Abstract
Little is known about the molecular mechanisms governing gonadal developmental processes in abalones. Here, we conducted transcriptome analysis of Pacific abalone Haliotis discus discus for gene discovery in the brain, ovary, testis, and unfertilized eggs. Among the annotated unigenes, 48.6% of unigenes were identified by Venn diagram analysis as having universal or tissue-specific expression. Twenty-three genes with gonad-biased gene ontology (GO) terms were first obtained. Secondly, 36 genes were found by screening known gene names related to germ cell development. Finally, 17 genes were obtained by querying the annotated unigene database for zygotically expressed gonadal genes (ovary and testis) and maternally expressed gonadal genes (ovary, testis, and unfertilized eggs) using keywords related to reproduction. To further verify tissue distribution pattern and subcellular localization of these genes, RT-PCR and in situ hybridization were performed using a unigene encoding a germ cell marker, vasa, as control. The results showed that vasa was expressed mainly in the early developmental stages of germ cells in both sexes. One of the candidate genes, vitelline envelope zona pellucida domain protein 12 (ZP12), was expressed in the primordial germ cells of immature gonad and early developmental stages of germ cells of the adult female. The results obtained from the present study suggest that vasa and ZP12 are involved in germ cell development of Pacific abalone and that ZP12 is an especially useful germ cell-specific marker in immature adults. The current gonadal transcriptome profile is an extensive resource for future reproductive molecular biology studies of this species.
Similar content being viewed by others
References
Aagaard JE, Yi XH, MacCoss MJ, Swanson W (2006) Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs. Proc Natl Acad Sci U S A 103:117302–117307
Aagaard JE, Vacquier VD, MacCoss MJ, Swanson W (2010) ZP domain protein in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins. Mol Biol Evol 27:193–203
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Arai K, Okumura S (2013) Aquaculture-oriented genetic researches in abalone: current status and future perspective. Afr J Biotechnol 12:4044–4052
Bar I, Cummins S, Elizur A (2016) Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the southern Bluefin tuna (Thunnus maccoyii). BMC Genomics 17:217
Barisone GA, Albertali IE, Sánchez M, Cabada MO (2003) The envelopes of amphibian oocytes: physiological modifications in bufo arenrum. Reprod Biol Endocrinol. https://doi.org/10.1186/1477-7827-1-18
Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188
Bester-van Der Merwe A, Blaauw S, Plessis JD, Roodt-wilding R (2013) Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using goldenGate medium-throughput genotyping assay. Int J Mol Sci 14:19341–19360
Chatchaiphan S, Srisapoome P, Kim J, Devlin RH, Na-Nakorn U (2017) De novo transcriptome characterization and growth-related gene expression profiling of diploid and triploid bighead catfish (Clrias macrocephalus Gunther, 1864). Mar Biotechnol (NY) 19:36–48
Chen X, Mei J, Wu JJ, Jing J, Ma WG, Zhang JZ, Dan C, Wang WM, Gui JF (2014) A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish. Mar Biotechnol (NY) 17:190–198
Choi MJ, Kim GD, Kim JM, Lim HK (2015) Differentially-expressed gene assocaited with faster growth of the Pacific abalone, Haliotis discus discus. Int J Mol Sci 16:27520–27534
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Cook PA (2014) The worldwide abalone industry. Mod Econ 5:1181–1186
Darie CC, Biniossek ML, Jovine L, Litscher ES, Wassarman PM (2004) Structural characterization of fish egg vitelline envelope proteins by mass spectrometry. Biochemistry 43:7459–7478
