Molecular characterisation of the complete nuclear ribosomal DNA sequence of the blacklip abalone Haliotis rubra

References

• Alter K, Andrewartha SJ, Morash AJ, Clark TD, Hellicar AD, León RI, Elliott NG. 2017. Hybrid abalone are more robust to multi-stressor environments than pure parental species. Aquaculture. 478:25–34. doi: 10.1016/j.aquaculture.2017.04.035
   Web of Science ®Google Scholar
• Ambrose CD, Crease TJ. 2011. Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. BMC Genetics. 12:13. doi: 10.1186/1471-2156-12-13
   PubMed Web of Science ®Google Scholar
• Appleyard SA, Carr NA, Elliott NG. 2009. Molecular analyses indicate homogenous structure of abalone across morphologically different Haliotis rubra collections in South Australia. Journal of Shellfish Research. 28:609–616. doi: 10.2983/035.028.0325
   Web of Science ®Google Scholar
• Baranski M, Loughnan S, Austin CM, Robinson N. 2006. A microsatellite linkage map of the blacklip abalone, Haliotis rubra. Animal Genetics. 37:563–570. doi: 10.1111/j.1365-2052.2006.01531.x
   PubMed Web of Science ®Google Scholar
• Baranski M, Rourke M, Loughnan S, Hayes B, Austin C, Robinson N. 2008. Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling. Animal Genetics. 39:606–614. doi: 10.1111/j.1365-2052.2008.01773.x
   PubMed Web of Science ®Google Scholar
• Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research. 27(2):573–580. doi: 10.1093/nar/27.2.573
   PubMed Web of Science ®Google Scholar
• Botwright NA. 2015. Karyotype comparison between Haliotis rubra, H. laevigata and the interspecific hybrid. Aquaculture Research. 46:236–241. doi: 10.1111/are.12156
   Web of Science ®Google Scholar
• Coleman AW, Vacquier VD. 2002. Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). Journal of Molecular Evolution. 54:246–257. doi: 10.1007/s00239-001-0006-0
   PubMed Web of Science ®Google Scholar
• Conod N, Bartlett JP, Evans BS, Elliott NG. 2002. Comparison of mitochondrial and nuclear DNA analyses of population structure in the blacklip abalone Haliotis rubra Leach. Marine and Freshwater Research. 53:711–718. doi: 10.1071/MF01197
   Web of Science ®Google Scholar
• Corbeil S, Williams LM, McColl KA, Crane MS. 2016. Australian abalone (Haliotis laevigata, H. rubra and H. conicopora) are susceptible to infection by multiple abalone herpesvirus genotypes. Diseases of Aquatic Organisms. 119:101–106. doi: 10.3354/dao02989
   PubMed Web of Science ®Google Scholar
• Dang VT, Speck P, Doroudi M, Smith B, Benkendorff K. 2011. Variation in the antiviral and antibacterial activity of abalone Haliotis laevigata, H. rubra and their hybrid in South Australia. Aquaculture. 315:242–249. doi: 10.1016/j.aquaculture.2011.03.005
   Web of Science ®Google Scholar
• Dyomin AG, Koshel EI, Kiselev AM, Saifitdinova AF, Galkina SA, Fukagawa T, Kostareva AA, Gaginskaya ER. 2016. Chicken rRNA gene cluster structure. Plos One. 11(6):e0157464. doi: 10.1371/journal.pone.0157464
   PubMed Web of Science ®Google Scholar
• Estes JA, Lindberg DR, Wray C. 2005. Evolution of large body size in abalones (Haliotis): patterns and implications. Paleobiology. 31:591–606. doi: 10.1666/04059.1
   Web of Science ®Google Scholar
• Feng S, Powell SM, Wilson R, Bowman JP. 2014. Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biology and Evolution. 6:133–148. doi: 10.1093/gbe/evt209
   PubMed Web of Science ®Google Scholar
• Fernández M, Polanco C, Ruiz ML, Pérez De La Vega M. 2000. A comparative study of the structure of the rDNA intergenic spacer of Lens culinaris Medik. and other legume species. Genome. 43:597–603. doi: 10.1139/g00-022
   PubMed Web of Science ®Google Scholar
• Geiger DL, Groves LT. 1999. Review of fossil abalone (Gastropoda: Vetigastropoda: Haliotidae) with comparison to recent species. Journal of Paleontology. 73:872–885. doi: 10.1017/S0022336000040713
   Web of Science ®Google Scholar
• Goodsell PJ, Underwood AJ, Chapman MG, Heasman MP. 2006. Seeding small numbers of cultured black-lip abalone (Haliotis rubra Leach) to match natural densities of wild populations. Marine and Freshwater Research. 57:747–756. doi: 10.1071/MF06039
   Web of Science ®Google Scholar
• Guindon S, Dufayard JF, 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. Systematic Biology. 59:307–321. doi: 10.1093/sysbio/syq010
   PubMed Web of Science ®Google Scholar
• Guo ZS, Ding Y, Zhang XH, Hou XG. 2017. Complete nuclear ribosomal DNA sequence analysis of Pacific abalone Haliotis discus hannai. Fisheries Science. 83:777–784. doi: 10.1007/s12562-017-1109-x
   Web of Science ®Google Scholar
• Guo ZS, Hou XG. 2016. Research progress on chromosome in family Haliotidae. Fisheries Science. 35:597–602. (In Chinese).
