC_02283 7) using the “Map to Reference” tool in 91 \nGeneious Prime. Protein-coding (PC), transport RNA (tRNA), and ribosomal RNA (rRNA) 92 \ngenes were annotated using the “Annotate and Predict” feature of Geneious Prime by 93 \n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 4 \ncomparing the novel A. ocellatus  mitogenome to other complete mitogenomes of closely 94 \nrelated species. The position of tRNAs was verified using tRNAscan -SE (Chan and Lowe 95 \n2019).  96 \nThe 20,217 bp consensus mitogenome of A. ocellatus (GenBank accession pending)  has a 97 \ntypical fish mitogenome organization  (Winn et al. 2024)  with 13 PC, two rRNA, 22 tRNA 98 \ngenes, and one putative control region, showing an overall nucleotide composition of A: 31.4%, 99 \nC: 27.1%, G: 15.5%, and T: 26%. All PCGs use the typical ATG start codon except for the 100 \nCOI which utilizes the alternative GTG start codon.  101 \nThe Bayesian phylogenetic analysis was performed using MrBayes 3.2 (Ronquist & 102 \nHuelsenbeck 2003) and consisted of a concatenated matrix of 13 PCGs (11,460 bp) from 15 103 \nmitogenomes of closely related species retrieved from the Gen Bank database. Substitution 104 \nsaturation in single codon positions from each PCG was analyzed using DAMBE 5 (Xia 2013). 105 \nThe software jModelTest 2 (Darriba et al. 2012) was used to find the best-fit model of evolution 106 \nfor each PCG. Figur e 1  shows the Bayesian phylogenetic tree in which all samples were 107 \ngrouped into 4 distinct family clades according to their taxonomy. Aetobatidae species formed 108 \na basal monophyletic clade with robust statistical support. A. ocellatus was clustered together 109 \nwith A. narinari into a discrete subclade (338 variable sites, genetic divergence 3.03%) , 110 \nreflecting their low estimated divergence age (from 2 to 5 mya, Sales et al. 2019). The genetic 111 \nmaterial analyzed herein (BioSample SAMN31811701) came from an organism collected in 112 \nthe Indo-West Pacific region ( Bohol Island, Philippines) originally identified as A. narinari. 113 \nHowever, the phylogenetic results obtained herein indicate that BioSample SAMN31811701 114 \nbelongs to A. ocellatus, supporting its species status as an Indo-West Pacific species (White et 115 \nal. 2010), while A. narinari is restricted to the Atlantic region (Sales et al. 2019). 116 \n 117 \n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 5 \nFigure 1. Bayesian ph ylogenetic tree inferred from 13  concatenated mitochondrial protein -118 \ncoding genes of Aetobatidae, Dasyatidae, Mobulidae, and Rhinopteridae species. The sequence 119 \nmatrix (11,460 nt) used in the phylogenetic analysi s consisted of unambiguously aligned 120 \nregions of the first, second, and third codon positions. The position of Aetobatus ocellatus is 121 \nhighlighted in bold. Pteroplatytrygon violacea and Dasyatis pastinaca (Dasyatidae) were used 122 \nas outgroups. Posterior probabilities are shown at each node. GenBank accession numbers for 123 \neach species are shown in parentheses. 124 \n 125 \n 126 \n 127 \n 128 \n 129 \nDASYATIDAE\n(OUTGROUP)\n0.05\nMobula alfredi (NC_068734.1)\nMobula birostris (KX151648)\nMobula mobular (KT203434.1)\nMobula tarapacana (KX151647)\nMobula eregoodootenke (NC_025954.1)\nMobula kuhlii (KX151651.1)\nMobula thurstoni (NC_037219.1)\nMobula hypostoma (PQ760241.1)\nMobula munkiana (KX151645.1)\nRhinoptera brasiliensis (NC_068668.1)\nRhinoptera bonasus (NC_082999.1)\nAetobatus narinari (KX151649.1)\nAetobatus ocellatus (PENDING)\nAetobatus flagellum (NC_022837.1)\nPteroplatytrygon violacea (KJ641617)\nDasyatis pastinaca (NC_057976.1)\nMOBULIDAE\nRHINOPTERIDAE\nAETOBATIDAE\n0.05\n1\n0.98\n0.99\n1\n1\n1\n11\n1\n1\n1\n1\n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 6 \nReferences 130 \n- Chan, P.P. , & Lowe, T. M. (2019) . tRNAscan-SE: Searching for tRNA Genes in 131 \nGenomic Sequences. Methods Mol Biol. 1962:1-14. 132 \n- Darriba, D.,  Taboada, G.L., Doallo , & R., Posada D. (2012). jModelTest  2: more 133 \nmodels, new heuristics and parallel computing. 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A new species of eagle ray 159 \nAetobatus narutob iei from the Northwest Pacific: an example of the critical role 160 \ntaxonomy plays in fisheries and ecological sciences. PLoS One. 8(12), e83785. 161 \n.CC-BY 4.0 International licenseperpetuity. It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint \n\nMitogenome Announcement \n 7 \n- White, W.T., & Moore, A. B. (2013). Redescription of Aetobatus flagellum (Bloch & 162 \nSchneider, 1801), an endangered e agle ray (Myliobatoidea: Myliobatidae) from  the 163 \nindo–West Pacific. Zootaxa 3752(1), 199-213. 164 \n- Winn, J.C., Maduna, S.N., & Bester -van der Merwe, A. E. (2024). 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It is made available under a \npreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in \nThe copyright holder for thisthis version posted January 15, 2025. ; https://doi.org/10.1101/2025.01.13.632509doi: bioRxiv preprint","source_license":"CC-BY-4.0","license_restricted":false}