1,026
Views
0
CrossRef citations to date
0
Altmetric
Mitogenome Announcement

The complete mitochondrial genome of the Reef Manta Ray, Mobula alfredi, from Hawaii

ORCID Icon, ORCID Icon &
Pages 197-203 | Received 20 Nov 2022, Accepted 07 Jan 2023, Published online: 02 Feb 2023

References

  • Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • Antaky CC, Kitamura PK, Knapp IS, Toonen RJ, Price MR. 2019. The complete mitochondrial genome of the band-rumped Storm Petrel (Oceanodroma castro). Mitochondrial DNA Part B. 4(1):1271–1272.
  • Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM, Naylor GJP. 2012. Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Mol Phylogenet Evol. 63(1):28–42.
  • Bustamante C, Barría C, Vargas-Caro C, Ovenden JR, Bennett MB. 2016. The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome. Mitochondrial DNA Part A. 27(5):3540–3541.
  • Chandrasekaran K, Dhinakarasamy I, Jayavel S, Rajendran T, Bhoopathy S, Gopal D, Ramalingam K, Ajmal Khan S. 2022. Complete sequence and characterization of the Mobula tarapacana (Sicklefin Devilray) mitochondrial genome and its phylogenetic implications. Journal of King Saud University - Science. 34(3):101909.doi:10.1016/j.jksus.2022.101909.
  • Croll DA, Dewar H, Dulvy NK, Fernando D, Francis MP, Galván‐Magaña F, Hall M, Heinrichs S, Marshall A, Mccauley D, et al. 2016. Vulnerabilities and fisheries impacts: the uncertain future of manta and devil rays. Aquatic Conserv Mar Freshw Ecosyst. 26(3):562–575.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772–772.
  • Deakos M, Baker J, Bejder L. 2011. Characteristics of a manta ray Manta alfredi population off Maui, Hawaii, and implications for management. Mar Ecol Prog Ser. 429:245–260.
  • Deakos MH. 2010. Paired-laser photogrammetry as a simple and accurate system for measuring the body size of free-ranging manta rays Manta alfredi. Aquat Biol. 10(1):1–10.
  • Deakos MH. 2012. The reproductive ecology of resident manta rays (Manta alfredi) off Maui, Hawaii, with an emphasis on body size. Environ Biol Fish. 94(2):443–456.
  • Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307–321.
  • Guindon S, Gascuel O. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst Biol. 5:696–704.
  • Hinojosa-Alvarez S, Díaz-Jaimes P, Marcet-Houben M, Gabaldón T. 2015. The complete mitochondrial genome of the Giant Manta ray, Manta birostris. Mitochondrial DNA. 26(5):787–788.
  • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17(8):754–755.
  • Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30(11):2531–2540.
  • Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241.
  • Knapp I, Puritz J, Bird C, Whitney J, Sudek M, Forsman Z, Toonen R. 2016. ezRAD- an accessible next-generation RAD sequencing protocol suitable for non-model organisms_v3.2. Protocols.io. doi:10.17504/protocols.io.e9pbh5n.
  • Last P, Stevens J. 2009. Sharks and rays of Australia. 2nd ed. Cambridge (MA): Harvard University Press.
  • Marshall A, Barreto R, Carlson J, Fernando D, Fordham S, Francis M, Herman K, Jabado R, Liu K, Pacoureau N, et al. 2019. Mobula alfredi. The IUCN red list of threatened species 2019: e.T195459A68632178. doi:10.2305/IUCN.UK.2019-3.RLTS.T195459A68632178.en.
  • Marshall AD, Bennett MB. 2010. Reproductive ecology of the reef manta ray Manta alfredi in southern Mozambique. J Fish Biol. 77(1):169–190.
  • Marshall AD, Compagno LJ, Bennett MB. 2009. Redescription of the genus Manta with resurrection of Manta alfredi. Zootaxa. 2301(1):1–28.
  • Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17(1):10–13.
  • Meng G, Li Y, Yang C, Liu S. 2019. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 47(11):e63.
  • O’Malley M p, Townsend KA, Hilton P, Heinrichs S, Stewart JD. 2017. Characterization of the trade in manta and devil ray gill plates in China and South‐east Asia through trader surveys. Aquatic Conserv Mar Freshw Ecosyst. 27(2):394–413.
  • Palumbi S, Martin A, Romano S, McMillan W, Stice L, Grabowski G. 1991. A simple fool’s guide to PCR, v2.0. Honolulu: University of Hawaii Department of Zoology and Kewalo Marine Laboratory, Special Publication; p. 1–23.
  • Pate J, Marshall A. 2020. Urban manta rays: potential manta ray nursery habitat along a highly developed Florida coastline. Endang Species Res. 43:51–64.
  • Poortvliet M, Hoarau G. 2013. The complete mitochondrial genome of the Spinetail Devilray, Mobula japanica. Mitochondrial DNA. 24(1):28–30.
  • Poortvliet M, Olsen JL, Croll DA, Bernardi G, Newton K, Kollias S, O’Sullivan J, Fernando D, Stevens G, Galván Magaña F, et al. 2015. A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences. Mol Phylogenet Evol. 83:72–85.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19(12):1572–1574.
  • Santillán-Lugo B, Llera-Herrera R, Corro-Espinosa D, Oñate-González EC, Rodríguez-Domínguez G, Saavedra-Sotelo NC. 2017. Complete mitochondrial genome of the Devil Ray, Mobula thurstoni (Lloyd, 1908) (Myliobatiformes: Myliobatidae). Mitochondrial DNA Part B. 2: 868–870.
  • Stecher G, Tamura K, Kumar S. 2020. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol Biol Evol. 37(4):1237–1239.
  • Stewart JD, Jaine FRA, Armstrong AJ, Armstrong AO, Bennett MB, Burgess KB, Couturier LIE, Croll DA, Cronin MR, Deakos MH, et al. 2018. Research priorities to support effective manta and devil ray conservation. Front Mar Sci. 5:314.
  • Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 38(7):3022–3027.
  • Terraneo TI, Arrigoni R, Benzoni F, Forsman ZH, Berumen ML. 2018. Using ezRAD to reconstruct the complete mitochondrial genome of Porites fontanesii (Cnidaria: Scleractinia). Mitochondrial DNA B Resour. 3(1):173–174.
  • Tisthammer KH, Forsman ZH, Sindorf VL, Massey TL, Bielecki CR, Toonen RJ. 2016. The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD. Mitochondrial DNA B Resour. 1(1):247–249.
  • Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE. 2013. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ. 1:e203.
  • White WT, Corrigan S, Yang L, Henderson A, Bazinet A, Swofford D, Naylor G. 2017. Phylogeny of the manta and devilrays (Chondrichthyes: Mobulidae), with an updated taxonomic arrangement for the family. Zool J Linn Soc. 182(1):50–75.
  • White WT, Giles J, Potter IC, Dharmadi . 2006. Data on the bycatch fishery and reproductive biology of mobulid rays (Myliobatiformes) in Indonesia. Fisheries Res. 82(1-3):65–73.