Abstract
Background
Haliotis discus hannai more commonly referred to as the Pacific Abalone is of significant commercial and economical value in South Korea, with it being the second largest producer in the world. Despite this significance there is a lack of genetic studies with regards to the species. Most existing studies focused mainly on environmental factors.
Objective
To provide a comprehensive review describing the genetic feature of Haliotis discus hannai by infection of vibrio and virus.
Methods
This review summarized the immune response in the Haliotis spp. with regards to immunological genes such as Cathepsin B, C-type lectin and Toll-like receptors. Genetic studies with regards to transposable elements and miRNAs are few and far between. A study identified LTR retrotransposon Ty3/gypsy in the species. As to miRNA, a single study identified numerous miRNAs in the Haliotis discus hannai.
Conclusion
This paper sought to provide an overview of genetic perspective with regards to immune response genes, transposable elements and miRNAs.
Similar content being viewed by others
References
Adachi K, Okumura S (2012) Determination of genome size of Haliotis discus hannai and H. diversicolor aquatilis (Haliotidae) and phylogenetic examination of this family. Fish Sci 78:849–852
Ayarpadikannan S, Kim H-S (2014) The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genom Inform 12:98–104
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233
Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS (2018) Ten things you should know about transposable elements. Genome Biol 19:199–210
Cai J, Li J, Thompson KD, Li C, Han H (2007) Isolation and characterization of pathogenic Vibrio parahaemolyticus from diseased post-larvae of abalone Haliotis diversicolor supertexta. J Basic Microbiol 47:84–86
Chadès I, Curtis JM, Martin TG (2012) Setting realistic recovery targets for two interacting endangered species, sea otter and northern abalone. Conserv Biol 26:1016–1025
Chen H, Wang L, Hou Z, Liu Z, Wang W, Gao D, Gao Q, Wang M, Song L (2015) The comprehensive immunomodulation of NeurimmiRs in haemocytes of oyster Crassostrea gigas after acetylcholine and norepinephrine stimulation. BMC Genomics 16:942–955
Chen H, Jiang S, Wang L, Wang L, Wang H, Qiu L, Song L (2016a) Cgi-miR-92d indirectly regulates TNF expression by targeting CDS region of lipopolysaccharide-induced TNF-α factor 3 (CgLITAF3) in oyster Crassostrea gigas. Fish Shellfish Immunol 55:577–584
Chen H, Zhou Z, Wang H, Wang L, Wang W, Liu R, Qiu L, Song L (2016b) An invertebrate-specific and immune-responsive microRNA augments oyster haemocyte phagocytosis by targeting CgIκB2. Sci Rep 6:29591–29600
Cheng P, Liu X, Zhang G, He J (2007) Cloning and expression analysis of a HSP70 gene from Pacific abalone (Haliotis discus hannai). Fish Shellfish Immunol 22:77–87
Cook PA (2016) Recent trends in worldwide abalone production. J Shellfish Res 35:581–584
Craven RC, Leure-duPree AE, Weldon RA, Wills JW (1995) Genetic analysis of the major homology region of the Rous sarcoma virus gag protein. J Virol 69:4213–4227
De Zoysa M, Nikapitiya C, Kim Y, Oh C, Kang DH, Whang I, Kim SJ, Lee JS, Choi CY, Lee J (2010) Allograft inflammatory factor-1 in disk abalone (Haliotis discus discus): molecular cloning, transcriptional regulation against immune challenge and tissue injury. Fish Shellfish Immunol 29:319–326
Djuranovic S, Nahvi A, Green R (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336:237–240
Duursma AM, Kedde M, Schrier M, le Sage C, Agami R (2008) miR-148 targets human DNMT3b protein coding region. RNA 14:872–877
Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang S, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E (2007) Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev 21:2558–2570
Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E (2009) Deadenylation is a widespread effect of miRNA regulation. RNA 15:21–32
Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105
Fu Y, Shi Z, Wu M, Zhang J, Jia L, Chen X (2011) Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One 6:e22957
Fu Y, Shi Z, Wang G, Li W, Zhang J, Jia L (2012) Expression and regulation of miR-1,-133a,-206a, and MRFs by thyroid hormone during larval development in Paralichthys olivaceus. Comp Biochem Physiol B Biochem Mol Biol 161:226–232
Fu Y, Shi Z, Wang G, Zhang J, Li W, Jia L (2013) Expression of let-7 microRNAs that are involved in Japanese flounder (Paralichthys olivaceus) metamorphosis. Comp Biochem Physiol B Biochem Mol Biol 165:106–113
Fukui Y, Saitoh S, Sawabe T (2010) Environmental determinants correlated to Vibrio harveyi-mediated death of marine gastropods. Environ Microbiol 12:124–133
Ghosh J, Lun CM, Majeske AJ, Sacchi S, Schrankel CS, Smith LC (2011) Invertebrate immune diversity. Dev Comp Immunol 35:959–974
Gu Y, Zhang L, Chen X (2014) Differential expression analysis of Paralichthys olivaceus microRNAs in adult ovary and testis by deep sequencing. Gen Comp Endocrinol 204:181–184
Guo H, Lu Z, Zhu X, Zhu C, Wang C, Shen Y, Wang W (2018) Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress. Fish Shellfish Immunol 74:152–161
Guo Z, Ding Y, Han L, Hou X (2019) Characterization of the complete mitochondrial genome of Pacific abalone Haliotis discus hannai. Fish Shellfish Immunol 4:717–718
Huang J, Luo X, Huang M, Liu G, You W, Ke C (2018) Identification and characteristics of muscle growth-related microRNA in the Pacific abalone, Haliotis discus hannai. BMC Genom 19:915–925
Kawasaki T, Kawai T (2014) Toll-like receptor signaling pathways. Front Immunol 5:461–468
Kim S-S, Kim J-D (2019) Overview on the development of aquaculture and aquafeed production in Korea. Aquac Indones 20:1–7
Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597–610
Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532
Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD (2009) New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites. Genome Res 19:1175–1183
Lee SI, Gim JA, Lim MJ, Kim HS, Nam BH, Kim NS (2018) Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis. Genes Genom 40:177–187
Lee HE, Jo A, Im J, Cha HJ, Kim WJ, Kim HH, Kim DS, Kim W, Yang TJ, Kim HS (2019) Characterization of the long terminal repeat of the endogenous retrovirus-derived microRNAs in the olive flounder. Sci Rep 9:14007–14016
Levin HL, Moran JV (2011) Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12:615–627
Long JM, Maloney B, Rogers JT, Lahiri DK (2019) Novel upregulation of amyloid-β precursor protein (APP) by microRNA-346 via targeting of APP mRNA 5′-untranslated region: implications in Alzheimer’s disease. Mol Psychiatry 24:345–363
Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11:1187–1197
Miller WJ, McDonald JF, Pinsker W (1997) Molecular domestication of mobile elements. Genetica 100:261–270
Najib A, Kim MS, Choi SH, Kang YJ, Kim KH (2016) Changes in microRNAs expression profile of olive flounder (Paralichthys olivaceus) in response to viral hemorrhagic septicemia virus (VHSV) infection. Fish Shellfish Immunol 51:384–391
Nam BH, Kwak W, Kim YO, Kim DK, Kong HJ, Kim WJ, Kang JH, Park JY, An CM, Moon JY (2017) Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae. Gigascience 6:1–8
Ørom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′ UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460–471
Park CJ, Kim SY (2013) Abalone aquaculture in Korea. J Shellfish Res 32:17–20
Pellicer J, Kelly LJ, Leitch IJ, Zomlefer WB, Fay MF (2014) A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae. N Phytol 201:1484–1497
Pritham EJ (2009) Transposable elements and factors influencing their success in eukaryotes. J Hered 100:648–655
