Element and carotenoid contents in the oyster Crassostrea gigas (Thunberg, 1793) with different shell pigmentation intensities

Aquaculture International, Journal Year: 2025, Volume and Issue: 33(2)

Published: Jan. 2, 2025

Language: Английский

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Role of NR5A2 in regulating sex differentiation, steroidogenesis, and gonadal development in Chlamys farreri

The Journal of Steroid Biochemistry and Molecular Biology, Journal Year: 2025, Volume and Issue: 248, P. 106690 - 106690

Published: Feb. 4, 2025

Language: Английский

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Shell Biosynthesis and Pigmentation as Revealed by the Expression of Tyrosinase and Tyrosinase-like Protein Genes in Pacific Oyster (Crassostrea gigas) with Different Shell Colors

Marine Biotechnology, Journal Year: 2021, Volume and Issue: 23(5), P. 777 - 789

Published: Sept. 6, 2021

Language: Английский

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Functional genomic tools for emerging model species

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(12), P. 1104 - 1115

Published: July 30, 2022

Understanding the molecular mechanisms underlying phenotypic evolution is a central goal in evolutionary biology.Unfortunately, causal associations between candidate loci and phenotype are rarely established because majority of never validated with functional tools.We describe latest developments use tools, particularly RNAi clustered regularly interspaced palindromic repeats (CRISPR)-Cas, to establish links genotype phenotype, discuss some methodological challenges when applying these tools that unique emerging model organisms.Specifically, we highlight significant issue current studies ecology biology date recapitulate ecologically relevant variation, suggest gene editing species should make more HDR pathway obtain insights thereby deeper understanding genetic basis traits. Most field aiming connect validate identified using tools. Recent RNA interference (RNAi) (CRISPR)-Cas genome have dramatically increased feasibility validation. However, methods come specific applied organisms, including limited spatial control silencing, low knock-in efficiencies, throughput Moreover, many do not this limits their scope for into processes. We therefore argue by allelic replacement through homology-directed repair (HDR) would greatly benefit evolution. A fundamental aim identify genomic variation underlies micro- macroevolutionary dynamics [1.Vitti J.J. et al.Detecting natural selection data.Annu. Rev. Genet. 2013; 47: 97-120Crossref PubMed Scopus (397) Google Scholar]. In present post-genomic era, diverse datasets routinely used purpose organisms (see Glossary), ranging from genome-wide population data various association approaches differential expression analysis chromatin accessibility assays [2.Jamann T.M. al.QTL mapping high-throughput sequencing.in: Alonso J.M. Stepanova A.N. Plant Functional Genomics: Methods Protocols. Springer, 2015: 257-285Crossref (20) Scholar,3.van der Burg K.R.L. al.Genomic architecture genetically assimilated seasonal color pattern.Science. 2020; 370: 721-725Crossref (24) Although such advancing our genotype–phenotype relationships traits involved adaptation speciation [3.van Scholar,4.Pardo-Diaz C. al.Towards identification adaptive evolution.Methods Ecol. Evol. 2015; 6: 445-464Crossref (93) Scholar], they also clear limitations, most obvious being lack ability rigorous inferences phenotypes genes or loci. manipulating function, as (CRISPR)–CRISPR-associated protein (Cas), recent years made it possible link organisms. review address growing need inferences, practical aspects validation future role CRISPR-Cas technologies evolution, strong emphasis on challenge importance establishing ecological relevance Rather than investing validation, genomics hasinstead predominantly resulted an increase sample sizes individuals, populations, quest speciation. The result ever-increasing number that, after identifying (e.g., tests selection, allele-frequency patterns, mapping, linkage analysis, transcriptomic studies), at length potential implications. These all inherent (reviewed [5.Schielzeth H. al.Success failure replication associations: How does help outbred populations?.Mol. Resour. 2018; 18: 739-754Crossref (19) Scholar, 6.Liu Y. al.On dependency cellular levels mRNA abundance.Cell. 2016; 165: 535-550Abstract Full Text PDF (1576) 7.Schielzeth Husby A. Challenges prospects quantitative trait standing populations.Ann. N. Acad. Sci. 2014; 1320: 35-57Crossref (41) 8.Wellenreuther M. Hansson B. Detecting polygenic evolution: problems, pitfalls, promises.Trends TIG. 32: 155-164Abstract (84) Scholar]), but common them limitation phenotype. Drawing conclusions body evidence challenging, interpretations be considered carefully attempting understand relationship. Given circumstances, raise two worth considering investigating First, although acknowledge implementation even desirable instances, wish stress absence proper allowing avoiding language. Imprecise language degrades insights, impedes how world works, bloats false positive results [9.Siddiq M.A. al.Experimental test refutation classic case Drosophila melanogaster.Nat. 2017; 1: 25Crossref (21) Second, relying upon existing annotations without perpetuates bias. Consider hypothetical scenario, wherein intersection SNP trait, where variants associated near coding sequences several differentially expressed genes. resulting list assessed, hypotheses formed based sequence element annotations, which turn overwhelmingly closest organism melanogaster insects, mouse Mus musculus mammals, zebrafish Danio rerio fish, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plants, so on). note duality approach: seems sound way forward homologous share functions over deep time, approach necessary no other possible, comes risk erroneous inferences. Model only important unknown function [10.Wu al.CRISPR/Cas9 mediated resource kinase phosphatase Drosophila.Sci. Rep. 10: 7383Crossref (3) Scholar] certainly change time orthologous [11.Verster A.J. al.Comparative screens elegans briggsae reveal impact developmental system drift function.PLoS 10e1004077Crossref Thus, solely annotation can restrict detect lineage-specific genes, moonlighting proteins, cases co-option evolved shape interest, especially subsequent changes alter biological [12.Tomczak al.Interpretation experiments Gene Ontology its annotations.Sci. 8: 5115Crossref (66) Equally problematic, selecting generates ascertainment bias assigned almost always avoided, though species-specific clearly magnitude problem huge ramifications vast – Homo sapiens <10% been focus >90% published papers [13.Stoeger T. al.Large-scale investigation reasons why potentially ignored.PLoS Biol. 16e2006643Crossref (125) bias, well aforementioned issues, demonstrate empowerment able functionally irrespective whether annotations. study van al. exemplifies issues elegance, authors investigated assimilation plasticity butterfly wing coloration, arriving 13 intersecting (GWAS) RNA-seq time-series results. They then manipulate four Knockout (KO) first choice, locus annotated wing-pattern (cortex), predictably affected color. Of one had effect (Dscam3) whereas did (trehalase). Finally, KO uncharacterized unannotated demonstrated causally coloration plasticity, was named herfst. Had chosen cortex, novel missed, (the metabolic trehalase) has unpredicted patterning. conducted neuronal Dscam3 patterning might generated line inquiry fact lacks support, trehalase possibly discounted. discovery herfst provides knowledge allows reanalysis previous work. With components types will synergistically improve across broader taxonomical range interest field. Establishing necessity stepwise process requires determination effort. amenable manipulation, others accomplished scale months, led impressive proliferation insightful knockdown techniques explore candidates were previously association-based [14.Klaassen al.CRISPR mutagenesis confirms oca2 melanin pigmentation Astyanax mexicanus.Dev. 441: 313-318Crossref (59) 15.Li X. al.Outbred sequencing CRISPR/Cas9 butterflies.Nat. Commun. 8212Crossref (133) 16.Mazo-Vargas al.Macroevolutionary shifts WntA potentiate diversity.Proc. Natl. U. S. 114: 10701-10706Crossref (99) 17.Santos M.E. al.Taxon-restricted origin access new environment.Science. 358: 386-390Crossref (56) 18.Woronik al.A transposable insertion alternative life history strategy.Nat. 2019; 5757Crossref (28) 19.Wucherpfennig J.I. al.Efficient CRISPR-Cas9 major sticklebacks.Evol. Res. 20: 107-132PubMed 20.Zhang L. al.Single master regulatory coordinates development iridescence.Proc. 10707-10712Crossref (97) taxonomically diverse, confirming butterflies [15.Li Scholar,16.Mazo-Vargas Scholar,20.Zhang albinism cave fish describing habitats water striders [17.Santos findings benefits bringing realm possibility behind processes documented populations difficult include phenomena migration [21.Zhan al.The genetics monarch warning colouration.Nature. 514: 317-321Crossref (186) exaggeration [22.Toubiana W. Khila Fluctuating strength intense male competition underlie strider's weapon.Proc. 28620182400PubMed innovations [23.Wagner G.P. Lynch V.J. Evolutionary novelties.Curr. 2010; R48-R52Abstract (184) polyphenisms [24.Casasa al.Nutrition-responsive insect polyphenism.Nat. 4: 970-978Crossref (17) name few. technique artificially downregulate assess level. downregulation occurs temporarily usually referred reduces rather eliminates production, opposed KO. largely relies proteins endogenous small pathways microRNA, interfering RNA, Piwi-interacting RNA) eukaryotic lineages [25.Shabalina S.A. Koonin E.V. Origins interference.Trends 2008; 23: 578-587Abstract (364) taxa highly divergent complex [26.Chapman E.J. Carrington J.C. Specialization pathways.Nat. 2007; 884-896Crossref (557) exogenously induced follow simplified conserved mechanism (Box 1) makes (although there notable exceptions; e.g., Lepidoptera [27.Terenius O. al.RNA Lepidoptera: overview successful unsuccessful implications experimental design.J. Insect Physiol. 2012; 57: 231-245Crossref (639) Scholar]).Box 1The nature enables sequence-specific knockdownsThe discovered plants Caenorhabditis [78.Fire al.Potent double-stranded elegans.Nature. 1998; 391: 806-811Crossref (12060) Scholar,79.Hamilton Baulcombe D.C. antisense posttranscriptional silencing plants.Science. 1999; 286: 950-952Crossref (2373) researchers observed reduction introduced (dsRNA) (asRNA) cells whole Research different systems since elucidated [80.Wilson R.C. Doudna J.A. Molecular interference.Annu. Biophys. 42: 217-239Crossref (732) core initiated cleavage dsRNA endonuclease Dicer smaller 20–25 nt fragments [81.Bernstein E. al.Role bidentate ribonuclease initiation step interference.Nature. 2001; 409: 363-366Crossref (3854) From fragments, strands associate Argonaut family and, together additional factors, form RNA-induced (RISC) [82.Hammond S.M. al.An RNA-directed nuclease mediates post-transcriptional cells.Nature. 2000; 404: 293-296Crossref (2443) Based RISC recognizes binds molecules interferes direct endonucleolytic cleavage, translational repression, directing formation heterochromatin corresponding [45.Podolska K. Svoboda P. Targeting living mammals interference.Brief. Funct. Genomics. 2011; 238-247Crossref (12) Scholar].The dependent transport cytosol described above initiated. groups efficient, vertebrates, cell membranes occur easily. cases, introduction aided exogenous agents viral vectors electroporation, delivering vehicle cationic lipids microinjection, solution injected directly tissue. This method efficient transport, systemic RNAi. strategy can, large extent, guided nearest organism. Apart generally broad applicability taxa, advantages stages tissue localization, both minimize negative pleiotropic effects. Further, tuned controlling dose completely ablated [28.Killiny al.Double-stranded uptake topical application, five CYP4 suppresses insecticide resistance Diaphorina citri.PLoS One. 9e110536Crossref (116) Scholar,29.Refki P.N. al.Emergence sensitivity Hox morphological trait.Dev. 392: 441-453Crossref (27) thus enabling survival phenotyping infer function. For example, insulin receptor polyphenism revealed [30.Xu H.J. al.Two receptors determine morphs planthoppers.Nature. 519: 464-467Crossref (308) alleles cause embryonic lethality homozygous state [31.Zhao al.Mutations NlInR1 affect normal growth lifespan brown planthopper Nilaparvata lugens.Insect Biochem. Mol. 115103246Crossref [32.Zhang C.-X. al.Molecular polymorphism insects.Annu. Entomol. 64: 297-314Crossref (64) studied classical large-scale normally [33.Liu al.Whole-animal screen identifies networks regulating germline stem Drosophila.Nat. 7: 12149Crossref Scholar,34.Wang G. al.RNAi tuning, microfluidic screening, recombineering improved production cerevisiae.Proc. 116: 9324-9332Crossref (37) tens [35.Toubiana factor BMP11 required exaggerated weapon fighting behavior strider.PLoS 2021; 19e3001157Crossref (6) Efficient rely overcoming hurdle organism, done time-consuming microinjections, targeting modest set (less ~50) achievable microinjection Scholar,35.Toubiana Some feeding [36.Feng D. Interference ingested dsRNA-expressing bacteria shell biosynthesis Crassostrea gigas.Mar. Biotechnol. 21: 526-536Crossref (23) Scholar,37.Whyard al.Ingested RNAs act insecticides.Insect 2009; 39: 824-832Crossref (456) time-efficient knockdowns [38.Forsthoefel D.J. reveals intestinal regulators branching morphogenesis, differentiation, planarians.Dev. Cell. 691-704Abstract (94) addition RNAi, application insects [39.Wang al.Second-generation supply effective targets pest control.PLoS 6e18644Google underutilized screens. One obstacle efficiency delivery within treated individual varies [40.Vogel insects: protecting beneficials pests.Front. 9: 1912Crossref (107) generating necessitates larger sizes. Another drawback lacking administration difficult. vertebrates resort via [41.Schepers Practice: Principles, Basics, Silencing elegans, Drosophila, Mammals. John Wiley & Sons,

