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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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Ohmori F, Kinoshita S, Funabara D, Koyama H, Nagai K, Maeyama K, Okamoto K, Asakawa S, Watabe S. Novel Isoforms of N16 and N19 Families Implicated for the Nacreous Layer Formation in the Pearl Oyster Pinctada fucata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:155-167. [PMID: 29340846 DOI: 10.1007/s10126-017-9793-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
Although a wide variety of proteins and genes possibly related to the shell formation in bivalve have been identified, their functions have been only partially approved. We have recently performed deep sequencing of expressed sequence tags (ESTs) from the pearl oyster Pinctada fucata using a next-generation sequencer, identifying a dozen of novel gene candidates which are possibly associated with the nacreous layer formation. Among the ESTs, we focused on three novel isoforms (N16-6, N16-7, and N19-2) of N16 and N19 families with reference to five known genes in the families and determined the full-length cDNA sequences of these isoforms. Reverse transcription-polymerase chain reaction revealed that N16-6 was expressed in gill, gonad, adductor muscle, and mantle, whereas N16-7 exclusively in mantle. N19-2 was expressed in all tissues examined. In situ hybridization demonstrated their regional expression in mantle and pearl sac, which well corresponded to those shown by EST analysis previously reported. Shells in the pearl oyster injected with dsRNAs of N16-7 and N19-2 showed abnormal surface appearance in the nacreous layer. Taken together, novel isoforms in N16 and N19 families shown in this study are essential to form the nacreous layer.
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Affiliation(s)
- Fumito Ohmori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Daisuke Funabara
- Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan
| | - Hiroki Koyama
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, 739-8528, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie, 517-0403, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Kikuhiko Okamoto
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie, 516-8581, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan.
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Delghandi M, Afzal H, Al Hinai MSN, Al-Breiki RDG, Jerry DR, Dao HT. Novel Polymorphic Microsatellite Markers for Panulirus ornatus and their Cross-species Primer Amplification in Panulirus homarus. Anim Biotechnol 2016; 27:310-4. [PMID: 27565876 DOI: 10.1080/10495398.2016.1190372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Polymorphic microsatellite loci were isolated for Panulirus ornatus using 454 GS-FLX Titanium pyrosequencing. Fifteen markers containing perfect di-, tri-, tetra-, and penta-nucleotide motifs were consistently co-amplified in five multiplexes in a panel of 91 randomly selected samples. Observed number of alleles varied from 2 to 14 per locus. Observed and expected heterozygosity ranged from 0.090 to 0.79 and 0.08 to 0.87, respectively. Ten loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between 11 loci. The microsatellite markers were also amplified successfully in related Panulirus homarus species with adequate level of polymorphism. The successful cross-species primer amplification of the 15 microsatellites indicates the potential of the developed markers to be transferred to other Panulirus species. The 15 novel microsatellite markers reported in this work add to the previously characterized markers by our group, exhibit adequate levels of polymorphism for wide range of future studies investigating population structure, genetic diversity, and evolutionary relationships among Panulirus species.
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Affiliation(s)
- Madjid Delghandi
- a Center of Excellence in Marine Biotechnology , Sultan Qaboos University , Al-Khoud , Sultanate of Oman
| | - Hasifa Afzal
- a Center of Excellence in Marine Biotechnology , Sultan Qaboos University , Al-Khoud , Sultanate of Oman
| | - Manal Saif Nasser Al Hinai
- a Center of Excellence in Marine Biotechnology , Sultan Qaboos University , Al-Khoud , Sultanate of Oman
| | | | - Dean R Jerry
- b Center for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental Science , James Cook University , Townsville , Queensland , Australia
| | - Hoc Tan Dao
- b Center for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental Science , James Cook University , Townsville , Queensland , Australia.,c Institute of Oceanography , Vietnam Academy of Science and Technology , Nha Trang , Vietnam
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Kocot KM, Aguilera F, McDougall C, Jackson DJ, Degnan BM. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Front Zool 2016; 13:23. [PMID: 27279892 PMCID: PMC4897951 DOI: 10.1186/s12983-016-0155-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.
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Affiliation(s)
- Kevin M Kocot
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama 35487 USA
| | - Felipe Aguilera
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia.,Current address: Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Carmel McDougall
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
| | - Daniel J Jackson
- Department of Geobiology, Goldschmidtstr.3, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072 Australia
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The use of -omic tools in the study of disease processes in marine bivalve mollusks. J Invertebr Pathol 2015; 131:137-54. [PMID: 26021714 DOI: 10.1016/j.jip.2015.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
Abstract
Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.
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Deng Y, Lei Q, Tian Q, Xie S, Du X, Li J, Wang L, Xiong Y. De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima. Biosci Biotechnol Biochem 2014; 78:1685-92. [PMID: 25047366 DOI: 10.1080/09168451.2014.936351] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We analyzed the mantle transcriptome of pearl oyster Pinctada maxima and developed EST-SSR markers using Illumina HiSeq 2000 paired-end sequencing technology. A total of 49,500,748 raw reads were generated. De novo assembly generated 108,704 unigenes with an average length of 407 bp. Sequence similarity search with known proteins or nucleotides revealed that 30,200 (27.78%) and 25,824 (23.76%) consensus sequences were homologous with the sequences in the non-redundant protein and Swiss-Prot databases, respectively, and that 19,701 (18.12%) of these unigenes were possibly involved in approximately 234 known signaling pathways in the Kyoto Encyclopedia of Genes and Genomes database. Ninety one biomineralization-related unigenes were detected. In a cultured stock, 1764 simple sequence repeats were identified and 56 primer pairs were randomly selected and tested. The rate of successful amplification was 68.3%. The developed molecular markers are helpful for further studies on genetic linkage analysis, gene localization, and quantitative trait loci mapping.
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Affiliation(s)
- Yuewen Deng
- a Fishery College , Guangdong Ocean University , Zhanjiang , China
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Development and multiplex PCR amplification of microsatellite markers in the commercial clam Venerupis rhomboides (Mollusca: Bivalvia). Mol Biol Rep 2012; 40:1625-30. [PMID: 23086276 DOI: 10.1007/s11033-012-2211-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022]
Abstract
Venerupis rhomboides is a commercial clam whose production could be enhanced through effective management of natural and hatchery stocks. This study provides the first panel of microsatellite markers for the exploitation of this species according to genetic criteria. A total of 22 polymorphic microsatellite loci were isolated and characterized from two genomic libraries enriched for different motifs. The number of alleles per locus ranged from 2 to 14 in a sample of 20 clams from Spain, and the observed and expected heterozygosity from 0 to 0.95 and 0.05-0.901, respectively. Sixteen loci were in agreement with Hardy-Weinberg equilibrium after sequential Bonferroni correction and linkage disequilibrium between loci pairs was not detected. To reduce the cost of the genotyping process, tri- and pentaplex PCRs, amplifying a total of 13 microsatellites loci were optimized. The microsatellites developed here represent the first nuclear markers described in V. rhomboides and will be useful tools for genetic studies involving assessment of genetic variation and population structure of natural and cultivated populations, assignment testing, construction of genetic linkage maps and dissection of production traits.
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