Eight New Mitogenomes Clarify the Phylogenetic Relationships of Stromboidea Within the Caenogastropod Phylogenetic Framework
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Eight new mitogenomes clarify the phylogenetic relationships of Stromboidea within the caenogastropod phylogenetic framework Alison R. Irwin a, b, *, Ellen E. Strong c , Yasunori Kano d , Elizabeth M. Harper e , Suzanne T. Williams a a Department of Life Sciences, Natural History Museum, Cromwell Rd, London, SW7 5BD, United Kingdom b School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, United Kingdom c Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington DC 20560, United States d Department of Marine Ecosystems Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan e Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom *Corresponding author: Alison Irwin Email: Alison Irwin: [email protected] Suzanne Williams: [email protected] Ellen Strong: [email protected] Yasunori Kano: [email protected] Elizabeth Harper: [email protected] Declarations of interest: none Supplementary Material 1. List of published sequences used in this study with species name and authority, mitogenome length, GenBank Accession number and publication reference, with complete reference list below table. Details for new sequences are in Table 2. Taxa used as outgroups in analyses are highlighted (bold), and superscript numbers mark (1) 18S and (2) 28S sequences included in mixed mitochondrial and nuclear gene trees, and (3) species name updated based on nomenclatural decisions in WoRMS (May 2020). The name Viviparus chui is in MolluscaBase as a taxon inquirendum, described as a fossil (Paracampeloma chui). Length GenBank Higher taxon Species name Reference (bp) Acc. no. Ifremeria nautilei Bouchet & Warén, 15,664 NC_024642 Osca et al. (2014) Caenogastropoda, 1991 Abyssochryssoidea Provanna sp. Dall, 1918 16,183 KM675481 T. Xu et al. (2016) Caenogastropoda, Pomacea maculata Perry, 1810 15,516 NC_027503 Yang et al. (2016) Architaenioglossa, Ampullarioidea Caenogastropoda, Pomacea bridgesii (Reeve, 1856) 16,640 NC_037691 J. Guo et al. (2017) Architaenioglossa, Ampullarioidea Caenogastropoda, Cyclophorus martensianus Möllendorff, Architaenioglossa, 15,308 MH700493 Xie et al. (2019) 1874 Cyclophoroidea Caenogastropoda, Architaenioglossa, Viviparus chui Yen, 1937 16,392 NC_035733 Wang et al. (2017) Viviparoidea Caenogastropoda, Nguyen et al. Cerithidea obtusa (Lamarck, 1822) 15,708 NC_039951 Cerithioidea (2018) Caenogastropoda, Littorinimorpha, Calyptraea chinensis (Linnaeus, 1758) 8,530 EU827193 Cunha et al. (2009) Calyptraeoidea Caenogastropoda, Cypraea tigris Linnaeus, 1758 16,177 MK783263 Pu et al. (2019) Littorinimorpha, Fukumori et al. Monetaria annulus (Linnaeus, 1758) 16,087 LC469295 Cypraeoidea (2019) Marques et al. Littorina saxatilis (Olivi, 1792) 16,887 NC_030595 Caenogastropoda, (2017) Winnepenninckx Littorinimorpha, Littorina saxatilis (Olivi, 1792)1 1,826 Y11751 Littorinoidea et al. (1998) Littorina saxatilis (Olivi, 1792)2 1,464 HE590811 Reid et al. (2012) Caenogastropoda, Littorinimorpha, Naticarius hebraeus (Martyn, 1786) 