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Complete mitochondrial genome of Callogorgia cf. gracilis (Octocorallia: Calcaxonia: Primnoidae)

Erin E. Easton & David Hicks

To cite this article: Erin E. Easton & David Hicks (2019) Complete mitochondrial genome of Callogorgia cf. gracilis (Octocorallia: Calcaxonia: Primnoidae), Mitochondrial DNA Part B, 4:1, 361-362, DOI: 10.1080/23802359.2018.1544042 To link to this article: https://doi.org/10.1080/23802359.2018.1544042

© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Published online: 10 Jan 2019.

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Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tmdn20 MITOCHONDRIAL DNA PART B 2019, VOL. 4, NO. 1, 361–362 https://doi.org/10.1080/23802359.2018.1544042

MITOGENOME ANNOUNCEMENT Complete mitochondrial genome of Callogorgia cf. gracilis (Octocorallia: Calcaxonia: Primnoidae)

Erin E. Easton and David Hicks School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA

ABSTRACT ARTICLE HISTORY We report the first complete mitochondrial genome of Callogorgia. Callogorgia cf. gracilis isolate Received 27 August 2018 DFH32_518B was collected by a remotely operated vehicle at 98 m on McGrail Bank (27.9840725N, Accepted 20 October 2018 92.604242W). The complete mitogenome is 18,937 bp (27.8% A, 18.3% C, 19.8% G, and 34.1% T) and KEYWORDS has the ancestral octocoral gene order for its 14 protein-coding genes, two rRNA genes, and one tRNA Mesophotic coral gene. It is sister to and 96.6% similar (uncorrected) to Narella hawaiiensis, the only other complete þ þ ecosystem; Cnidaria; Gulf mitogenome reported for Primnoidae. The cox1 igr1 mtMutS region differs by two base pairs of Mexico (0.12%) from the only reported C. gracilis haplotype.

Callogorgia consists of 27 valid species (Cairns et al. 2018), annotated by manually adjusting Narella hawaiiensis four of which occur in the northwestern Gulf of Mexico (NC026192) annotations mapped to the consensus sequence. (Cairns and Bayer 2002; Etnoyer and Cairns 2017): C. ameri- The complete mitogenome was aligned with default MUSCLE cana, C. delta, C. gracilis, and C. linguimaris. C. gracilis is the (Edgar 2004) parameters to eight representative species with only one reported shallower than 180 m (Quattrini et al. the octocoral ancestral mitochondrial gene order and com- 2013; Etnoyer and Cairns 2017) and is distinguishable by its plete mitogenomes available in GenBank: all Calcaxonia spe- stiff, straight main stem, cylindrical (vs. clavate) polyps, num- cies, one randomly selected representative from each ber of sclerites, and unique mitochondrial molecular barcode Alcyonacea subclass, and all Helioporacea and Pennatulacea (cox1þigr1þmtMutS) (Cairns and Bayer 2002; Quattrini et al. species. The latter two taxa generally are sister to the clade 2013). The collected specimen is morphologically consistent containing Primnoidae (Brockman and McFadden 2012; with C. gracilis but differs by two base pairs (0.12%) from the Poliseno et al. 2017). A maximum-likelihood, phylogenetic single cox1þigr1þmtMutS haplotype reported in Quattrini tree was constructed in RAxML 8.2.11 (Stamatakis 2014) þ þ et al. (2013) for C. gracilis (DOI: 10.6084/m9.figshare.6998459). (Figure 1). Extended methods and cox1 igr1 mtMutS align- Because additional specimens are required to delineate spe- ment are available at figshare (DOI: 10.6084/ m9.figshare.6998459). cies within the C. gracilis complex (see Cairns and Bayer The complete mitogenome is 18,937 bp (27.8% A, 18.3% 2002), we assigned this specimen to C. cf. gracilis. C, 19.8% G, and 34.1% T), has the ancestral octocoral gene The specimen was collected by remotely operated vehicle order, and has one tRNA, two rRNA, and 14 protein-coding (SubAtlantic Mohawk 18 operated by University of North genes. Despite the utility of gene-sequence data in resolving Carolina – Wilmington, Undersea Vehicles Program) at 98 m coral phylogenies (e.g. Soler-Hurtado et al. 2017), this mitoge- on McGrail Bank (27.9840725N, 92.604242W) on 24 nome report is the first for Callogorgia and second for September 2017. DNA was extracted with GeneJET Genomic Primnoidae. C. cf. gracilis is sister to and 96.6% similar DNA Purification Kit (ThermoFisher Scientific Waltham, MA) (uncorrected) to the only other Primnoidae, N. hawaiiensis, ’ per manufacture s protocol and submitted to Biopolymers but the relative position of Primnoidae among octocoral fam- Facility at Harvard Medical School for library preparation and ilies is not well supported (Figure 1). The C. cf. gracilis mito- next-generation sequencing (NextSeq 500). Trimmed reads genome was deposited in GenBank (MH719202) and the (Trimmomatic-0.32, Bolger et al. 2014) were assembled de specimen in the Smithsonian National Museum of National novo with SPAdes (Bankevich et al. 2012) on the University of History (USNM1507967). New Hampshire Bioinformatics Core facility ron server. After circularizing and editing overlapping ends of the SPAdes con- tig in Geneious R10.2.6 (Kearse et al. 2012), trimmed reads Disclosure statement (BBDuk v. 37.25) were mapped to the resulting reference The authors report no conflicts of interest. The authors alone are respon- sequence to generate a consensus sequence. Genes were sible for the content and writing of this article.

