Skip to main content
SpringerLink
Log in

Molluscan Genomics: Implications for Biology and Aquaculture

  • Enhancing Agricultural Production (A Rooney, Section Editor)
  • Published:
Current Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Purpose of Review

As a result of advances in DNA sequencing technology, molluscan genome research, which initially lagged behind that of many other animal groups, has recently seen a rapid succession of decoded genomes. Since molluscs are highly divergent, the subjects of genome projects have been highly variable, including evolution, neuroscience, and ecology. In this review, recent findings of molluscan genome projects are summarized, and their applications to aquaculture are discussed.

Recent Findings

Recently, 14 molluscan genomes have been published. All bivalve genomes show high heterozygosity rates, making genome assembly difficult. Unique gene expansions were evident in each species, corresponding to their specialized features, including shell formation, adaptation to the environment, and complex neural systems. To construct genetic maps and to explore quantitative trait loci (QTL) and genes of economic importance, genome-wide genotyping using massively parallel, targeted sequencing of cultured molluscs was employed.

Summary

Molluscan genomics provides information fundamental to both biology and industry. Modern genomic studies facilitate molluscan biology, genetics, and aquaculture.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

Papers of particular interest, published recently, have been highlighted as: •• Of major importance

  1. Rosenberg G. A new critical estimate of named species-level diversity of the recent Mollusca. Am Malacol Bull. 2014;32(2):308–22. https://doi.org/10.4003/006.032.0204.

    Article  Google Scholar 

  2. FAO. The state of world fisheries and aquaculture 2016: contributing to food security and nutrition for all. Rome: Food and Agriculture Organization; 2016.

  3. FAO. The state of world fisheries and aquaculture 2006. Rome: Food Agriculture Organization; 2007.

  4. FAO. FAO yearbook. Fishery and aquaculture statistics 2011. Rome: Food and Agriculture Organization; 2013.

  5. Saavedra C, Bachère E. Bivalve genomics. Aquaculture. 2006;256(1–4):1–14. https://doi.org/10.1016/j.aquaculture.2006.02.023.

    Article  CAS  Google Scholar 

  6. Meuwissen T, Hayes B, Goddard M. Genomic selection: a paradigm shift in animal breeding. Anim Front. 2016;6(1):6–14. https://doi.org/10.2527/af.2016-0002.

    Article  Google Scholar 

  7. García-Ruiz A, Cole JB, VanRaden PM, Wiggans GR, Ruiz-López FJ, Van Tassell CP. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection. Proc Natl Acad Sci. 2016;113(28):E3995–4004. https://doi.org/10.1073/pnas.1519061113.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333–51. https://doi.org/10.1038/nrg.2016.49.

    Article  PubMed  CAS  Google Scholar 

  9. •• Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, et al. Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res. 2012;19(2):117–30. https://doi.org/10.1093/dnares/dss005. This is the first published molluscan genome article. It showed high heterozygosity in the bivalve genome

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. •• Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 2012;490(7418):49–54. https://doi.org/10.1038/nature11413. In this study of the Pacific oyster genome, expansion of specific gene family such as HSP70 and IAPs reinforces their adaptation ability to harsh environmental stresses in the intertidal zone

    Article  PubMed  CAS  Google Scholar 

  11. Simakov O, Marletaz F, Cho S-J, Edsinger-Gonzales E, Havlak P, Hellsten U, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 2013;493(7433):526–31. https://doi.org/10.1038/nature11696.

    Article  PubMed  CAS  Google Scholar 

  12. Albertin CB, Simakov O, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, et al. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 2015;524(7564):220–4. https://doi.org/10.1038/nature14668.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Takeuchi T, Koyanagi R, Gyoja F, Kanda M, Hisata K, Fujie M, et al. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. Zool Lett. 2016;2(1):3. https://doi.org/10.1186/s40851-016-0039-2.

    Article  Google Scholar 

  14. Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C. A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialis. PLoS One. 2016;11(3):e0151561. https://doi.org/10.1371/journal.pone.0151561.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nat Commun. 2017;8:15451. https://doi.org/10.1038/ncomms15451.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Schell T, Feldmeyer B, Schmidt H, Greshake B, Tills O, Truebano M, et al. An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). Genome Biol Evol. 2017;9(3):585–92. https://doi.org/10.1093/gbe/evx032.

    Article  CAS  Google Scholar 

  17. Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol. 2017;1:0121. https://doi.org/10.1038/s41559-017-0121.