Di G, Luo X, You W, Zhao J, Kong X, Ke C (2015) Proteomic analysis of muscle between hybrid abalone and patental lines Haliotis gigantea reeve and Haliotis discus hannai ino. Heredity 114:564–574
Fabioux C, Huvet A, Lelong C, Robert R, Pouvreau S, Daniel JY (2004) Oyster vasa-like gene as a marker of the germline cell development in Crassostrea gigas. Biochem Biophys Res Commun 320:592–598
Fabioux C, Corporeau C, Quillien V, Favrel P, Huvet A (2009) In vivo RNA interference in oyster-vasa silencing inhibits germ cell development. FEBS J 276:2566–2573
Franchini P, Van der Merwe M, Roodt-wilding R (2011) Transcriptome characterization of the south African abalone Haliotis midae using sequencing-by-synthesis. BMC Res Notes. https://doi.org/10.1186/1756-0500-4-59
Fu Y, Jia L, Shi Z, Zhang J, Li W (2017) Gene expression patterns regulating embryogenesis based on the integrated de novo transcriptome assembly of the Japanese flounder. Comp Biochem Physiol Part D Genomics Proteomics 22:58–66
Fujimoto T, Nishimura T, Goto-kazeto R, Kawakami Y, Yamaha E, Arai K (2010) Sexual dimorphism of gonadal structure and gene expression in germ cell-deficient loach, a teleost fish. Proc Natl Acad Sci U S A 107:17211–17216
Gleason LU, Burton RS (2015) RNA-Seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis. Mol Ecol 24:610–627
Grabherr MG, Hass BJ, Yassour M, Levin JZ, Thompson DA (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (NY) 19:644–652
Huang ZX, Chen ZS, Ke CH, Zhao J, You WW, Zhang J, Dong WT, Chen J (2012) Pyroseqencing of haliotis diversicolor transcriptome: insights into early development molluscan gene expression. PLoS One 7:e51279
Huang JQ, Chen SL, Liu Y, Shao CW, Lin F, Wang N, Hu QM (2014) Molecular characterization, sexually dimorphic expression, and functional analysis of 3’untranslated region of vasa gene in half-smooth tongue sole (Cynoglossus semilaevis). Theriogenology 82:213–224
Hyllner SJ, Westerlund L, Olsson PE, Schopen A (2001) Cloning of rainbow trout egg envelope proteins: members of a unique group of structural proteins. Biol Reprod 64:805–811
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999:138–148
Jiang LK, You WW, Zhang XJ, Xu J, Jiang YL, Wang K, Zhao ZX, Chen BH, Zhao YF, Mahboob S, Al-Ghanim KA, Ke CH, Xu P (2015) Construction of the BAC library of small abalone (Haliotis diversicolor) for gene screening and genome characterization. Mar Biotechnol (NY) 18:49–56
Kanamori A, Naruse K, Mitani H, Shima A, Hori H (2003) Genomic organization of ZP domain containing egg envelope genes in medaka (Oryzias latipes). Gene 305:35–45
Kranz AM, Tollenaere A, Norris BJ, Degnan BM, Degnan SM (2010) Identifying the germline in an equally cleaving mollusk: vasa and nanos expression during embryonic and larval development of the vetigastropod Haliotis asinina. J Exp Zool 314B:267–279
Kurakawa H, Saito D, Nakamura S, Katoh-Fukui Y, Ohta K, Baba T, Morohashi K, Tanaka M (2007) Germ cells are essential for sexual dimorphism in the medaka gonad. Proc Natl Acad Sci U S A 104:16958–16963
Li Y, Lai S, Wang R, Zhao Y, Qin H, Jiang L, Li N, Fu Q, Li C (2017a) RNA-Seq analysis of the antioxidant status and immune response of Portunus trituberculatus following aerial exposure. Mar Biotechnol (NY) 19:89–101
Li JQ, Wang ML, Fang JQ, Liu X, Mao YZ, Liu GM, Bian DP (2017b) Reproductive performance of one-year-old Pacific abalone (Haliotis discus hannai) and its crossbreeding effect on offspring growth and survival. Aquaculture 473:110–114
Linhartova Z, Satio T, Kaspar V, Rodina M, Praskova E, Haqihara S, Psenicka M (2015) Sterilization of sterlet Acipenser ruthenus by using knockdown agent, antisense morpholino oligonucleotide against dead end gene. Theriogenology. https://doi.org/10.1016/j.theriogenology.07.003
Liu XJ, Wang H, Gong ZY (2006) Tandem-repeated zebrafish zp3 genes possess oocyte-specific promoters and are insensitive to estrogen induction. Biol Reprod 74:1016–1025
