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Complete Mitogenomes for Two Lineages of the Australian Smelt, Retropinna Semoni (Osmeriformes: Retropinnidae)

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Complete Mitogenomes for Two Lineages of the Australian Smelt, Retropinna Semoni (Osmeriformes: Retropinnidae) Complete mitogenomes for two lineages of the Australian smelt, Retropinna semoni (Osmeriformes: Retropinnidae) Author Schmidt, Daniel J, Islam, Md Rakeb-Ul, Hughes, Jane M Published 2016 Journal Title Mitochondrial DNA Part B: Resources Version Version of Record (VoR) DOI https://doi.org/10.1080/23802359.2016.1209097 Copyright Statement © 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Downloaded from http://hdl.handle.net/10072/394528 Griffith Research Online https://research-repository.griffith.edu.au Mitochondrial DNA Part B Resources ISSN: (Print) 2380-2359 (Online) Journal homepage: https://www.tandfonline.com/loi/tmdn20 Complete mitogenomes for two lineages of the Australian smelt, Retropinna semoni (Osmeriformes: Retropinnidae) Daniel J. Schmidt, Md. Rakeb-Ul Islam & Jane M. Hughes To cite this article: Daniel J. Schmidt, Md. Rakeb-Ul Islam & Jane M. Hughes (2016) Complete mitogenomes for two lineages of the Australian smelt, Retropinnasemoni (Osmeriformes: Retropinnidae), Mitochondrial DNA Part B, 1:1, 615-616, DOI: 10.1080/23802359.2016.1209097 To link to this article: https://doi.org/10.1080/23802359.2016.1209097 © 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Published online: 05 Sep 2016. Submit your article to this journal Article views: 283 View related articles View Crossmark data Citing articles: 4 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tmdn20 MITOCHONDRIAL DNA PART B: RESOURCES, 2016 VOL. 1, NO. 1, 615–616 http://dx.doi.org/10.1080/23802359.2016.1209097 MITOGENOME ANNOUNCEMENT Complete mitogenomes for two lineages of the Australian smelt, Retropinna semoni (Osmeriformes: Retropinnidae) Daniel J. Schmidt , Md. Rakeb-Ul Islam and Jane M. Hughes Australian Rivers Institute, Griffith University, Nathan, QLD, Australia ABSTRACT ARTICLE HISTORY Complete mitochondrial genome sequences were determined for two lineages (‘‘CEQ’’ and ‘‘SEQ’’) of the Received 22 June 2016 Australian smelt, Retropinna semoni. Both mitogenomes contain the typical vertebrate arrangement of 13 Accepted 30 June 2016 protein-coding genes, 22 tRNA genes, 2 rRNA genes and control region. A conventional start codon for ND2 was not present in either lineage; instead CTG (Leucine) was present at this position. These sequen- KEYWORDS Freshwater fish; ces will be a useful resource for evolutionary studies of a significant species complex in the Australian mitochondrial genome; freshwater fish fauna. MiSeq; cryptic species; next- generation sequencing The Australian smelt (Retropinna semoni) is an Australian as the longest contig with circular topology. The putative endemic freshwater fish, widely distributed across the south- mitogenome assembly was visually checked for errors derived east of the continent. Genetic analyses using allozymes, micro- from heteroplasmy or paralogues using the Geneious genome satellites and mtDNA indicate this species may comprise a browser. An initial annotation was achieved using MitoFish complex of at least five taxa (Hammer et al. 2007; Hughes (Iwasaki et al. 2013) and subsequently inspected by eye. et al. 2014). Here, we present complete mitochondrial genome The complete mitogenome of Retropinna semoni ‘‘lineage sequences of two northern lineages that correspond geo- CEQ’’ (GenBank accession: KX421785) was 16,582 bp in length, graphically to informal ‘‘CEQ’’ and ‘‘SEQ’’ groups designated based on 5755 reads and mean coverage of 105. The com- by Hammer et al. (2007). Genomic DNA was isolated from tis- plete mitogenome of R. semoni ‘‘lineage SEQ’’ (GenBank acces- sue voucher GUB433 (¼ lineage SEQ, Twin Bridges Reserve, sion: KX421784) was 16,577 bp in length based on 13,412 Brisbane River, À27.430457 152.639357) and voucher GUM433 reads and mean coverage of 234. Both mitogenomes con- (¼ lineage CEQ, Conondale Bridge, Mary River, À26.727511 tained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a con- 152.713604). DNA was sheared to an approximate mean trol region in the standard vertebrate order. A start codon for length of 400 bp and an Illumina MiSeq-compatible sequenc- ND2 was not determined for either of the new mitogenomes. ing library was prepared using the iTru protocol (Travis Glenn, The first ND2 codon was annotated as CTG (Leucine) in both pers. comm.). Sequencing was performed on a MiSeq instru- taxa despite the presence of a conventional ATG start codon ment (Illumina, San Diego, CA), producing 2 