Guangyu Ge’s research while affiliated with Chinese Academy of Fishery Sciences and other places

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Publications (4)


Sampling information of H. discus hannai.
Description of basic information about the SSR locus in H. discus hannai.
Sequences of primers for 13 polymorphic EST-SSR of H. discus hannai.
Cont.
The main genetic parameters of six populations in H. discus hannai.

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Population Genetics of Haliotis discus hannai in China Inferred Through EST-SSR Markers
  • Article
  • Full-text available

January 2025

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4 Reads

Genes

Hongsu Yang

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Zhou Wu

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Guangyu Ge

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[...]

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Liqing Zhou

Background/Objectives: The Pacific abalone Haliotis discus hannai originated in cold waters and is an economically important aquaculture shellfish in China. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. Methods: In this study, eighteen polymorphic EST-SSR loci were successfully developed based on the hemolymph transcriptome data of Pacific abalone, and thirteen highly polymorphic EST-SSR loci were selected for the genetic variation analysis of the six populations collected. Results: The results showed that the average number of observed alleles was 8.0769 (RC)-11.3848 (DQ) in each population. The number of observed alleles in the DQ, NH, and TJ populations was significantly higher than that in the RC population. The cultivated population outside the Changshan Islands has experienced a 22.79% reduction in allele diversity compared to the wild population of DQ. The pairwise Fst values and analysis of molecular variance (AMOVA) revealed significant population differentiation among all populations except DQ and NH populations, with RC and ZZ cultured populations exhibiting the largest population differentiation (Fst = 0.1334). The phylogenetic tree and structural analysis divided the six populations into two groups (group 1: NH, DQ, and ZZ; group 2: DL, TJ, and RC), and there was no relationship between geographical distance and genetic distance. Conclusions: These results may reflect the large-scale culture from different populations in China and the exchange of juveniles between hatcheries. Different breeding conditions have led to a higher degree of genetic differentiation between the RC and ZZ populations. This study enables a better understanding of the genetic diversity and structure of current Pacific abalone populations.

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Sampling information of Haliotis discus hannai
Sequences of primers for 13 polymorphic EST-SSR sites of Haliotis discus hannai
Inferring the impact of large-scale aquaculture of Haliotis discus hannai in northern and southern China using EST-SSR markers

March 2024

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42 Reads

The Pacific abalone Haliotis discus hannai originated in cold waters, but as an economically important aquaculture shellfish in China, there has been a large-scale transfer of fish to Fujian Province in southern China for culture. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. In this study, eighteen polymorphic EST-SSR loci were successfully developed based on the hemolymph transcriptome data of Pacific abalone, and thirteen highly polymorphic EST-SSR loci were selected for the genetic variation analysis of six populations collected from Zhangzhou in Fujian Province (ZZ), Dalian in Liaoning Province (DL), Rongcheng in Shandong Province (RC), and the Changshan Archipelago, including Nanhuangcheng Island (NH), Daqin Island (DQ), and Tuoji Island (TJ). The results showed that the average number of observed alleles was 8.0769 (RC)-11.3848 (DQ) in each population. The number of observed alleles in the DQ, NH, and TJ populations was significantly higher than that in the RC population. If the NH and TJ cultured populations of the Changshan Archipelago were excluded, then compared with the DQ wild population, the number of alleles in the cultured population decreased by 22.79%. The pairwise Fst values and analysis of molecular variance (AMOVA) revealed significant population differentiation among most populations, with the RC and ZZ cultured populations exhibiting the largest population differentiation (Fst = 0.1334). The UPGMA phylogenetic tree and structural analysis divided the six populations into two groups (group 1: NH, DQ, and ZZ; group 2: DL, TJ, and RC), and there was no relationship between geographical distance and genetic distance. These results may reflect the large-scale culture from north to south in China and the exchange of juveniles between hatcheries. Different breeding conditions have led to a higher degree of genetic differentiation between the RC and ZZ populations. In conclusion, this study provides valuable information on the genetic structure of Pacific abalone populations in China and contributes to the management and restoration of Pacific abalone.


Figure 5. Relative expression levels of aminotransferase class I and II gene family members in gills of C. ariakensis. Asterisks indicate significant differences compared to the 0 h time poin follows: * indicated p < 0.05 or ** indicated p < 0.001.
Primers used in qRT-PCR experiments.
Cont.
Protein composition and physicochemical properties of the Aminotransferase class I and II gene family in C. ariakensis.
Aminotransferase Class I and II Gene Family in the Jinjiang Oyster (Crassostrea ariakensis): Genomewide Identification, Phylogenetic Analysis and Expression Profiles after Salinity Stress

