Integrated application of transcriptomics and metabolomics provides insights into unsynchronized growth in pearl oyster Pinctada fucata martensii

Hao, Ruijuan; Du, Xin; Yang, Chuangye; Deng, Yuewen; Zheng, Zhe; Wang, Qingheng

doi:10.1016/j.scitotenv.2019.02.221

Cited by 88 publications

(48 citation statements)

References 65 publications

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“…A total of 226 metabolites were identified by mass spectrum matching and 80 reliable metabolites were determined based on spectral similarity values >700 (Hao et al, 2019). The differential variables among groups were selected based on VIP scores >1.0 from OPLS-DA and p < 0.05 from ANOVA.…”

Section: Identification Of Significantly Different Metabolites and Anmentioning

confidence: 99%

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

et al. 2020

Front. Microbiol.

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Panxian ham, a traditional Chinese dry-cured ham, is protected by national geographical indication. Similar to other fermented foods, the microbial population of dry-cured ham is pivotal to taste and flavor formation. This study aimed to establish the relationship between microorganisms and metabolites during the spontaneous fermentation of Panxian ham. Multivariate analysis based on metabolomics data revealed that continuous metabolic changes occurred during the entire fermentation process, with the most significant changes occurring in the initial stage of ripening. Thirty-one significantly different metabolites (SDMs) were identified as discriminant factor, and pathway analysis suggested that these metabolites were involved in 30 pathways, including alanine, aspartate, and glutamate metabolism; glycine, serine, and threonine metabolism; and arginine and proline metabolism. Microbial community analysis using the Illumina MiSeq platform indicated that the bacterial community was more complex than the fungal community, and their succession regulation differed during processing. At the genus level, 11 bacteria and five fungi were identified as core microbes, of which Staphylococcus was the dominant bacteria and Debaryomyces and Aspergillus were the dominant fungi. Further, statistical redundancy analysis (RDA) indicated that Staphylococcus, Debaryomyces, and Chromohalobacter promoted the production of amino and fatty acids; Cobetia and Aspergillus were associated with sugar metabolism, and Kushneria, Penicillium, and Yamadazyma were closely related with organic acids. These findings provide fundamental knowledge regarding the metabolically active microorganisms in Panxian ham, helping industrial processors to develop effective strategies for standardizing quality parameters.

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Section: Identification Of Significantly Different Metabolites and Anmentioning

confidence: 99%

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

et al. 2020

Front. Microbiol.

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“…Calmodulin, collagen, CSAD, GST, L‐rhamnonate dehydratase, regucalcin, SRAP, SCDGT, solute carrier family 23 member 2, somatostatin receptor, P450, nacre and shematrin‐5 were upregulated in small‐sized oysters than big ones whiles angiopoietin, zonadhesin, C1q, lectin and myostatin were upregulated in bigger pearl oysters than the smaller ones with these genes functioning in shell and cell growth (Shi & He, ). Hao et al () also reported ECM‐related proteins and integrin‐related genes in the growth of pearl oysters. Although some of these genes have their roles documented, little is known about the specific regulatory pathways utilized during the growth processes and hence needs to be investigated giving room for new research.…”

Section: Growth Regulatorsmentioning

confidence: 93%

“…One major problem found in pearl oyster stocks is the variability in growth performance when pearl oysters are cultured under same environmental conditions (Hao et al, ). This unsynchronized growth was related to an unexplainable variance (Tamayo, Ibarrola, Urrutia, & Navarro, ) and in an attempt to understand and explain the variance, transcriptome and metabolomics studies have been used to investigate this mechanism in pearl oysters (Hao et al, , ; Wang et al, ). The results have provided insights into candidate genes and vital pathways involved in controlling the physiology of phenotypic traits.…”

Section: Unsynchronized Growth In Pearl Oystersmentioning

confidence: 99%

“…Differential expression of certain genes has also been reported to be responsible for the unsynchronized growth of pearl oysters. ECM‐related proteins and integrin‐related genes were significantly increased in the fast growers of P. maxima than the slow growers (Hao et al, ). ECM‐related proteins are known to be involved in biomineralization and integrins mediate definite interaction among ECM and cells (Huang, ; Reddy & Mangale, ).…”

Section: Unsynchronized Growth In Pearl Oystersmentioning

confidence: 99%

“…During the immune response, immune and antioxidant enzymes and genes such as lysozyme and glutathione are expressed. In the slow growers of P. maxima , glutathione content was significantly expressed (Hao et al, ). Glutathione is known to prevent oxidative damage of tissues by conserving the cellular redox status (Wen, Jin, Chen, & Gao, ) hence high glutathione levels in the slow growers demonstrate increased immune activity.…”

Section: Unsynchronized Growth In Pearl Oystersmentioning

confidence: 99%

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Growth in pearl oysters: A review of genetic and environmental influences

et al. 2019

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Pearl oysters have high economic value. These species have gained much interest of research in growth, producing disease resistant and viable stocks for aquaculture facilities. Growth‐related genes, such as insulin‐related peptide receptor and the IGF system, and its components ERKs and MKK4 have been documented to influence growth in pearl oysters. Temperature, salinity, culture condition among other environmental factors were also reported to influence growth by influencing the physiological functions of pearl oysters such as clearance rate, oxygen consumption, respiration rate, excretion rate and expressed in parameters such as the scope of growth and the net growth efficiency. Genetic and artificial breeding techniques have been utilized in breeding programmes to improve growth and pearl quality in pearl oysters with mass selection and hybridization documented as efficient methods to improve growth traits. One problem observed during the growth of pearl oysters is the unsynchronized growth. Transcriptome and metabolomics studies have been undertaken to understand the underlying mechanism of this problem. The pearl oyster immune response to stress has also been reported to cause growth differences and needs to be thoroughly investigated to help produce viable stocks with synchronized growth for the aquaculture industry.

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A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf

Tang

Luo

et al. 2020

Plant Cell Rep

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Integrated application of transcriptomics and metabolomics provides insights into unsynchronized growth in pearl oyster Pinctada fucata martensii

Cited by 88 publications

References 65 publications

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

Growth in pearl oysters: A review of genetic and environmental influences

A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf

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