Â 300 bp paired- in the reference sequence. Mean read depth at the first codon end reads. The two libraries each generated 1.18 Â 107 paired- position of ND2 was >97, with >99% pairwise identity. end reads. Mitogenome assembly was performed using Pairwise divergence between CEQ and SEQ lineages across Geneious v9.1.5 (Kearse et al. 2012). For each taxon, overlap- the full mitogenome was 3.6%, ranging from 1.8% for ATPase ping paired reads were merged using the BBMerge tool and 6, up to 7.3% for ND6. Phylogenetic analysis using complete 6 Â 105 merged reads in size range 250–590 bp were mitochondrial genome matches from GenBank showed the sampled. Reference-guided assembly was implemented in closest relationship of the two new mitogenomes with the Geneious v9.1.5 (Auckland, New Zealand) using the iterative congeneric New Zealand smelt, Retropinna retropinna map to reference function with Retropinna retropinna as refer- (Figure 1). The new R. semoni mitogenomes (GenBank: ence sequence (GenBank accession: AP004108; Ishiguro et al. KX421785; KX421784) matched with 100% identity to frag- 2003). De Novo assembly was implemented in Geneious using ments of cyt b from R. semoni collected in the Brisbane and medium sensitivity settings and allowing contigs with match- Mary River catchments (GenBank: JX914063; JX914057; see ing ends to circularize. A putative mitogenome was identified Page & Hughes 2014). CONTACT Daniel J. Schmidt [email protected] Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia ß 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, dis- tribution, and reproduction in any medium, provided the original work is properly cited. 616 D. J. SCHMIDT ET AL. KP281293 Hypomesus olidus 100 38 HM106489 Hypomesus nipponensis 100 HM106491 Mallotus villosus HM106493 Osmerus mordax 100 AB047553 Plecoglossus altivelis 51 KJ645978 Salanx cuvieri 100 100 KJ645979 Hemisalanx brachyrostralis KM517200 Salanx ariakensis KX421784 Retropinna semoni, SEQ lineage 100 KX421785 Retropinna semoni, CEQ lineage 100 NC_004598 Retropinna retropinna* 100 KR048706 Galaxias truttaceus 100 DQ288271 Oncorhynchus mykiss 0.1 substitutions/site Figure 1. Phylogenetic placement of two Retropinna semoni mitogenomes with the top mitogenome hits from a blastn query of the NCBI nucleotide database. Tip labels include GenBank accession number with species name and node labels show bootstrap results. New mitogenome sequences highlighted in bold font; reference genome used for assembly denoted by an asterisk. Alignment of mitogenomes was performed using MAFFT v7.017 (Katoh et al. 2002) and excluded the d-loop which aligned poorly across taxa. A maximum likelihood phylogenetic analysis was performed on the final alignment of 15,805 bp with RAxML v7.2.8 using the GTR þ GAMMA substitution model with 1000 bootstrap replicates (Stamatakis 2006). Acknowledgements Hughes JM, Schmidt DJ, Macdonald JI, Huey JA, Crook DA. 2014. Low interbasin connectivity in a facultatively diadromous fish: evidence Nicole Hogg and Fraxa Caraiani (Griffith University DNA Sequencing from genetics and otolith chemistry. Mol Ecol. 23:1000–1013. Facility) provided access to the ultrasonicator and MiSeq. Travis Glenn Ishiguro NB, Miya M, Nishida M. 2003. Basal euteleostean relationships: a advised on library preparation using the iTru protocol. Leo Lee assisted mitogenomic perspective on the phylogenetic reality of the with fieldwork and Kathryn Real performed the DNA extraction. ‘‘Protacanthopterygii’’. Mol Phylogenetics Evol. 27:476–488. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Disclosure statement Mabuchi K, Takeshima H, Miya M, Nishida M. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accur- No conflict of interest. The project complies with Australian animal ethics ate and automatic annotation pipeline. Mol Biol Evol. 30:2531–2540. permit number ENV/23/14/AEC. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for ORCID rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059–3066. Daniel J. Schmidt http://orcid.org/0000-0001-5638-497X Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an inte- grated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28:1647–1649. References Page TJ, Hughes JM. 2014. Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study. Hammer MP, Adams M, Unmack PJ, Walker KF. 2007. A rethink on Biol J Linnean Soc. 111:554–569. Retropinna: conservation implications of new taxa and significant gen- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogen- etic sub-structure in Australian smelts (Pisces: Retropinnidae). Mar etic analyses with thousands of taxa and mixed models. Bioinformatics. Freshwater Res. 58:327–341. 22:2688–2690..
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