    Article  Google Scholar 

  18. •• Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, et al. Scallop genome provides insights into evolution of bilaterian karyotype and development. Nat Ecol Evol. 2017;1:0120. https://doi.org/10.1038/s41559-017-0120. In this study, three bivalve genome assemblies including the scallop, the Pacific oyster, and the pearl oyster were reconstructed to chromosomal level by using genetic maps. They showed the scallop genome retains bilaterian ancestral state

    Article  Google Scholar 

  19. Du X, Song K, Wang J, Cong R, Li L, Zhang G. Draft genome and SNPs associated with carotenoid accumulation in adductor muscles of bay scallop (Argopecten irradians). J Genom. 2017;5:83–90. https://doi.org/10.7150/jgen.19146.

    Article  Google Scholar 

  20. Du X, Fan G, Jiao Y, Zhang H, Guo X, Huang R, et al. The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization. GigaScience. 2017;6(8):1–12. https://doi.org/10.1093/gigascience/gix059.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Mun S, Kim Y-J, Markkandan K, Shin W, Oh S, Woo J, et al. The whole-genome and transcriptome of the Manila clam (Ruditapes philippinarum). Genome Biol Evol. 2017;9(6):1487–98. https://doi.org/10.1093/gbe/evx096.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Nam B-H, Kwak W, Kim Y-O, Kim D-G, Kong HJ, Kim W-J, et al. Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae. GigaScience. 2017;6(5):1–8. https://doi.org/10.1093/gigascience/gix014.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Consortium TGP. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061–73. https://doi.org/10.1038/nature09534.

    Article  CAS  Google Scholar 

  24. Guo X, He Y, Zhang L, Lelong C, Jouaux A. Immune and stress responses in oysters with insights on adaptation. Fish Shellfish Immunol. 2015;46(1):107–19. https://doi.org/10.1016/j.fsi.2015.05.018.

    Article  PubMed  CAS  Google Scholar 

  25. Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature. 2014;515(7526):261–3. https://doi.org/10.1038/nature13685.

    Article  PubMed  CAS  Google Scholar 

  26. Curole JP, Hedgecock D. Bivalve genomics: complications, challenges, and future perspectives. In: Aquaculture genome technologies. Oxford: Blackwell Publishing Ltd; 2007.

    Google Scholar 

  27. Compeau PEC, Pevzner PA, Tesler G. How to apply de Bruijn graphs to genome assembly. Nat Biotech. 2011;29(11):987–91. https://doi.org/10.1038/nbt.2023.

    Article  CAS  Google Scholar 

  28. Henson J, Tischler G, Ning Z. Next-generation sequencing and large genome assemblies. Pharmacogenomics. 2012;13(8):901–15. https://doi.org/10.2217/pgs.12.72.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience. 2013;2(1):10. https://doi.org/10.1186/2047-217X-2-10.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24(8):1384–95. https://doi.org/10.1101/gr.170720.113.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol. 2010;11(3):R28. https://doi.org/10.1186/gb-2010-11-3-r28.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Zheng H, Li L, Zhang G. Inbreeding depression for fitness-related traits and purging the genetic load in the hermaphroditic bay scallop Argopecten irradians irradians (Mollusca: Bivalvia). Aquaculture. 2012;366:27–33. https://doi.org/10.1016/j.aquaculture.2012.08.029.

    Article  Google Scholar 

  33. Kocot KM, Jeffery NW, Mulligan K, Halanych KM, Gregory TR. Genome size estimates for Aplacophora, Polyplacophora and Scaphopoda: small solenogasters and sizeable scaphopods. J Molluscan Stud. 2016;82(1):216–9. https://doi.org/10.1093/mollus/eyv054.

    Article  Google Scholar 

  34. Ieyama H, Ogaito H. Chromosomes and nuclear DNA contents of two subspecies in the Diplommatinidae. Venus:Jpn J Malacology. 1998;57(2):133–6.

    Google Scholar 

  35. Bonnaud L, Ozouf-Costaz C, Boucher-Rodoni R. A molecular and karyological approach to the taxonomy of Nautilus. C R Biol. 2004;327(2):133–8. https://doi.org/10.1016/j.crvi.2003.12.004.