Lu JG, Zheng M, Zheng JJ, Liu J, Liu YZ, Peng LP, Zhang XF, Wang QS, Luan PX, Mahbooband S, Sun XW (2015) Transcriptomic analyses reveal novel genes with sexually dimorphic expression in yellow catfish (Pelteobagrus fulvidraco) brain. Mar Biotechnol (NY) 17:613–623
Matsumoto T, Masaoka T, Fujiwara A, Nakamura Y, Satoh N, Awaji M (2013) Reproduction-related genes in the pearl oyster genome. Zool Sci 30:826–850
McCombie H, Leud C, Phelipot P, Lapegue S, Boudry P, Gerard A (2005) A complementary method for production of tetraploid Crassostrea gigas using crosses between dipliod and tetraploids with cytochalasin B treatments. Mar Biotechnol (NY) 7:318–330
Miao Y, Zhang L, Sun Y, Jiao W, Li Y, Sun J, Wang Y, Wang S, Bao S, Liu W (2015) Integration of transcriptomic and proteomic approaches provides a core set of genes for understanding of scallop attachment. Mar Biotechnol (NY) 17:523–532
Miura T, Miura C, Fukushima E, Iwai T, Celino F, Watanabe N, Uehara M, Ohashi H, Yoshida K, Hosokawa H, Urasaki S, Kuwayama K, Uchimura Y, Sone K, Odawara K, Ido A (2013) In: Watabe S, Maeyama K, Nagasawa H (eds) Recent advances in pearl research. Tokyo, Terrapub
Modig C, Modesto T, Canario A, Cerda J, Hofsten J, Olsson P (2006) Molecular characterization and expression pattern of zona pellucida proteins in gilthead seabream (Sparus aurata). Biol Reprod 75:717–725
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Nagasawa K, Takeuchi Y, Miwa M, Higuchi K, Morita T, Mitsuboshi T, Miyaki K, Kadomura K, Yoshizaki G (2009) cDNA cloning and expression analysis of a vasa-like gene in Pacific bluefin tuna Thunnus orientalis. Fish Sci 75:71–79
Nam BH, Kwak W, Kim Y, Kim D, Kong HJ, Kim W, Kang J, Park JY, An CM, Moon J, Park CJ, Yu JW, Yoon J, Seo M, Kim K, Kim DK, Lee S, Sung S, Lee C, Shin Y, Jung M, Kang B, Shin G, Ka S, Caetano-Anolles K, Cho S, Kim H (2017) Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotide. GigaScience 6:1–8
Nekrutenko A, Taylor J (2015) Next-generation sequencing date interpretation: enhancing reproducibility and accessibility. Nat Rev Genet 13:667–672
Obata M, Sano N, Kimata S, Nagasawa K, Yoshizaki G, Komaru A (2010) The proliferation and migration of immature germ cells in the mussel, Mytilus galloprovincialis vasa-like gene (Myvlg) by in situ hybridization. Dev Genes Evol 220:139–149
Okumura S, Arai K, Harigaya Y, Eguchi H, Sakai M, Senbokuya H, Fukukawa S, Yamamori K (2007) Highly efficient induction of triploid Pacific abalone Haliotis discus hannai by caffeine treatment. Fish Sci 73:237–243
Olson DJ, Hulstrand AM, Houston DW (2012) Maternal mRNA knockdown studies: antisense experiments using the host-transfer technique in X. Laevis and X. Tropicalis. Methods Mol Biol 917:167–182
Pertea G, Huang X, Liang F, Antonescu V, Sultana R (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652
Plant TM (2015) 60 years of neuroendocrinology: the hypothalamo-pituitary-gonadal axis. J Endocrinol 226:T41–T54
Raz E (2000) The function and regulation of vasa-like genes in germ-cell development. Genome Biol 1:reviews 1017.1–reviews 1017.6
Robalino J, Browdy CL, Prior S, Metz A, Parnell P, Gross P, Warr G (2004) Induction of antiviral immunity by double-stranded RNA in a marine invertebrate. J Virol 78:10442–1044
Roux A, Lambrechts H, Roodt-wilding R (2013) Reproductive histology of cultured Haliotis midae (linnaeus, 1758) and preliminary evaluation of maturation. J Shellfish Res 32:143–153
Shao C, Bao B, Xie Z, Chen X, Li B, Jia X, Yao Q, Orti G, Li W, Li X, Hamre K, Xu J, Wang L, Chen F, Tian Y, Schreiber AM, Wang N, Shi Q, Li H, Xiu Y, Li Y, Xu W, Shi Z, Zhang G, Power DM, Wang Q, Schartl M, Chen S (2016) The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry. Nat Genet 49:119–124