September 2023

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120 Reads

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4 Citations

Fishes

Aminotransferases are enzymes found in living organisms that catalyze transfer reactions between amino acids and keto acids, crucial for amino acid metabolism and synthesis. Aminotransferase classes I and II play a vital role in regulating osmolarity, protecting cells, and improving metabolic homeostasis and cellular fitness. To investigate the characteristics of the aminotransferase class I and II gene family and their roles in osmotic pressure regulation in the Jinjiang oyster (Crassostrea ariakensis), the gene structure, chromosomal localization, and phylogeny were characterized and the genes’ expression in the gill under high-salt stress was analyzed. In this study, eighteen Aminotransferase class I and II genes, including SPTLCa and SPTLCb, SPTa and SPTb, ALAT2a and ALAT2b, KAT3a and KAT3b, and ASTa, ASTb and ASTc, were identified. The physicochemical properties of 11 family members were stable, with their instability factors less than 40. Subcellular localization prediction showed that aminotransferase classes I and II were localized in the cytoplasm or mitochondria. Chromosomal localization results showed that the 18 aminotransferase class I and II genes were located on eight chromosomes. All members of this gene family had the Aminotran_1_2 structural domain which is associated with osmotic pressure regulation by adjusting the conversion reaction between amino acids and keto acids. Most gene expressions showed an initial increase followed by a decrease from 0 h to 12 h when the oysters were challenged by acute stress using artificial seawater with a salinity of 40. However, the expression of CarAGT2 and CarKAT3b genes showed an increased trend with increasing stress time. This study systematically investigated the bioinformatics characteristics of the aminotransferase class I and II gene family in C. ariakensis and their role in osmotic pressure regulation, which provides scientific data for understanding the potential functions of these genes in physiological adaptation, thereby expanding the research on osmoregulation in bivalves.


Figure 1 Statistic of DEGs.
Figure 2 Partial differential gene heat map under hypoxia stress.
Figure 3 KEGG enrichment analysis of A_VS_B. Note: Red indicates a high correlation, and green indicates a low correlation. A large bubble indicates a high number of differential genes, and a small bubble indicates a low number of differential genes.
Figure 6 Results of fluorescent quantitative verification of DEGs. Note: The horizontal coordinate indicates the gene, and the vertical coordinate indicates the relative expression of the gene. Those above the horizontal coordinate indicate up-regulation, and those below indicate down-regulation.
Transcriptome analysis reveals the molecular basis of the response to acute hypoxic stress in blood clam Scapharca broughtonii

December 2022

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119 Reads

Israeli Journal of Aquaculture - Bamidgeh

Hypoxia tolerance and adaptive regulation are important for aquatic animals, especially for species with poor mobility, such as most bivalves. Previous studies have confirmed that the blood clam Scapharca broughtonii has strong hypoxia resistance. However, the molecular mechanism supporting its hypoxic tolerance is still largely limited. To further screen the genes and their potential regulation of hypoxia tolerance, the transcriptome changes of S. broughtonii after acute hypoxic stress were explored by RNA sequencing. In this study, the average value of Q30 is 92.89%, indicating that the quality of sequencing is relatively high. The Unigenes obtained were annotated using four databases, namely Interpo, KEGG, Swisspro and TrEMBL. The annotation rates in these four databases were 71.82%, 75.95%, 92.98%, and 79.26%, respectively. And also, there were 649 DEGs in group B (dissolved oxygen (DO) of 2.5 mg/L) compared with group D (DO of 7.5 mg/L), among which 252 were up-regulated, and 397 were down-regulated. There were 965 DEGs in group A (DO of 0.5 mg/L), 2.5 mg/L, and 7.5 mg/L, compared with group B, among which 530 were up-regulated, and 435 were down-regulated. Meanwhile, there were 2,040 DEGs in group A compared with group D, among which 901 were up-regulated, and 1,139 were down-regulated. The main metabolic-related pathways of KEGG enriched in this study included Insulin secretion, Insulin signaling pathway, MAPK signal transduction pathway, and PPAR signaling pathway. These pathways may be critical metabolic pathways to solve energy demand and rebuild energy balance in S. broughtonii under hypoxic conditions. This study preliminarily clarified the response of S. broughtonii to hypoxia stress on the molecular levels, providing a reference for the following study on the response laws of related genes and pathways under environmental stress of S. broughtonii.

Citations (1)


... The phylogenetic analysis grouped the aminotransferase class into 5 different classes, with 94, 23, 26, 79 and 43 aminotransferase proteins in the I, II, III, IV, and V groups, respectively. In the Jinjiang oyster, 18 aminotransferase class I and II genes were identified, and their expression varied under salinity stress [32]. Aminotransferases are categorized into five classes: I, II, III, IV, and V. Classes I and II include alanine aminotransferase, aromatic amino acid aminotransferase, aspartate aminotransferase, and histidine phosphate aminotransferase [32,33]. ...

Reference:

Insights into the Role of GhTAT2 Genes in Tyrosine Metabolism and Drought Stress Tolerance in Cotton
Aminotransferase Class I and II Gene Family in the Jinjiang Oyster (Crassostrea ariakensis): Genomewide Identification, Phylogenetic Analysis and Expression Profiles after Salinity Stress

Fishes