15,384 NC_028002 Osca et al. (2015) Naticoidea Márquez, Aliger gigas (Linnaeus, 1758)3 15,461 NC_024932 et al. (2016) Aliger gigas (Linnaeus, 1758)1, 3 638 GU198749 Spade et al. (2010) Lambis lambis (Linnaeus, 1758) 15,481 MH115428 Jiang et al. (2019) Caenogastropoda, Littorinimorpha, Lambis lambis (Linnaeus, 1758)1 1,887 HQ833996 Zou et al. (2011) Stromboidea, Strombidae Harpago chiragra (Linnaeus, 1758) 15,460 MH122656 Jiang et al. (2019) Conomurex luhuanus (Linnaeus, 1758) 15,799 NC_035726 Zhao et al. (2018) Criscione and Conomurex luhuanus (Linnaeus, 1758)2 1,373 KC110029 Ponder (2013) Caenogastropoda, Littorinimorpha, Onustus exutus (Reeve, 1842) 16,043 MK327366 M. Xu et al. (2019) Stromboidea, Xenophoridae Monoplex parthenopeus (Salis 15,270 NC_013247 Cunha et al. (2009) Marschlins, 1793) Caenogastropoda, Galeodea echinophora (Linnaeus, Littorinimorpha, 15,388 NC_028003 Osca et al. (2015) Tonnoidea 1758) Charonia lampas (Linnaeus, 1758) 15,405 NC_037188 Cho et al. (2017) Peretolchina et al. Korotnewia korotnevi (Lindholm, 1909)3 15,171 KY697389 (2020) Caenogastropoda, Littorinimorpha, Oncomelania hupensis Gredler, 1881 15,182 NC_013073 Li and Zhou (2009) Truncatelloidea Potamopyrgus antipodarum (Gray, Neiman et al. 15,110 NC_020790 1843) (2010) Eualetes tulipa (Rousseau in Chenu, Rawlings et al. 15,078 NC_014585 Caenogastropoda, 1843) (2010) Littorinimorpha, Ceraesignum maximum (G. B. Sowerby Rawlings et al. Vermetoidea 15,578 NC_014583 I, 1825) (2010) Caenogastropoda, Babylonia borneensis (G. B. Sowerby 15,556 KT211493 Sung et al. (2016) Neogastropoda, II, 1864) Babyloniidae Babylonia lutosa (Lamarck, 1816) 15,346 NC_028628 Xiong et al. (2015) Caenogastropoda, Jónsson et al. Buccinum undatum Linnaeus, 1758 15,265 NC_040940 Neogastropoda, (2019) Buccinoidea Reishia clavigera (Küster, 1860) 15,285 NC_010090 Ki et al. (2010) Caenogastropoda, Clionella kraussii (E. A. Smith, 1877) 15,760 MH308390 Uribe et al. (2018) Neogastropoda, Conus tribblei Walls, 1977 15,570 NC_027957 Barghi et al. (2016) Conoidea Caenogastropoda, Zhong et al. Neogastropoda, Murex trapa Röding, 1798 15,408 MN462589 (2019b) Muricoidea Caenogastropoda, McComish et al. Neogastropoda, Amalda northlandica Hart, 1995 15,354 NC_014403 (2010) Olivoidea Bivetiella cancellata (Linnaeus, 1767) 16,648 NC_013241 Cunha et al. (2009) Neptuneopsis gilchristi G. B. Sowerby Harasewych et al. 15,312 MN125492 Caenogastropoda, III, 1898 (2019) Neogastropoda, Volutoidea Cymbium olla (Linnaeus, 1758) 15,375 NC_013245 Cunha et al. (2009) Zhong et al. Melo melo (Lightfoot, 1786) 15,721 MN462590 (2019a) Z. Guo et al. Vetigastropoda Haliotis iris Gmelin, 1791 17,131 NC_031361 (2019) References Barghi, N., Concepcion, G.P., Olivera, B.M., Lluisma, A.O., 2016. Characterization of the complete mitochondrial genome of Conus tribblei Walls, 1977. Mitochondrial DNA A 27, 4451 –4452. https://doi.org/10.3109/19401736.2015.1089566. Cho, I.-Y., Kim, K.-Y., Yi, C.H., Kim, I.H., Jung, Y.-H., Hwang, S.-J., Bae, J., Yoon, M., Kim, M.