Analysis of transcriptome difference between rapid-growing and slow-growing in Penaeus vannamei

Huang, Yongyu; Wang, Guodong; Liu, Junsheng; Zhang, Lili; Huang, Shi-Yu; Wang, Yilei; Yang, Zhang-wu; Ge, Hui

doi:10.1016/j.gene.2021.145642

Cited by 17 publications

(7 citation statements)

References 118 publications

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“…All 566 functional genes (FGs) that contained these candidate SNPs were extracted. In Figure 4, the 2292 DEGs (differentially expressed genes) are shown, which were identified in previous a previous study [52]. The Venn diagram shows that these 566 functional genes include 75 DEGs.…”

Section: Snp Annotation and Functional Analysismentioning

confidence: 79%

“…Additionally, "protein processing in the endoplasmic reticulum", "phagosome", and "lysosome" pathways enriched some of the FGs. High levels of oxidative stress inhibit organism growth [52]. Oxidative stress induces misfolding of endoplasmic reticulum proteins, while the protein processing in the endoplasmic reticulum pathway mainly plays a role in maintaining protein homeostasis [90].…”

Section: Functional Analysis Of Snpsmentioning

confidence: 99%

“…In this work, SNPs were detected using transcriptome data [52]. In order to identify high-quality SNPs that might be related to growth performance, while resequencing of DNA pools was used to assess the reliability of these SNPs.…”

Section: Introductionmentioning

confidence: 99%

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SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

Huang

Zhang

et al. 2021

Fishes

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Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.

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Section: Snp Annotation and Functional Analysismentioning

confidence: 79%

Section: Functional Analysis Of Snpsmentioning

confidence: 99%

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SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

Huang

Zhang

et al. 2021

Fishes

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“…Excessive inflammatory responses in the body can lead to oxidative stress in animals [ 60 ]. It has been confirmed that arachidonic acid metabolism pathway is closely linked to stress processes and plays an important role in signal transduction pathways as well [ 61 , 62 , 63 , 64 ]. Arachidonic acid metabolism was also significantly enriched in unsynchronously growing red swamp crayfish (Procambarus clarkii) [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

Integrative Application of Transcriptomics and Metabolomics Provides Insights into Unsynchronized Growth in Sea Cucumber (Stichopus monotuberculatus)

Liu

Pan

et al. 2022

IJMS

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Ever-increasing consumer demand for sea cucumbers mainly leads to huge damage to wild sea cucumber resources, including Stichopus monotuberculatus, which in turn exerts negative impacts on marine environments due to the lack of ecological functions performed by sea cucumbers. Aquaculture of sea cucumbers is an effective way to meet consumer demand and restore their resources. Unsynchronous growth is a prominent problem in the aquaculture of sea cucumbers which has concealed unelucidated molecular mechanisms until now. In this study, we carried out an integrative analysis of transcriptomics and metabolomics on fast-growing (SMF) and slow-growing (SMS) groups of S. monotuberculatus cultured in the same environmental conditions. The results revealed that a total of 2054 significantly differentially expressed genes (DEGs) were identified, which are mainly involved in fat digestion and absorption, histidine metabolism, arachidonic acid metabolism, and glutathione metabolism. 368 differential metabolites (DMs) were screened out between the SMF group and the SMS group; these metabolites are mainly involved in glycerophospholipid metabolism, purine metabolism, biosynthesis of unsaturated fatty acids, pyrimidine metabolism, arachidonic acid metabolism, and other metabolic pathways. The integrative analysis of transcriptomics and metabolomics of S. monotuberculatus suggested that the SMF group had a higher capacity for lipid metabolism and protein synthesis, and had a more frequent occurrence of apoptosis events, which are likely to be related to coping with environmental stresses. The results of this study provide potential values for the aquaculture of sea cucumbers which may promote their resource enhancement.

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“…

Penaeus vannamei constitutes approximately 70% of the world's cultured shrimp production owing to its high-commercial value (Huang et al, 2021). However, aquaculture is always threatened by diseases caused by pathogens, resulting in serious global economic losses.With the development of various models, such as polyculture and intensification, and the increase in the circulation of shrimp products and fry, the number of pathogens affecting P. vannamei is increasing (Tandel et al, 2017).

…”

mentioning

confidence: 99%

A loop‐mediated isothermal amplification‐based microfluidic chip for triplex detection of shrimp pathogens

Wang

et al. 2022

Journal of Fish Diseases

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Penaeus vannamei constitutes approximately 70% of the world's cultured shrimp production owing to its high-commercial value (Huang et al., 2021). However, aquaculture is always threatened by diseases caused by pathogens, resulting in serious global economic losses.With the development of various models, such as polyculture and intensification, and the increase in the circulation of shrimp products and fry, the number of pathogens affecting P. vannamei is increasing (Tandel et al., 2017). These include viral pathogens, such as white spot syndrome virus (WSSV), infectious hypodermal and haematopoietic necrosis virus (IHHNV), Taura syndrome virus (TSV), infectious myonecrosis virus (IMNV), yellow head virus (YHV), Decapod iridescent virus 1 (DIV1); parasitic pathogens, such as Enterocytozoon hepatopenaei (EHP); and bacterial pathogens, such as Vibrio parahaemolyticus that cause Acute Hepatopancreatic Necrosis Disease (AHPND) and V. harveyi. Of these, diseases caused by WSSV, IHHNV, IMNV, YHV, and DIV1 are regarded as Class II animal epidemic disease in 2020. Additionally, diseases caused by EHP and DIV1 have been characterized as new, and along with WSSV, these three pathogens have become urgent threats to the shrimp farming industry. To control them, the general belief is to detect the diseases as early as possible and then take measures to prevent their spread.Therefore, establishing an accurate, sensitive, fast, and convenient

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Analysis of transcriptome difference between rapid-growing and slow-growing in Penaeus vannamei

Cited by 17 publications

References 118 publications

SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

Integrative Application of Transcriptomics and Metabolomics Provides Insights into Unsynchronized Growth in Sea Cucumber (Stichopus monotuberculatus)

A loop‐mediated isothermal amplification‐based microfluidic chip for triplex detection of shrimp pathogens

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