   Google Scholar
• Guo ZS, Hou XG, Han L. 2017. Complete nuclear ribosomal DNA (nrDNA) sequence analyses of the black-footed abalone Haliotis iris. New Zealand Journal of Marine and Freshwater Research. 1–15. doi:10.1080/00288330.2017.1363790.
   Web of Science ®Google Scholar
• He Y, Shen SD, Shen ZG. 2017. Cloning and application of the complete nuclear ribosomal DNA (nrDNA) cistron sequence of Pyropia haitanensis (Bangiales, Rhodophyta). Botanica Marina. 60:327–337. doi: 10.1515/bot-2016-0079
   Web of Science ®Google Scholar
• Hooper C, Hardy-Smith P, Handlinger J. 2007. Ganglioneuritis causing high mortalities in farmed Australian abalone (Haliotis laevigata and Haliotis rubra). Australian Veterinary Journal. 85:188–193. doi: 10.1111/j.1751-0813.2007.00155.x
   PubMed Web of Science ®Google Scholar
• Jang HM, Erf GF, Rowland KC, Kong BW. 2014. Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model. BMC Genomics. 15:707. doi: 10.1186/1471-2164-15-707
   PubMed Web of Science ®Google Scholar
• Kakou B, Angers B, Glémet H. 2015. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens). Genome. 59:149–158. doi: 10.1139/gen-2015-0114
   PubMed Web of Science ®Google Scholar
• Ki JS, Kim IC, Lee JS. 2009. Comparative analysis of nuclear ribosomal DNA from the moon jelly Aurelia sp.1 (Cnidaria: Scyphozoa) with characterizations of the 18S, 28S genes, and the intergenic spacer (IGS). Hydrobiologia. 616:229–239. doi: 10.1007/s10750-008-9596-5
   Web of Science ®Google Scholar
• Knudsen S. 1999. Promoter 2.0: for the recognition of Pol II promoter sequences. Bioinformatics. 15:356–361. doi: 10.1093/bioinformatics/15.5.356
   PubMed Web of Science ®Google Scholar
• Li ZB, Appleyard SA, Elliott NG. 2006. Population structure of Haliotis rubra from south Australia inferred from nuclear and mtDNA analyses. Acta Oceanologica Sinica. 25:99–112.
   Web of Science ®Google Scholar
• Li YY, Shen SD, He LH, Xu P, Lu S. 2010. Sequence analysis of rDNA intergenic spacer (IGS) of Porphyra haitanensis. Journal of Applied Phycology. 22:187–193. doi: 10.1007/s10811-009-9441-x
   Web of Science ®Google Scholar
• Li YY, Shen SD, He LH, Xu P, Wang GC. 2009. Sequence analysis of the ITS region and 5.8S rDNA of Porphyra haitanensis. Chinese Journal of Oceanology and Limnology. 27(3):493–501. doi: 10.1007/s00343-009-9168-1
   Web of Science ®Google Scholar
• Li XC, Xu JJ, He Y, Shen SS, Zhu JY, Shen ZG. 2016. The complete nuclear ribosomal DNA (nrDNA) cistron sequence of Pyropia yezoensis (Bangiales, Rhodophyta). Journal of Applied Phycology. 28:663–669. doi: 10.1007/s10811-015-0522-8
   Web of Science ®Google Scholar
• Li L, Zhong CH, Bian YB. 2014. The molecular diversity analysis of Auricularia auricula-judae in China by nuclear ribosomal DNA intergenic spacer. Electronic Journal of Biotechnology. 17:27–33. doi: 10.1016/j.ejbt.2013.12.005
   Web of Science ®Google Scholar
• Ling SD. 2008. Range expansion of a habitat-modifying species leads to loss of taxonomic diversity: a new and impoverished reef state. Oecologia. 156:883–894. doi: 10.1007/s00442-008-1043-9
   PubMed Web of Science ®Google Scholar
• Liu W, Heasman M, Simpson R. 2009. Growth and reproductive performance of triploid and diploid blacklip abalone, Haliotis rubra (Leach, 1814). Aquaculture Research. 40:188–203. doi: 10.1111/j.1365-2109.2008.02082.x
   Web of Science ®Google Scholar
• Liu W, Heasman M, Simpson R, Dworjanyn S, Pirozzi I. 2006. Growth and feeding in juvenile triploid and diploid blacklip abalone, Haliotis rubra (Leach, 1814), at two temperatures. Aquaculture Nutrition. 12:410–417. doi: 10.1111/j.1365-2095.2006.00442.x
   Web of Science ®Google Scholar
• Liu Y, Xu T, Robinson N, Qin J, Li X. 2015. Cryopreservation of sperm in farmed blacklip abalone (Haliotis rubra Leach, 1814). Aquaculture Research. 46:2628–2636. doi: 10.1111/are.12415
   Web of Science ®Google Scholar
• Maggini F, Gelati MT, Spolverini M, Frediani M. 2008. The intergenic spacer region of the rDNA in Olea europaea L. Tree Genetics & Genomes. 4:293–298. doi: 10.1007/s11295-007-0109-x
   Web of Science ®Google Scholar