Priyathilaka TT, Bathige S, Lee S, Nam BH, Lee J (2019) Transcriptome-wide identification, functional characterization, and expression analysis of two novel invertebrate-type Toll-like receptors from disk abalone (Haliotis discus discus). Fish Shellfish Immunol 84:802–815
Qiu R, Liu X, Hu Y, Sun B (2013) Expression characterization and activity analysis of a cathepsin B from Pacific abalone Haliotis discus hannai. Fish Shellfish Immunol 34:1376–1382
Ramachandran V, Chen X (2008) Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321:1490–1492
Robert J (2003) Evolution of heat shock protein and immunity. Dev Comp Immunol 27:449–464
Sawabe T, Inoue S, Fukui Y, Yoshie K, Nishihara Y, Miura H (2007) Mass mortality of Japanese abalone Haliotis discus hannai caused by Vibrio harveyi infection. Microbes Environ 22:300–308
Silva LC, Ortigosa LC, Benard G (2010) Anti-TNF-α agents in the treatment of immune-mediated inflammatory diseases: mechanisms of action and pitfalls. Immunotherapy. 2:817–833
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G (2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet 50:1282–1288
Sun X, Liu Q, Yang B, Huang J (2016) Differential expression of microRNAs of Litopenaeus vannamei in response to different virulence WSSV infection. Fish Shellfish Immunol 58:18–23
Turk V, Stoka V, Vasiljeva O, Renko M, Sun T, Turk B, Turk D (2012) Cysteine cathepsins: from structure, function and regulation to new frontiers. Biochim Biophys Acta 1824:68–88
Wang R, Wang J, Sun Y, Yang B, Wang A (2015) Antibiotic resistance monitoring in Vibrio spp. isolated from rearing environment and intestines of abalone Haliotis diversicolor. Mar Pollut Bull 101:701–706
Weis WI, Taylor ME, Drickamer K (1998) The C-type lectin superfamily in the immune system. Immunol Rev 163:19–34
Wu C, Zhang W, Mai K, Xu W, Wang X, Ma H, Liufu Z (2010) Transcriptional up-regulation of a novel ferritin homolog in abalone Haliotis discus hannai Ino by dietary iron. Comp Biochem Physiol 152:424–432
Xi Q, Xiong Y, Wang Y, Cheng X, Qi E, Shu G, Wang SB, Gao L, Zhu X, Jiang Q (2015) Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei). Mol Biol Rep 42:61–69
Xu F, Wang X, Feng Y, Huang W, Wang W, Li L, Fang X, Que H, Zhang G (2014) Identification of conserved and novel microRNAs in the pacific oyster Crassostrea gigas by deep sequencing. PLoS One 9:e104371
Xu X, Yuan J, Yang L, Weng S, He J, Zuo H (2016) The Dorsal/miR-1959/Cactus feedback loop facilitates the infection of WSSV in Litopenaeus vannamei. Fish Shellfish Immunol 56:397–401
Zhang J, Qiu R, Hu Y (2014) HdhCTL1 is a novel C-type lectin of abalone Haliotis discus hannai that agglutinates Gram-negative bacterial pathogens. Fish Shellfish Immunol 41:466–472
Zhang H, Fu Y, Su Y, Shi Z, Zhang J (2015) Identification and expression of HDAC4 targeted by miR-1 and miR-133a during early development in Paralichthys olivaceus. Comp Biochem Physiol 179:1–8
Zhang B, Zhou Z, Sun L (2016) pol-miR-731, a teleost miRNA upregulated by megalocytivirus, negatively regulates virus-induced type I interferon response, apoptosis, and cell cycle arrest. Sci Rep 6:28354–28367
Zhou H, Rigoutsos I (2014) Mir-103a-3p targets the 5'UTR of GPRC5A in pancreatic cells. RNA 20:1431–1439
Zuo H, Yuan J, Chen Y, Li S, Su Z, Wei E, Li C, Weng S, Xu X, He J (2016) A microRNA-mediated positive feedback regulatory loop of the NF-kappaB pathway in Litopenaeus vannamei. J Immunol 196:3842–3853
Acknowledgements
This research was a part of the project titled “Omics based on fishery disease control technology development and industrialization (20150242) funded by the Ministry of Oceans and Fisheries, South Korea.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors has no conflicting interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Im, J., Kim, HS. Genetic features of Haliotis discus hannai by infection of vibrio and virus. Genes Genom 42, 117–125 (2020). https://doi.org/10.1007/s13258-019-00892-w
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-019-00892-w