Language: Английский

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siRNA-Mediated MrIAG Silencing Induces Sex Reversal in Macrobrachium rosenbergii

Marine Biotechnology, Journal Year: 2020, Volume and Issue: 22(3), P. 456 - 466

Published: April 27, 2020

Language: Английский

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Examination of the roles of Foxl2 and Dmrt1 in sex differentiation and gonadal development of oysters by using RNA interference

Aquaculture, Journal Year: 2021, Volume and Issue: 548, P. 737732 - 737732

Published: Nov. 19, 2021

Language: Английский

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Outer fold is sole effective tissue among three mantle folds with regard to oyster shell colour

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 241, P. 124655 - 124655

Published: April 28, 2023

Language: Английский

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Pigment Distribution and Secretion in the Mantle of the Pacific Oyster (Crassostrea gigas)

Journal of Ocean University of China, Journal Year: 2023, Volume and Issue: 22(3), P. 813 - 820

Published: May 13, 2023

Language: Английский

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Molecular characterization of transcription factor CREB3L2 and CREB3L3 and their role in melanogenesis in Pacific oysters (Crassostrea gigas)

Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology, Journal Year: 2024, Volume and Issue: 273, P. 110970 - 110970

Published: April 10, 2024

Language: Английский

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Morpholino oligomer delivery via bath immersion for use in reverse genetic studies on the early development of eastern oysters (Crassostrea virginica)

Aquaculture, Journal Year: 2025, Volume and Issue: 600, P. 742261 - 742261

Published: Feb. 5, 2025

Language: Английский

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