CONTACT Erin E. Easton [email protected] UTRGV-SEEMS, 100 Marine Lab Dr., South Padre Island, TX 78597, USA ß 2019 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. 362 E. E. EASTON AND D. HICKS

Callogorgia cf. gracilis (Alcyonacea: Calcaxonia: Primnoidae) MH719202 100 0.03 Narella hawaiiensis (Alcyonacea: Calcaxonia: Primnoidae) NC026192

Renilla muelleri (Pennatulacea: Renillidae) NC018378 44 100

100 Stylatula elongata (Pennatulacea: Virgulariidae) NC018380

100 44 Junceella fragilis (Alcyonacea: Calcaxonia: Ellisellidae) NC024181

Sibogagorgia cauliflora (Alcyonacea: Scleraxonia: Paragorgiidae) NC026193

Heliopora coerulea (Helioporacea: Helioporidae) NC020375

Leptogorgia sarmentosa (Alcyonacea: Holaxania: Gorgoniidae) NC035670

Scleronephthya gracllimum (Alcyonacea: Alcyoniina: Neptheidae) NC023344 Figure 1. Maximum-likelihood, phylogenetic tree of the complete mitogenomes of Callogorgia cf. gracilis (this study) and eight representative octocorals (taxonomic position and GenBank accession numbers in tip labels). In Geneious R10.2.6, complete mitogenomes were aligned with default MUSCLE parameters; the resulting alignment was used to construct the phylogenetic tree in RAxML 8.2.11 with the following changes to the default settings: bootstrap replicates ¼1000, algo- rithm ¼ rapid bootstrapping and search for best-scoring ML tree, outgroup ¼ NC023344, nucleotide model ¼ GTR CAT I. Bootstrap values are reported at the nodes. See figshare (DOI: 10.6084/m9.figshare.6998459) for extended methods.

Funding rearrangement in octocoral mitochondrial genomes. Genome Biol Evol. 4:994–1006. Research cruise and ROV operations funding provided by NOAA’s Deep Cairns SD, Bayer FM. 2002. Studies on western Atlantic Octocorallia Sea Coral Research and Technology Program, Flower Garden Banks (Coelenterata: Anthozoa). Part 2: The genus Callogorgia Gray, 1858. National Marine Sanctuary, and National Marine Sanctuary Foundation. Proceedings of the Biological Society of Washington. 115:840–867. This publication was made possible by the National Oceanic and Cairns SD, Stone RP, Moon H-W, Lee JH. 2018. Primnoidae (Octocorallia: Atmospheric Administration, Office of Education Educational Partnership Calcaxonia) from the Emperor Seamounts, with notes on Callogorgia Program award NA16SEC4810009. Its contents are solely the responsibil- elegans (Gray, 1870). Pac Sci. 72:125–142. ity of the award recipient and do not necessarily represent the official Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accur- views of the U.S. Department of Commerce, National Oceanic and acy and high throughput. Nucleic Acids Res. 32:1792–1797. Atmospheric Administration. Research supported in part by an Etnoyer PJ, Cairns SD. 2017. Deep-sea coral taxa in the US Gulf of Institutional Grant (NA14OAR4170102) to the Texas Sea Grant College Mexico: depth and geographical distribution. https://deepseacoraldata. Program from the National Sea Grant Office, National Oceanic and noaa.gov/. [Last accessed on 6 August 2018]. Atmospheric Administration, U.S. Department of Commerce. 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 integrated and extendable desktop software platform for the ORCID organization and analysis of sequence data. Bioinformatics. 28: – Erin E. Easton http://orcid.org/0000-0003-4853-6026 1647 1649. Poliseno A, Feregrino C, Sartoretto S, Aurelle D, Worheide€ G, McFadden CS, Vargas S. 2017. Comparative mitogenomics, phylogeny and evolu- tionary history of Leptogorgia (Gorgoniidae). Mol Phylogenet Evol. – References 115:181 189. Quattrini AM, Georgian SE, Byrnes L, Stevens A, Falco R, Cordes EE. 2013. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Niche divergence by deep-sea octocorals in the genus Callogorgia Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a across the continental slope of the Gulf of Mexico. Mol Ecol. 22: new genome assembly algorithm and its applications to single-cell 4123–4140. sequencing. J Comput Biol. 19:455–477. Soler-Hurtado MM, Lopez-Gonz alez PJ, Machordom A. 2017. Molecular Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for phylogenetic relationships reveal contrasting evolutionary patterns in Illumina sequence data. Bioinformatics. 30:2114–2120. Gorgoniidae (Octocorallia) in the Eastern Pacific. Mol Phylogenet Evol. Brockman SA, McFadden CS. 2012. The mitochondrial genome of 111:219–230. Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis intramolecular recombination as the primary mechanism of gene and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313.