Genome of Kumamoto Oyster Crassostrea sikamea Provides Insights Into Bivalve Evolution and Environmental Adaptation

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(4)

Published: April 1, 2025

ABSTRACT The Kumamoto oyster, Crassostrea sikamea , is a marine bivalve naturally distributed along the coasts of southern China and Japan, with hatchery population that has been under domestication in United States since its introduction from Japan 1940s. To understand evolutionary history environmental adaptation, we produced chromosome‐level genome assembly C. conducted whole‐genome resequencing 141 individuals US six wild populations Japan. assembled size 616 Mb covering all 10 chromosomes contig N50 4.21 scaffold 62.25 Mb. Phylogenetic analysis indicated diverged angulata gigas clade about 9.9 million years ago. Synteny revealed significant chromosomal rearrangements during evolution leading to oysters, but remarkable conservation oyster over ~180 years, surprising disparity evolution. three distinct clusters for US, Japanese, Chinese populations, closer Japanese population, confirming origin. No differentiation was detected among five indicating strong gene flow. Between 402 genes exhibited selection signals, including myosin heavy chain were also differentiated domesticated lines eastern suggesting changes these may be important domestic production. Among 768 showing signals between natural China, related stress response are most enriched, responding critical local adaptation. These findings provide insights into as well useful resources comparative genomics genetic improvement cultured stocks.

Language: Английский

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Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Nov. 12, 2021

Abstract Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology important for assessing adaptive potential species under climate change. Analysis a chromosome-level assembly resequencing individuals across wide latitude distribution estuarine oyster ( Crassostrea ariakensis ) revealed unexpectedly low genomic diversity population structures shaped by historical glaciation, geological events oceanographic forces. Strong selection signals were detected genes responding temperature salinity stress, especially expanded solute carrier families, highlighting importance gene expansion environmental adaptation. Genes exhibiting high showed strong upstream regulatory regions that modulate transcription, indicating favoring plasticity. Our findings suggest variation structure marine bivalves are heavily influenced history physical forces, may enhance critical rapidly changing environments.

Language: Английский

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Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(11), P. 5144 - 5155

Published: Aug. 11, 2021

Genetic variation and phenotypic plasticity are both important to adaptive evolution. However, how they act together on particular traits remains poorly understood. Here, we integrated phenotypic, genomic, transcriptomic data from two allopatric but closely related congeneric oyster species, Crassostrea angulata southern/warm environments gigas northern/cold environments, investigate the roles of genetic divergence in thermal adaptation. Reciprocal transplantation experiments showed that species had higher fitness their native habitats than nonnative indicating strong divergence. The southern evolved transcriptional plasticity, was adaptive, suggesting increased is for adaptation warm climates. Genome-wide comparisons between revealed genes under selection tended respond environmental changes sequence noncoding regions. All energy metabolism exhibited habitat-specific expression with involved ATP production lipid catabolism highly expressed warm/southern habitats, consumption synthesis were cold/northern habitats. gene acyl-CoA desaturase, a key enzyme synthesis, selective sweep upstream region lower transcription species. These results further supported by free fatty acid (FFA) content habitat, pointing significance ATP/FFA trade-off. Our findings provide evidence play shaping oysters.

Language: Английский

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DNA methylation differences between male and female gonads of the oyster reveal the role of epigenetics in sex determination

Gene, Journal Year: 2022, Volume and Issue: 820, P. 146260 - 146260

Published: Feb. 1, 2022

Language: Английский

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Transgenerational effects of intertidal environment on physiological phenotypes and DNA methylation in Pacific oysters

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 871, P. 162112 - 162112

Published: Feb. 9, 2023

Language: Английский

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Cis- andTrans-variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(2)

Published: Jan. 19, 2023

The evolution of phenotypic plasticity plays an essential role in adaptive responses to climate change; however, its regulatory mechanisms marine organisms which exhibit high still remain poorly understood. temperature-responsive trait oleic acid content and major gene stearoyl-CoA desaturase (Scd) expression have diverged two allopatric congeneric oyster species, cold-adapted Crassostrea gigas warm-adapted angulata. In this study, genetic molecular methods were used characterize fatty desaturation membrane fluidity regulated by Scd. Sixteen causative single-nucleotide polymorphisms (SNPs) identified the promoter/cis-region Scd between wild C. Further functional experiments showed that SNP (g.-333C [C. allele] >T angulata allele]) may influence transcription creating/disrupting binding motif positive trans-factor Y-box factor gigas/C. angulata, mediates higher/lower constitutive Additionally, sterol-regulatory element-binding proteins (Srebp) specifically bind promoter both downregulated during cold stress compared upregulated This partly explains relatively lower environmental sensitivity (plasticity) gigas. study serves as experimental case reveal cis- trans-variations shape pattern plasticity, provides new insights into formation traits prediction potential future change.

