A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads

References

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410.
   PubMed Web of Science ®Google Scholar
• Arnason U, Gullberg A, Janke A. 2001. Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage. Zool Scripta. 30(4):249–255.
   Web of Science ®Google Scholar
• Bañon R, Arronte JC, Rodríguez-Cabello C, Piñeiro C-G, Punzón A, Serrano A. 2016. Commented checklist of marine fishes from the Galicia Bank seamount (NW Spain). Zootaxa. 4067(3):293–333.
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319.
   PubMed Web of Science ®Google Scholar
• Blasdale T, Newton AW. 1998. Estimates of discards from two deep water fleets in the Rockall Trough. ICES Document CM 1998/O: 11. Available at: http://www.ices.dk/sites/pub/CM%20Doccuments/1998/O/O1198.pdf.
   Google Scholar
• Boisvert CA, Johnston P, Trinajstic K, Johanson Z. 2019. Chondrichthyan evolution, diversity, and senses. Springer, Cham; p. 65–91
   Google Scholar
• Calis E, Jackson EH, Nolan CP, Jeal F. 2005. Preliminary age and growth estimates of the rabbit fish, Chimaera monstrosa, with implications for future resource management. J Northw Atl Fish Sci. 35:15–26.
   Google Scholar
• Catarino D, Jakobsen K, Jakobsen J, Giacomello E, Menezes GM, Diogo H, Canha Â, Porteiro FM, Melo O, Stefanni S. 2020. First record of the opal chimaera, Chimaera opalescens (Holocephali: Chimaeridae) and revision of the occurrence of the rabbit fish Chimaera monstrosa in the Azores waters. J Fish Biol. 97(3):763–775.
   PubMed Web of Science ®Google Scholar
• Cavanagh RD, Gibson C. 2007. Overview of the conservation status of cartilaginous fishes (Chondrichthyans) in the Mediterranean Sea, Gland, Switzerland and Malaga, Spain, IUCN Species Survival Commission Shark Specialist Group.
   Google Scholar
• Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 18(2):170–175.
   PubMed Web of Science ®Google Scholar
• Dagit DD, Hareide N, Clò S. 2007. Chimaera monstrosa. The IUCN Red List of Threatened Species. 2007. e.T63114A12610445.
   Google Scholar
• Didier DA, Kemper JM, Ebert DA. 2012. Phylogeny, biology, andclassification of extant holocephalans. In: Carrier JC, Musick JA, Heithaus MR, editors. The biology of sharks and their relatives, Vol. 1. Boca Raton, FL: CRC Press; p. 97–122.
   Google Scholar
• Dulvy NK, Fowler SL, Musick JA, Cavanagh RD, Kyne PM, Harrison LR, Carlson JK, Nk Davidson L, Fordham SV, Francis MP, et al. 2014. Extinction risk and conservation of the world’s sharks and rays. eLife. 3(3):1–34.
   Google Scholar
• Dulvy NK, Trebilco R. 2018. Size-based insights into the ecosystem role of sharks and rays. In: Carrier J, Heithaus MR, Simpfendorfer CA, eds. Shark research: emerging technologies and applications for the field and laboratory, Vol. 1. Boca Ranton: CRC Press; p. 25–44.
   Google Scholar
• Formenti G, The Vertebrate Genomes Project Consortium, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Jarvis ED. 2021. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol. 22(1):1–22.
   PubMed Web of Science ®Google Scholar
• Freitas M, Vieira S, Costa L, Delgado J, Biscoito M, González J. 2017. First records of Chimaera opalescens (Holocephali: Chimaeriformes: Chimaeridae) from Madeira and north-west African coast. Acta Ichthyol Piscat. 47(1):81–84.
   Web of Science ®Google Scholar
• Gomes-dos-Santos A, Arrondo NV, Machado AM, Veríssimo A, Pérez M, Román E, Castro LFC, Froufe E. 2020. The complete mitochondrial genome of the deep-water cartilaginous fish Hydrolagus affinis (deBrito Capello, 1868) (Holocephali: Chimaeridae). Mitochondrial DNA Part B. 5(2):1810–1812.
   Web of Science ®Google Scholar
• Gomes-Dos-Santos A, Vilas-Arrondo N, Machado AM, Veríssimo A, Pérez M, Baldó F, Castro LFC, Froufe E. 2021. Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae). Mitochondrial DNA B Resour. 6(2):420–422.
   PubMed Web of Science ®Google Scholar
• Iglésias SP, Kemper JM, Naylor GJP. 2022. Chimaera compacta, a new species from southern Indian Ocean, and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae). Ichthyol Res. 69(1):31–45.
   Web of Science ®Google Scholar
• Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B. 2010. Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol Biol Evol. 27(11):2576–2586.
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Kousteni V, Mazzoleni S, Vasileiadou K, Rovatsos M. 2021. Complete mitochondrial DNA genome of nine species of sharks and rays and their phylogenetic placement among modern elasmobranchs. Genes. 12(3):324.
   PubMed Web of Science ®Google Scholar
• Kraft DW, Conklin EE, Barba EW, Hutchinson M, Toonen RJ, Forsman ZH, Bowen BW. 2020. Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinusfalciformis). PeerJ. 8:e10186.
   PubMed Web of Science ®Google Scholar
• Luchetti EA, Iglésias SP, Sellos DY. 2011. Chimaera opalescens n. sp., a new chimaeroid (Chondrichthyes: Holocephali) from the north-eastern Atlantic Ocean. J Fish Biol. 79(2):399–417.
   PubMed Web of Science ®Google Scholar
• Moura T, Figueiredo I, Machado PB, Gordo LS. 2004. Growth pattern and reproductive strategy of the holocephalan Chimaera monstrosa along the Portuguese continental shelf. J Mar Biol Ass. 84(4):801–804.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Oliver S, Braccini M, Newman SJ, Harvey ES. 2015. Global patterns in the bycatch of sharks and rays. Marine Policy. 54:86–97.
   Web of Science ®Google Scholar
• Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genomics. 17(1):719.
   PubMed Web of Science ®Google Scholar
• Vieira RP, Cunha MR. 2014. In situ observation of chimaerid speciesin the Gorringe Bank: New distribution records for the north-EastAtlantic Ocean. J Fish Biol. 85(3):927–932.
   PubMed Web of Science ®Google Scholar
• Weigmann S. 2016. Annotated checklist of the living sharks, batoids and chimaeras (Chondrichthyes) of the world, with a focus on biogeographical diversity. J Fish Biol. 88(3):837–1037.
   PubMed Web of Science ®Google Scholar
• Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13(6):e1005595.
   PubMed Web of Science ®Google Scholar
• Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. 2014. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Research. 3:191.
   Google Scholar