Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis

Gene, Journal Year: 2024, Volume and Issue: 911, P. 148346 - 148346

Published: March 6, 2024

Language: Английский

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Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 24, 2024

Abstract Background In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth highly polygenic trait, typically regulated by genes with small to moderate effects. Due its complexity, growth variability in such shellfish remains poorly understood. this study, we aimed investigate differential gene expression among spat pearl oyster Pinctada margaritifera distinct phenotypes. Results We selected two groups P. belonging same F2 cohort based on performance 5.5 months old. Transcriptome profile analysis identified total 394 differentially expressed between these Fast-growing (F) and Slow-growing (S) According enrichment analysis, S oysters overexpressed associated stress-pathways regulation innate immune responses. contrast, F up-regulated cytoskeleton activity, cell proliferation, apoptosis. Analysis genome polymorphism 16 single nucleotide polymorphisms (SNPs) significantly SNP effect categorization revealed one for high annotated stop codon gained mutation. Interestingly, located within scavenger receptor class member 1 (SRF1), known modulate Our analyses also that all showed up-regulation were homozygous stop-codon Conversely, had heterozygous genotype reduced gene. Conclusions Altogether, our findings suggest differences may be explained contrasted metabolic allocation regulatory pathways system. This study provides valuable contribution towards understanding molecular components bivalves general.

Language: Английский

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Multi-tissue metabolomic profiling reveals the crucial metabolites and pathways associated with scallop growth

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 15, 2024

Bivalves represent a vital economic resource in aquaculture for their high productivity and extensive market demand. Growth is one of the most important desired traits bivalves, regulated by multiple levels, notably intricate metabolic processes. However, understanding profiles that influence bivalve growth limited, particularly from multi-tissue perspective. In this study, tissues Chlamys farreri with different performance were systematically investigated ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Through comparing variation between fast-growing (FG) scallops slow-growing (SG) scallops, 613, 509, 105, 192 significantly metabolites (SDMs) identified mantle, gill, adductor muscle, digestive gland, respectively. Growth-related pathways including sphingolipid metabolism, fatty acid biosynthesis, ABC transporter pathway, along 11 SDMs associated all four tissues, implying they involved scallops. Tissue-specific profiling indicated sulfur-containing amino metabolism mantle potentially contributed to shell growth, while gill synergistically participated through various processes, such as tyrosine glycine, serine, threonine melanogenesis; energy was crucial muscle growth; nutrients digestion absorption gland linked scallop growth. Our results first comprehensive analysis C. farreri, offering valuable insights future production.

Language: Английский

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Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis

iScience, Journal Year: 2022, Volume and Issue: 25(8), P. 104677 - 104677

Published: June 27, 2022

Predicting the potential for species adaption to climate change is challenged by need identify physiological mechanisms that underpin vulnerability. Here, we investigated sensitivity ocean acidification in marine mussels during early development, and specifically trochophore stage. Using RNA DNA sequencing situ hybridization, identified developmental processes associated with abnormal development rapid adaptation low pH. Trochophores exposed pH seawater exhibited 43 differentially expressed genes. Gene annotation hybridization of genes point (1) shell field (2) cellular stress response. Five within these two shifts allele frequencies indicative a adaptation. This case study contributes direct evidence protecting species' existing genetic diversity critical management action facilitate resilience change.

Language: Английский

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Transcriptional regulation analysis reveals the complexity of metamorphosis in the Pacific oyster (Crassostrea gigas)

Marine Life Science & Technology, Journal Year: 2023, Volume and Issue: 5(4), P. 467 - 477

Published: Nov. 25, 2023

Language: Английский

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Single nucleotide polymorphisms of the SIF gene and their association with growth traits in swimming crab (Portunus trituberculatus)

Aquaculture Reports, Journal Year: 2023, Volume and Issue: 33, P. 101792 - 101792

Published: Oct. 23, 2023

The swimming crab (Portunus trituberculatus) is an economically important aquaculture species in China. Mining candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits of P. trituberculatus great importance for the genetic breeding this species. Among traits, "protein still life, isoforms C/SIF type 2 (SIF)" thought to be gene affecting animal development. In current study, we investigated SIF from better understand its biological function. full-length cDNA was 6185 bp, a 5208 bp open reading frame encoding 1735 amino acids. Homology analysis showed that shared 90.07% identity Procambarus clarkii 40.25–86.95% other Expression pattern fast- slow-growing groups revealed significantly higher expression level former than latter (P < 0.05). qPCR studies ubiquitous seven tissues tested, but most abundantly heart compared muscle, testis, ovary, seminal vesicle, gill, hepatopancreas A total 38 SNPs UTRs exons were screened genotyped 184 individuals crabs by targeted resequencing. Association four (full carapace width, length, body height, weight; P Two out shaped as haploblock containing three haplotypes (GC, TA, TC), TA haplotype GC haplotype. Overall, results provided potential SNP markers improvement breeding.

Language: Английский

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Spatial-temporal expression analysis of lineage-restricted shell matrix proteins reveals shell field regionalization and distinct cell populations in the slipper snailCrepidula atrasolea

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 21, 2023

Molluscs are one of the most morphologically diverse clades metazoans, exhibiting an immense diversification calcium carbonate structures, such as shell. Biomineralization calcified shell is dependent on matrix proteins (SMPs). While SMP diversity hypothesized to drive molluscan diversity, we just starting unravel evolutionary history and biology. Here leveraged two complementary model mollusc systems, Crepidula fornicata atrasolea , determine lineage-specificity 185 SMPs. We found that 95% adult C. proteome belongs conserved metazoan orthogroups, with molluscan-restricted orthogroups containing half all SMPs in proteome. The low number -restricted contradicts generally-held notion animal’s biomineralization toolkit dominated by mostly novel genes. Next, selected a subset lineage-restricted for spatial-temporal analysis using situ hybridization chain reaction (HCR) during larval stages . 12 out 18 analyzed expressed field. Notably, these genes present 5 expression patterns, which define at least three distinct cell populations within These results represent comprehensive gastropod age field patterns date. Collectively, data lay foundation future work interrogate molecular mechanisms fate decisions underlying mantle specification diversification.

Language: Английский

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