    Article  PubMed  CAS  Google Scholar 

  36. Hallinan NM, Lindberg DR. Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca. Genome Biol Evol. 2011;3:1150–63. https://doi.org/10.1093/gbe/evr087.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6(1):11. https://doi.org/10.1186/s13100-015-0041-9.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Nagai KA. History of the cultured pearl industry. Zool Sci. 2013;30(10):783–93. https://doi.org/10.2108/zsj.30.783.

    Article  PubMed  Google Scholar 

  39. Gyoja F, Satoh N. Evolutionary aspects of variability in bHLH orthologous families: insights from the pearl oyster, Pinctada fucata. Zool Sci. 2013;30(10):868–76. https://doi.org/10.2108/zsj.30.868.

    Article  PubMed  CAS  Google Scholar 

  40. Koga H, Hashimoto N, Suzuki DG, Ono H, Yoshimura M, Suguro T, et al. A genome-wide survey of genes encoding transcription factors in Japanese pearl oyster Pinctada fucata: II. Tbx, Fox, Ets, HMG, NFκB, bZIP, and C2H2 zinc fingers. Zool Sci. 2013;30(10):858–67. https://doi.org/10.2108/zsj.30.858.

    Article  PubMed  CAS  Google Scholar 

  41. Morino Y, Okada K, Niikura M, Honda M, Satoh N, Wada H. A genome-wide survey of genes encoding transcription factors in the Japanese pearl oyster, Pinctada fucata: I. Homeobox genes. Zool Sci. 2013;30(10):851–7. https://doi.org/10.2108/zsj.30.851.

    Article  PubMed  CAS  Google Scholar 

  42. Setiamarga DHE, Shimizu K, Kuroda J, Inamura K, Sato K, Isowa Y, et al. An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata. Zool Sci. 2013;30(10):877–88. https://doi.org/10.2108/zsj.30.877.

    Article  PubMed  CAS  Google Scholar 

  43. Funabara D, Watanabe D, Satoh N, Kanoh S. Genome-wide survey of genes encoding muscle proteins in the pearl oyster, Pinctada fucata. Zool Sci. 2013;30(10):817–25. https://doi.org/10.2108/zsj.30.817.

    Article  PubMed  CAS  Google Scholar 

  44. Matsumoto T, Masaoka T, Fujiwara A, Nakamura Y, Satoh N, Awaji M. Reproduction-related genes in the pearl oyster genome. Zool Sci. 2013;30(10):826–50. https://doi.org/10.2108/zsj.30.826.

    Article  PubMed  CAS  Google Scholar 

  45. Miyamoto H, Endo H, Hashimoto N, limura K, Isowa Y, Kinoshita S, et al. The diversity of shell matrix proteins: genome-wide investigation of the pearl oyster, Pinctada fucata. Zool Sci. 2013;30(10):801–16. https://doi.org/10.2108/zsj.30.801.

    Article  PubMed  CAS  Google Scholar 

  46. Kinoshita S, Ning W, Inoue H, Maeyama K, Okamoto K, Nagai K, et al. Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster. PLoS One. 2011;6(6):e21238. https://doi.org/10.1371/journal.pone.0021238.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Marie B, Joubert C, Tayalé A, Zanella-Cléon I, Belliard C, Piquemal D, et al. Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell. Proc Natl Acad Sci. 2012;109(51):20986–91. https://doi.org/10.1073/pnas.1210552109.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Liu C, Li S, Kong J, Liu Y, Wang T, Xie L, et al. In-depth proteomic analysis of shell matrix proteins of Pinctada fucata. Sci Rep. 2015;5:17269. https://doi.org/10.1038/srep17269.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Suzuki M, Saruwatari K, Kogure T, Yamamoto Y, Nishimura T, Kato T, et al. An acidic matrix protein, Pif, is a key macromolecule for nacre formation. Science. 2009;325(5946):1388–90.

    Article  PubMed  CAS  Google Scholar 

  50. Funabara D, Ohmori F, Kinoshita S, Koyama H, Mizutani S, Ota A, et al. Novel genes participating in the formation of prismatic and nacreous layers in the pearl oyster as revealed by their tissue distribution and RNA interference knockdown. PLoS One. 2014;9(1):e84706. https://doi.org/10.1371/journal.pone.0084706.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Marie B, Jackson DJ, Ramos-Silva P, Zanella-Cléon I, Guichard N, Marin F. The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties. FEBS J. 2013;280(1):214–32. https://doi.org/10.1111/febs.12062.