Language: Английский

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Chromosome‐level reference genome for European flat oyster (Ostrea edulis L.)

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(11), P. 1713 - 1729

Published: Aug. 4, 2022

Abstract The European flat oyster ( Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite growing interest in genetic applications to support population management aquaculture, reference genome this species lacking date. Here, we report chromosome‐level assembly annotation the Flat genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation RNA sequencing. A contig (N50: 2.38 Mb) scaffolded into expected karyotype 10 pseudochromosomes. final 935.13 Mb, with scaffold‐N50 95.56 predicted repeat landscape dominated by unclassified elements specific O. . verified accuracy completeness multiple approaches, including novel linkage map built ddRAD‐Seq technology, comprising 4016 SNPs from four full‐sib families (eight parents 163 F1 offspring). Annotation integrating multitissue transcriptome data, comparative protein evidence ab‐initio gene prediction identified 35,699 protein‐coding genes. Chromosome‐level synteny demonstrated against high‐quality assemblies, independently French individual. Comparative genomics used characterize family expansions during evolution that potentially facilitated adaptation. This new will enable high‐resolution conservation aquaculture initiatives, improves our understanding evolution.

Language: Английский

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Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas

Aquaculture, Journal Year: 2023, Volume and Issue: 576, P. 739878 - 739878

Published: July 8, 2023

Language: Английский

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Exploration of Molecular Mechanisms of Immunity in the Pacific Oyster (Crassostrea gigas) in Response to Vibrio alginolyticus Invasion

Animals, Journal Year: 2024, Volume and Issue: 14(11), P. 1707 - 1707

Published: June 6, 2024

Over the years, oysters have faced recurring mass mortality issues during summer breeding season, with Vibrio infection emerging as a significant contributing factor. Tubules of gill filaments were confirmed to be in hematopoietic position Crassostrea gigas, which produce hemocytes immune defense capabilities. Additionally, epithelial cells oyster gills effectors defend against pathogens. In light this, we performed transcriptome analysis tissues obtained from C. gigas infected alginolyticus for 12 h and 48 h. Through this analysis, identified 1024 differentially expressed genes (DEGs) at post-injection 1079 DEGs post-injection. Enrichment these revealed association immune-related Gene Ontology (GO) terms Kyoto Encyclopedia Genes Genomes (KEGG) pathways. To further investigate response, constructed protein–protein interaction (PPI) network using enriched immune-associated KEGG This provided insights into interactions relationships among genes, shedding on underlying mechanisms innate mechanism gills. ensure accuracy our findings, validated 16 key quantitative RT-PCR. Overall, study represents first exploration PPI approach. The findings provide valuable future research pathogen control development enhanced antimicrobial resistance.

Language: Английский

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Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(4), P. 1529 - 1544

Published: Nov. 20, 2021

The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species China. However, studies on its genomics population genetics remain lacking. Here, we assembled the chromosome-level genome of a female C. ariakensis re-sequenced 261 individuals from five locations China representing three typical habitats. was 662.9 Mb contig N50 length 5.9 using PacBio HiFi-CCS long reads, 99.83% sequences were anchored onto 10 pseudochromosomes Hi-C data. A total 26,354 protein-coding genes predicted. We identified significantly expanded gene families which are closely associated osmotic pressure regulation, including CDO, SLC13 SDR. Population structure analysis revealed that clustered into groups (northern, southern Shanghai) (K = 3) their phylogenetic relationship consistently correlated to geographical distribution. Furtherly, differentiation between northern clearly demonstrated by estimated coefficient (FST 0.1154), PSMC distribution showed two effective size separated at 0.1 Ma. Meanwhile flow Shanghai detected. Selective sweep group detected heat response salinity adaptation. This study could provide valuable genomic resources information for further research molecular evolution, genetic breeding, biological function evolutionary adaptation ariakensis.

Language: Английский

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