• Mayfield S, Mundy C, Gorfine H, Hart AM, Worthington D. 2012. Fifty years of sustained production from the Australian abalone fisheries. Review in Fisheries Science. 20:220–250. doi: 10.1080/10641262.2012.725434
   Web of Science ®Google Scholar
• Maynard BT, Kerr LJ, McKiernan JM, Jansen ES, Hanna PJ. 2005. Mitochondrial DNA sequence and gene organization in the Australian blacklip abalone Haliotis rubra (Leach). Marine Biotechnology. 7:645–658. doi: 10.1007/s10126-005-0013-z
   PubMed Web of Science ®Google Scholar
• Miller KJ, Mundy CN, Mayfield S. 2014. Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian Greenlip Abalone. Molecular Ecology. 23:4958–4975. doi: 10.1111/mec.12914
   PubMed Web of Science ®Google Scholar
• Miller AD, van Rooyen A, Rašić G, Ierodiaconou DA, Gorfine HK, Day R, Wong C, Hoffmann AA, Weeks AR. 2016. Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data. Molecular Ecology. 25:3845–3864. doi: 10.1111/mec.13734
   PubMed Web of Science ®Google Scholar
• Notredame C, Higgins DG, Heringa J. 2000. T-Cofee: a novel method for multiple sequence alignments. Journal of Molecular Biology. 302:205–217. doi: 10.1006/jmbi.2000.4042
   PubMed Web of Science ®Google Scholar
• Parvaresh M, Talebi M, Sayed-Tabatabaei BE. 2014. Molecular characterization of ribosomal DNA intergenic spacer (IGS) region in pomegranate (Punica granatum L.). Plant Systematics and Evolution. 300:899–908. doi: 10.1007/s00606-013-0928-1
   Web of Science ®Google Scholar
• Pederson HG, Barrett NS, Frusher SD, Buxton CD. 2008. Effect of predator–prey and competitive interactions on size at emergence in the black-lip abalone Haliotis rubra in a Tasmanian MPA. Marine Ecology Progress Series. 366:91–98. doi: 10.3354/meps07521
   Web of Science ®Google Scholar
• Posada D. 2009. Selection of models of DNA evolution with jModelTest. bioinformatics for DNA sequence analysis. Methods in Molecular Biology. 537:93–112. doi: 10.1007/978-1-59745-251-9_5
   PubMedGoogle Scholar
• Sanders MJ, Beinssen KH. 1998. A comparison of management strategies for the rehabilitation of a fishery: applied to the fishery for blacklip abalone Haliotis rubra in the Western Zone of Victoria (Australia). Fisheries Research. 38:283–301. doi: 10.1016/S0165-7836(98)00158-1
   Web of Science ®Google Scholar
• Santoni S, Bervillé A. 1992. Characterization of the nuclear ribosomal DNA units and phylogeny of Beta L. wild forms and cultivated beets. Theoretical and Applied Genetics. 83(5):533–542. doi: 10.1007/BF00226896
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA 6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution. 30(12):2725–2729. doi: 10.1093/molbev/mst197
   PubMed Web of Science ®Google Scholar
• Valentine JP, Tarbath DB, Frusher SD, Mundy CN, Buxton CD. 2010. Limited evidence for ecosystem-level change on reefs exposed to Haliotis rubra (‘blacklip abalone’) exploitation. Austral Ecology. 35:806–817. doi: 10.1111/j.1442-9993.2009.02088.x
   Web of Science ®Google Scholar
• Van Wormhoudt A, Gaume B, Le Bras Y, Roussel V, Huchette S. 2011. Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata: tissue differential expression. Genetica. 139:1217–1227. doi: 10.1007/s10709-011-9623-8
   PubMed Web of Science ®Google Scholar
• Xu JJ, Jiang B, Chai SM, He Y, Zhu JY, Shen ZG, Shen SD. 2016. Complete nuclear ribosomal DNA sequence amplification and molecular analyses of Bangia (Bangiales, Rhodophyta) from China. Chinese Journal of Oceanology and Limnology. 34(5):1044–1053. doi: 10.1007/s00343-016-5033-1
   Web of Science ®Google Scholar
• Yu JH, Li HX, Ge XP, Li JL, Tang YK. 2010. Characteristics analysis of complete ribosomal DNA sequence in Chinese mitten crab (Eriocheir sinensis). Journal of Fisheries of China. 34(5):698–703. (In Chinese with English Abstract). doi: 10.3724/SP.J.1231.2010.06659
   Google Scholar
• Zheng X, Chang QC, Zhang Y, Tian SQ, Lou Y, Duan H, Guo DH, Wang CR, Zhu XQ. 2014. Characterization of the complete nuclear ribosomal DNA sequences of Paramphistomum cervi. Scientific World Journal. 2014:751907.
   Google Scholar