==== Front Mitochondrial DNA B Resour Mitochondrial DNA B Resour Mitochondrial DNA. Part B, Resources 2380-2359 Taylor & Francis 10.1080/23802359.2019.1677526 1677526 Version of RecordResearch Article Mitogenome Announcement The mitochondrial genome of the black-tailed dasyure (Murexia melanurus) R. Tian et al.https://orcid.org/0000-0002-4564-1886Tian Ran a* Geng Yuepan a* https://orcid.org/0000-0002-3649-7923Thomas Patrick B. bcd https://orcid.org/0000-0003-1229-8724Jeffery Penny L. bc Mutton Thomas Y. e Chopin Lisa K. bc https://orcid.org/0000-0001-8825-1522Baker Andrew M. ef https://orcid.org/0000-0001-8594-7217Seim Inge abcg a Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China; b Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia; c Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute – Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia; d Queensland Bladder Cancer Initiative, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia; e School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia; f Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia; g Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia * These authors contributed equally to this work. CONTACT Inge Seim inge@seimlab.orgIntegrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing210046, Jiangsu, China 16 10 2019 2019 4 2 3598 3600 © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.2019The Author(s)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.http://creativecommons.org/licenses/by/4.0/Abstract In this study, we report the mitochondrial genome of the black-tailed dasyure (Murexia melanurus) of New Guinea. The circular genome is 17,736 bp in length and has an AT content of 60.5%. Its gene content – 13 protein-coding genes (PCGs), 2 ribosomal (rRNA) genes, 21 transfer RNA (tRNA) genes, a tRNA pseudogene (tRNALys), and a non-coding control region (CR) – and gene arrangement are consistent with previous marsupial mitogenome assemblies. Keywords Mitochondrial genomemarsupialdasyureDasyuridaeNew GuineaMurexia ==== Body The marsupial family Dasyuridae (or carnivorous marsupials) includes ∼75 species native to mainland Australia and Tasmania, New Guinea, and other adjacent islands (Baker and Dickman 2018). The dasyurid subfamily Phascogalinae comprises three genera: Antechinus and Phascogale of Australia, and Murexia of New Guinea. Although morphological similarities exist, the current evidence suggests these genera derived from a common ancestor some 12.5 million years ago (Mutton et al. 2019). Murexia spp. have not received as much attention in evolutionary studies as their Australian counterparts within Phascogalinae, and genetic information on the various constituent species within Murexia is poorly represented. Here, we describe the complete mitochondrial genome of the black-tailed dasyure (Murexia melanurus). Murexia melanurus genomic DNA was extracted from ear tissue (voucher specimen ABTC46020) collected from Tibi, Papua New Guinea. Paired-end short-insert (200 bp) DNA libraries were sequenced by BGI (Hong Kong, China), to generate ∼30× genome coverage. Raw data were filtered using Flexbar v3.4.0 (Roehr et al. 2017). To remove microbial contaminants, we used bowtie2 v2.3.4.1 (Langmead and Salzberg 2012) to map reads to all bacterial and fungal sequences in NCBI Genomes, retaining 99.68% of reads. Two to 95 million reads were assembled using NOVOPlasty v2.7.2 (Dierckxsens et al. 2017), with the ND1 coding sequence from a partial M. melanurus mitogenome (GenBank: KJ868127) (Mitchell et al. 2014) as a seed sequence and the parameters ‘Type = mito, K-mer = 39, Genome range = 16,000–22,000’. The subset with the lowest number of reads which yielded a circular genome was retained (here: 12 M reads; 0.26% were assembled into a 17,736 bp contig at 179× coverage). Geneious Prime v2019.1.3 (Biomatters Ltd., Auckland, New Zealand) was used to align 95 M reads against the assembled contig and generate a consensus genome sequence, with a 75% masking threshold. The genome was annotated using GenBank features of the northern quoll (Dasyurus hallucatus; accession no. NC_007630). Various genome features were compared to the Virginia opossum (Didelphis virginiana), a seminal species