Complete mitochondrial genome of Paralvinella palmiformis (Polychaeta: Alvinellidae)

References

• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology. 19(5):786–477.
   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
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
   PubMed Web of Science ®Google Scholar
• Bushnell B. 2014. BBMap: a fast, accurate, splice-aware aligner. Berkeley, CA (United States): Lawrence Berkeley National Lab.(LBNL).
   Google Scholar
• Desbruyères D, Laubier L. 1986. Les Alvinellidae, une famille nouvelle d'annélides polychètes inféodées aux sources hydrothermales sous-marines: systématique, biologie et écologie. Can J Zool. 64(10):2227–2245. doi:https://doi.org/10.1139/z86-337.
   Google Scholar
• Desbruyères D, Laubier L. 1982. Paralvinella grasslei, new genus, new species of Alvinellinae (Polychaeta: Ampharetidae) from the Galapagos rift geothermal vents. Vol. 95. Proceedings of the Biological Society of Washington, Washington. p. 484–494.
   Google Scholar
• Desbruyères D, Laubier L. 1989. Paralvinella hessleri, new species of Alvinellidae (Polychaeta) from the Mariana back-arc basin hydrothermal vents. Vol. 102. Proceedings of the Biological Society of Washington, Washington. p. 761–767.
   Google Scholar
• Desbruyères D, Laubier L. 1993. New species of Alvinellidae (Polychaeta) from the North Fiji back-arc basin hydrothermal vents (southwestern Pacific). Vol. 106. Proceedings of the Biological Society of Washington, Washington. p. 225–236.
   Google Scholar
• Dilly GF, Young CR, Lane WS, Pangilinan J, Girguis PR. 2012. Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes. Proceedings of the Royal Society of London B: Biological Sciences, London. rspb20120098.
   Google Scholar
• Fontanillas E, Galzitskaya OV, Lecompte O, Lobanov MY, Tanguy A, Mary J, Girguis PR, Hourdez S, Jollivet D. 2017. Proteome evolution of deep-Sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages. Genome Biol Evol. 9(2):279–296.
   PubMedGoogle Scholar
• Grelon D, Morineaux M, Desrosiers G, Juniper SK. 2006. Feeding and territorial behavior of Paralvinella sulfincola, a polychaete worm at deep-sea hydrothermal vents of the Northeast Pacific Ocean. J Exp Marine Biol Ecol. 329(2):174–186.
   Google Scholar
• Han Y, Zhang D, Wang C, Zhou Y. 2021. Out of the Pacific: a new alvinellid worm (Annelida: Terebellida) from the northern Indian Ocean hydrothermal vents. Front Mar Sci. 8:8.
   Google Scholar
• 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 organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
   PubMed Web of Science ®Google Scholar
• Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27(5):722–736.
   PubMed Web of Science ®Google Scholar
• Larget BR, Kotha SK, Dewey CN, Ané C. 2010. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics. 26(22):2910–2911.
   PubMedGoogle Scholar
• Laslett D, Canbäck B. 2008. ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics. 24(2):172–175.
   PubMed Web of Science ®Google Scholar
• Lee RW. 2003. Thermal tolerances of deep-sea hydrothermal vent animals from the northeast Pacific. Biol Bull. 205(2):98–101.
   PubMedGoogle Scholar
• Lelièvre Y, Legendre P, Matabos M, Mihály S, Lee RW, Sarradin P-M, Arango CP, Sarrazin J. 2017. Astronomical and atmospheric impacts on deep-sea hydrothermal vent invertebrates. Proc Biol Sci. 284(1852):20162123.
   Google Scholar
• Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 34(18):3094–3100.
   PubMed Web of Science ®Google Scholar
• McHugh D. 1989. Population structure and reproductive biology of two sympatric hydrothermal vent polychaetes, Paralvinella pandorae and P. palmiformis. Marine Biology. 103(1):95–106.
   Google Scholar
• Rinke C, Lee RW. 2009. Pathways, activities and thermal stability of anaerobic and aerobic enzymes in thermophilic vent paralvinellid worms. Mar Ecol Prog Ser. 382:99–112.
   Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. New York, NY: Cold Spring Harbor Laboratory Press..
   Google Scholar
• Sarrazin J, Juniper SK, Massoth G, Legendre P. 1999. Physical and chemical factors influencing species distributions on hydrothermal sulfide edifices of the Juan de Fuca Ridge, northeast Pacific. Mar Ecol Prog Ser. 190:89–112.
   Web of Science ®Google Scholar
• Stiller J, Tilic E, Rousset V, Pleijel F, Rouse GW. 2020. Spaghetti to a Tree: A robust phylogeny for Terebelliformia (Annelida) based on transcriptomes, molecular and morphological data. Biology. 9(4):73.
   PubMed Web of Science ®Google Scholar
• Tunnicliffe V, Desbruyères D, Jollivet D, Laubier L. 1993. Systematic and ecological characteristics of Paralvinella sulfincola Desbruyères and Laubier, a new polychaete (family Alvinellidae) from northeast Pacific hydrothermal vents. Can J Zool. 71(2):286–297.
   Google Scholar
• Tunnicliffe V. 1988. Biogeography and evolution of hydrothermal-vent fauna in the eastern Pacific Ocean. Vol. 233. Proceedings of the Royal Society of London B: Biological Sciences, London, p. 347–366.
   Google Scholar
• Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS One. 9(11):e112963.
   PubMed Web of Science ®Google Scholar
• Wang JR, Holt J, McMillan L, Jones CD. 2018. FMLRC: Hybrid long read error correction using an FM-index. BMC Bioinformatics. 19(1):50.
   PubMedGoogle Scholar
• Zhong M, Hansen B, Nesnidal M, Golombek A, Halanych KM, Struck TH. 2011. Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids. BMC Evol Biol. 11:369.
   PubMedGoogle Scholar