    Article  PubMed  CAS  Google Scholar 

  52. Feng D, Li Q, Yu H, Kong L, Du S. Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation. Sci Rep. 2017;7:45754. https://doi.org/10.1038/srep45754.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Mann K, Edsinger-Gonzales E, Mann M. In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea. Proteome Sci. 2012;10(1):28. https://doi.org/10.1186/1477-5956-10-28.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Mann K, Edsinger E. The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. Proteome Sci. 2014;12(1):28. https://doi.org/10.1186/1477-5956-12-28.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. McDougall C, Aguilera F, Degnan BM. Rapid evolution of pearl oyster shell matrix proteins with repetitive, low-complexity domains. J R Soc Interface. 2013;10(82):20130041. https://doi.org/10.1098/rsif.2013.0041.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Rohfritsch A, Bierne N, Boudry P, Heurtebise S, Cornette F, Lapègue S. Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas. Evol Appl. 2013;6(7):1064–78. https://doi.org/10.1111/eva.12086.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Ruesink JL, Lenihan HS, Trimble AC, Heiman KW, Micheli F, Byers JE, et al. Introduction of non-native oysters: ecosystem effects and restoration implications. Annu Rev Ecol Evol Syst. 2005;36:643–89.

    Article  Google Scholar 

  58. Orensanz JM, Schwindt E, Pastorino G, Bortolus A, Casas G, Darrigran G, et al. No longer the pristine confines of the world ocean: a survey of exotic marine species in the southwestern Atlantic. Biol Invasions. 2002;4(1):115–43. https://doi.org/10.1023/A:1020596916153.

    Article  Google Scholar 

  59. Guo X. Use and exchange of genetic resources in molluscan aquaculture. Rev Aquac. 2009;1(3–4):251–9. https://doi.org/10.1111/j.1753-5131.2009.01014.x.

    Article  Google Scholar 

  60. Galil BSA. Sea under siege—alien species in the Mediterranean. Biol Invasions. 2000;2(2):177–86. https://doi.org/10.1023/A:1010057010476.

    Article  Google Scholar 

  61. FAO. FAO yearbook. Fishery and aquaculture statistics 2014. Rome: Food and Agriculture Organization; 2016.

  62. Gerdol M, Venier P, Pallavicini A. The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia. Dev Comp Immunol. 2015;49(1):59–71. https://doi.org/10.1016/j.dci.2014.11.007.

    Article  PubMed  CAS  Google Scholar 

  63. Zhang L, Li L, Guo X, Litman GW, Dishaw LJ, Zhang G. Massive expansion and functional divergence of innate immune genes in a protostome. Sci Rep. 2015;5:8693. https://doi.org/10.1038/srep08693.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. He Y, Jouaux A, Ford SE, Lelong C, Sourdaine P, Mathieu M, et al. Transcriptome analysis reveals strong and complex antiviral response in a mollusc. Fish Shellfish Immunol. 2015;46(1):131–44. https://doi.org/10.1016/j.fsi.2015.05.023.

    Article  PubMed  CAS  Google Scholar 

  65. Rosenthal Joshua JC, Seeburg Peter H. A-to-I RNA editing: effects on proteins key to neural excitability. Neuron. 2012;74(3):432–9. https://doi.org/10.1016/j.neuron.2012.04.010.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. •• Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376. https://doi.org/10.1371/journal.pone.0003376. They developed reduced representation sequencing method with high-throuput sequencing technology. The method called restriction-site-associated DNA sequencing or RAD-seq is modified and actively utilized for SNP discovery in non-model aquacultuer animals

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379. https://doi.org/10.1371/journal.pone.0019379.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Wang S, Meyer E, McKay JK, Matz MV. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat Meth. 2012;9(8):808–10. https://doi.org/10.1038/nmeth.2023.

    Article  CAS  Google Scholar 

  69. Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, et al. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One. 2013;8(3):e58700. https://doi.org/10.1371/journal.pone.0058700.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Jiao W, Fu X, Dou J, Li H, Su H, Mao J, et al. High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc. DNA Res. 2014;21(1):85–101. https://doi.org/10.1093/dnares/dst043.

    Article  PubMed  CAS  Google Scholar 

  71. Shi Y, Wang S, Gu Z, Lv J, Zhan X, Yu C, et al. High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker. Aquaculture. 2014;434:376–84. https://doi.org/10.1016/j.aquaculture.2014.08.044.