Shi JW, Sheng JQ, Peng K, Wang JH, Yi WJ, Wu HJ, Gu Q, Hong YJ (2013) Expression pattern of the zona pellucida 3 (ZP3) gene during ovarian development and the location of ZP3 protein in oocytes in natural, wild triploid crucian carp mutant, Carassius auratus var. Pingxiangnensis. Genet Mol Res 12:5640–5650
Shiel BP, Hall NE, Cooke IR, Robinson NA, Strugnell JM (2015) De novo characterization of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family. Mar Biotechnol (NY) 17:23–32
Smith J, Paton IR, Hughes DC, Burt DW (2005) Isolation and mapping the chicken zona pellucida genes: an insight into the evolution of orthologous genes in different species. Mol Reprod Dev 70:133–145
Song K, Li L, Zhang GF (2017) Bias and correction in RNA-Seq data for marine species. Mar Biotechnol (NY) 19(5):541–550
Swartz SZ, Chan XY, Lambert JD (2008) Localization of vasa mRNA during early cleavage of the snail llyanassa. Dev Genes Evol 218:107–113
Tsutsui K, Ubuka T (2014) Breakthrough in neuroendocrinology by discovering novel neuropeptides and neurosteroids: 1. Discovery of gonadotropin-inhibitory hormone (GnIH) across vertebrates. Gen Comp Endocrinol 205:4–10
Valenzuela-Miranda D, Del Río-Portilla MA, Gallardo-Escárate C (2015) Characterization of the growth-related transcriptome in California red abalone (Haliotis rufescens) through RNA-Seq analysis. Mar Genomics 3:199–202
Van Wielendaele P, Badisco L, Vanden Broeck J (2013) Neuropeptidergic regulation of reproduction in insects. Gen Comp Endocrinol 188:23–34
Vicose GC, Viera MP, Bilbao A, Izquierdo MS (2007) Embryonic and larval development of Haliotis tuberculate coccineareeve: an indexed micro-photographic sequence. J Shellfish Res 26:847–854
Wang M, Liu M, Wang B, Jiang K, Jia Z, Wang L, Wang L (2018) Transcriptomic analysis of exosomal shuttle mRNA in pacific oyster Crassostrea gigas during bacterial stimulation. Fish Shellfish Immunol 74:540–550
Wassarman PM, Jovine L, Litscher ES (2001) A profile of fertilization in mammals. Nat Cell Biol 3:E59–E64
Yang X, Ikhwanuddin M, Li X, Lin F, Wu Q, Zhang Y, You C, Liu W, Cheng Y, Shi X, Wang S, Ma H (2017) Comparative transcriptome analysis provides insights into differentially expressed genes and long non-coding RNAs between ovary and testis of the mud crab (Scylla paramamosain). Mar Biotechnol (NY). https://doi.org/10.1007/s10126-017-9784-2
Yoshizaki G, Sakatani S, Tominaga H, Takeuchi T (2000) Cloning and characterization of a vasa-like gene in rainbow trout and its expression in the germ cell lineage. Mol Reprod Dev 55:364–371
Yue HM, Li CJ, Du H, Zhang SH, Wei QW (2015) Sequencing and de novo assembly of the gonadal transcriptome of the endangered chinese sturgeon (Acipenser sinensis). PLoS One 10:e0127332
Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B (2015) A practical comparison of De novo genome assembly software tools for next-generation sequencing technologies. PLoS One 6:e17915
Zhao ZY, Wu GQ, Wang J, Liu CL, Qiu LH (2013) Next-generation sequencing-based transcriptome analysis of Helicoverpa armigera larvae immune-primed with Photorhabdus luminescens TT01. PLoS One 8:e80146
Zheng P, Wang M, Li C, Sun X, Wang X, Sun Y, Sun S (2017) Insights into deep-sea adaptations and host-symbiont interactions: a comparative transcriptome study on Bathymodiolus mussels and their coastal relatives. Mol Ecol 26(19):5133–5148
Zohar Y, Muñoz-Cueto JA, Elizur A, Kah O (2010) Neuroendocrinology of reproduction in teleost fish. Gen Comp Endocrinol 165:438–455
Acknowledgements
This work was supported by JSPS Grant-in-Aid for Challenging Exploratory Research Grant Number 15K14802.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Yu, L., Xu, D., Ye, H. et al. Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development. Mar Biotechnol 20, 467–480 (2018). https://doi.org/10.1007/s10126-018-9809-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-018-9809-5