-S., 2017. Full-length mitochondrial genome of the triton trumpet Charonia lampas (Littorinimorpha: Ranellidae). Mitochondrial DNA B 2, 759–760. https://doi.org/10.1080/23802359.2017.1398610. Criscione, F., Ponder, W.F., 2013. A phylogenetic analysis of rissooidean and cingulopsoidean families (Gastropoda: Caenogastropoda). Mol. Phylogen. Evol. 66, 1075–1082. https://doi.org/10.1016/j.ympev.2012.11.026. Cunha, R.L., Grande, C., Zardoya, R., 2009. Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol. Biol. 9, 210. https://doi.org/10.1186/1471-2148-9- 210. Fukumori, H., Itoh, H., Irie, T., 2019. The mitochondrial genome of the gold-ringed cowry Monetaria annulus (Mollusca: Gastropoda: Cypraeidae) determined by whole-genome sequencing. Mitochondrial DNA B 4, 2305–2307. https://doi.org/10.1080/23802359.2019.1627946. Guo, J., Yang, H., Zhang, C., Xue, H., Xia, Y., Zhang, J.E., 2017. Complete mitochondrial genome of the apple snail Pomacea diffusa (Gastropoda, Ampullariidae) with phylogenetic consideration. Mitochondrial DNA B 2, 865-867. https://doi.org/10.1080/23802359.2017.1407683. Guo, Z., Jiang, Z., Han, L., Ding, Y., Hou, X., 2019. Characterisation of the complete mitochondrial genome of the black-footed abalone Haliotis iris. N. Z. J. Zool. 46, 74–86. https://doi.org/10.1080/03014223.2018.1495655. Harasewych, M., Sei, M., Wirshing, H.H., González, V.L., Uribe, J.E., 2019. The complete mitochondrial genome of Neptuneopsis gilchristi GB Sowerby III, 1898 (Neogastropoda: Volutidae: Calliotectinae). Nautilus 133, 67–73. Jiang, D., Zheng, X., Zeng, X., Kong, L., Li, Q., 2019. The complete mitochondrial genome of Harpago chiragra and Lambis lambis (Gastropoda: Stromboidea): implications on the Littorinimorpha phylogeny. Scientific reports 9, 1-9. https://doi.org/10.1038/s41598-019- 54141-x. Jónsson, Z.O., Pálsson, S., Westfall, K.M., Magnúsdóttir, H., Goodall, J., Ornolfsdottir, E.B., 2019. The mitochondrial genome of common whelk Buccinum undatum (Neogastropoda: Buccinidae). Mitochondrial DNA B 4, 457–459. https://doi.org/10.1080/23802359.2018.1545534. Ki, J.S., Lee, Y.M., Jung, S.O., Horiguchi, T., Cho, H.S., Lee, J.S., 2010. Mitochondrial genome of Thais clavigera (Mollusca: Gastropoda): Affirmation of the conserved, ancestral gene pattern within the mollusks. Mol. Phylogeneti. Evol. 54, 1016-1020. https://doi.org/10.1016/j.ympev.2009.12.003. Li, S., Zhou, X., 2009. The mitochondrial genome of the Oncomelania hupensis, the snail intermediate host of Schistosoma japonicum in mainland China. Direct submission to the Genome Project NCBI record NC_013073–2009. https://www.ncbi.nlm.nih.gov/nuccore/NC_013073. Marques, J.P., Sotelo, G., Larsson, T., Johannesson, K., Panova, M., Faria, R., 2017. Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis. Marine Genomics 32, 41–47. https://doi.org/10.1016/j.margen.2016.10.006. Márquez, E.J., Castro, E.R., Alzate, J.F., 2016. Mitochondrial genome of the endangered marine gastropod Strombus gigas Linnaeus, 1758 (Mollusca: Gastropoda). Mitochondrial DNA A 27, 1516–1517. https://doi.org/10.3109/19401736.2014.953118. McComish, B.J., Hills, S.F.K., Biggs, P.J., Penny, D., 2010. Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol. Evol. 2, 410–424. https://doi.org/10.1093/gbe/evq029.