in the marsupial mitochondrial genetics literature [e.g. see Janke et al. (1994) and Nilsson (2009)]. The M. melanurus mitochondrial genome (GenBank: MK977600) is 17,736 bp and has a base composition of 32% A, 28.5% T, 14.1% G, and 25.4% C. As in other marsupials, the genome has 13 protein-coding genes (PSGs), 2 ribosomal (rRNA) genes, and 21 transfer RNA (tRNA) genes. The genome shares unique features with all marsupial mitogenomes reported to date. These include: an ‘ACWNY’ tRNA gene re-arrangement (Paabo et al. 1991); a tRNALys pseudogene (Janke et al. 1994; Dorner et al. 2001); and lack of an anticodon for aspartic acid, which is likely rescued by RNA-editing (Janke and Paabo 1993). In agreement with a recent molecular appraisal (Mitchell et al. 2014; Westerman et al. 2016), phylogenetic analysis revealed that M. melanurus and Murexia habbema are sisters, to the exclusion of the closely-related genera Phascogale and Antechinus (Figure 1). Maximum-likelihood (ML; estimated using IQ-TREE (Nguyen et al. 2015)) and Bayesian Interference (BI; implemented in MrBayes v3.2.7 (Ronquist and Huelsenbeck 2003)) gave the same tree topology. Figure 1. Phylogenetic tree of black-tailed dasyure (Murexia melanurus; indicated in bold blue font), nine other species in the marsupial family Dasyuridae, and the outgroup species Thylacinus cynocephalus. Because there are no complete mitogenomes from the genera Antechinus and Murexia in GenBank, phylogenetic reconstruction was performed with coding sequences of 12 protein-coding genes (excluding ND6). The number at each node is ML/BI bootstrap support value. Acknowledgements We thank Leanne Wheaton (South Australian Museum) for providing the M. melanurus ear tissue sample. Geolocation information Geospatial coordinates for the black-tailed dasyure (Murexia melanurus) ear tissue collection: 6°11′S, 143°9′E Disclosure statement The authors declare that they have no competing interests. ==== Refs References Baker A , Dickman C 2018 Secret lives of carnivorous marsupials . Clayton (Australia) : CSIRO Publishing . Dierckxsens N , Mardulyn P , Smits G 2017 NOVOPlasty: de novo assembly of organelle genomes from whole genome data . Nucl Acids Res . 45 (4 ):e18 .28204566 Dorner M , Altmann M , Paabo S , Morl M 2001 Evidence for import of a lysyl-tRNA into marsupial mitochondria . MBoC . 12 (9 ):2688 –2698 .11553708 Janke A , Feldmaier-Fuchs G , Thomas WK , von Haeseler A , Paabo S 1994 The marsupial mitochondrial genome and the evolution of placental mammals . Genetics . 137 (1 ):243 –256 .8056314 Janke A , Paabo S 1993 Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition . Nucl Acids Res . 21 (7 ):1523 –1525 .8479901 Langmead B , Salzberg SL 2012 Fast gapped-read alignment with Bowtie 2 . Nat Methods . 9 (4 ):357 –359 .22388286 Mitchell KJ , Pratt RC , Watson LN , Gibb GC , Llamas B , Kasper M , Edson J , Hopwood B , Male D , Armstrong KN , et al. 2014 Molecular phylogeny, biogeography, and habitat preference evolution of marsupials . Mol Biol Evol . 31 (9 ):2322 –2330 .24881050 Mutton TY , Phillips MJ , Fuller SJ , Bryant LM , Baker AM 2019 Systematics, biogeography and ancestral state of the Australian marsupial genus Antechinus (Dasyuromorphia: Dasyuridae) . Zool J Linn Soc . 186 (2 ):553 –568 . Nguyen LT , Schmidt HA , von Haeseler A , Minh BQ 2015 IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies . Mol Biol Evol . 32 (1 ):268 –274 .25371430 Nilsson MA 2009 The structure of the Australian and South American marsupial mitochondrial control region . Mitochondrial DNA . 20 (5–6 ):126 –138 .19900062 Paabo S , Thomas WK , Whitfield KM , Kumazawa Y , Wilson AC 1991 Rearrangements of mitochondrial transfer RNA genes in marsupials . J Mol Evol . 33 (5 ):426 –430 .1720466 Roehr JT , Dieterich C , Reinert K 2017 Flexbar 3.0 - SIMD and multicore parallelization . Bioinformatics . 33 (18 ):2941 –2942 .28541403 Ronquist F , Huelsenbeck JP 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models . Bioinformatics . 19 (12 ):1572 –1574 .12912839 Westerman M , Krajewski C , Kear BP , Meehan L , Meredith RW , Emerling CA , Springer MS 2016 Phylogenetic relationships of Dasyuromorphian marsupials revisited . Zool J Linn Soc . 176 (3 ):686 –701 .