    Article  Google Scholar 

  72. Li Y, He M. Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing. PLoS One. 2014;9(11):e111707. https://doi.org/10.1371/journal.pone.0111707.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Wang J, Li L, Zhang GA. A high-density SNP genetic linkage map and QTL analysis of growth-related traits in a hybrid family of oysters (Crassostrea gigas × Crassostrea angulata) using genotyping-by-sequencing. G3: Genes|Genomes|Genetics. 2016;6(5):1417.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Bai Z, Han X, Luo M, Lin J, Wang G, Li J. Constructing a microsatellite-based linkage map and identifying QTL for pearl quality traits in triangle pearl mussel (Hyriopsis cumingii). Aquaculture. 2015;437:102–10. https://doi.org/10.1016/j.aquaculture.2014.11.008.

    Article  CAS  Google Scholar 

  75. Nie H, Yan X, Huo Z, Jiang L, Chen P, Liu H, et al. Construction of a high-density genetic map and quantitative trait locus mapping in the Manila clam Ruditapes philippinarum. Sci Rep. 2017;7:229. https://doi.org/10.1038/s41598-017-00246-0.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Ren P, Peng W, You W, Huang Z, Guo Q, Chen N, et al. Genetic mapping and quantitative trait loci analysis of growth-related traits in the small abalone Haliotis diversicolor using restriction-site-associated DNA sequencing. Aquaculture. 2016;454:163–70. https://doi.org/10.1016/j.aquaculture.2015.12.026.

    Article  CAS  Google Scholar 

  77. Bai Z-Y, Han X-K, Liu X-J, Li Q-Q, Li J-L. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii. Sci Rep. 2016;6:32608. https://doi.org/10.1038/srep32608.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Gutierrez AP, Turner F, Gharbi K, Talbot R, Lowe NR, Peñaloza C, et al. Development of a medium density combined-species SNP Array for Pacific and European oysters (Crassostrea gigas and Ostrea edulis). G3: Genes|Genomes|Genetics. 2017;7(7):2209.

    Article  PubMed  PubMed Central  Google Scholar 

  79. Qi H, Song K, Li C, Wang W, Li B, Li L, et al. Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas). PLoS One. 2017;12(3):e0174007. https://doi.org/10.1371/journal.pone.0174007.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  80. Jones DB, Jerry DR, Forêt S, Konovalov DA, Zenger KR. Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima. Mar Biotechnol. 2013;15(6):647–58. https://doi.org/10.1007/s10126-013-9514-3.

    Article  PubMed  CAS  Google Scholar 

  81. Zhong X, Li Q, Guo X, Yu H, Kong L. QTL mapping for glycogen content and shell pigmentation in the Pacific oyster Crassostrea gigas using microsatellites and SNPs. Aquac Int. 2014;22(6):1877–89. https://doi.org/10.1007/s10499-014-9789-z.

    Article  CAS  Google Scholar 

  82. Sauvage C, Boudry P, De Koning DJ, Haley CS, Heurtebise S, Lapègue S. QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas). Anim Genet. 2010;41(4):390–9. https://doi.org/10.1111/j.1365-2052.2009.02018.x.

    Article  PubMed  CAS  Google Scholar 

  83. Hedgecock D, Shin G, Gracey AY, Den Berg DV, Samanta MP. Second-generation linkage maps for the Pacific oyster Crassostrea gigas reveal errors in assembly of genome scaffolds. G3: Genes|Genomes|Genetics. 2015, 2007;5(10)

Download references

Acknowledgements

I am grateful to all members of Marine Genomics Unit at OIST for their support. I also thank Dr. Steven D. Aird for editing the manuscript.

Funding

This research was supported by grants from the Project to Advance Institutional Bio-oriented Technology Research, NARO (special project on advanced research and development for next-generation technology), and by internal funds from the Okinawa Institute of Science and Technology (OIST).

Author information

Authors and Affiliations

  1. Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan

    Takeshi Takeuchi

Authors
  1. Takeshi Takeuchi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Takeshi Takeuchi.

Ethics declarations

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by the author.

Additional information

This article is part of the Topical Collection on Enhancing Agricultural Production

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Takeuchi, T. Molluscan Genomics: Implications for Biology and Aquaculture. Curr Mol Bio Rep 3, 297–305 (2017). https://doi.org/10.1007/s40610-017-0077-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40610-017-0077-3

Keywords

Search

Navigation