Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Liu, Wenbin; Yuan, Xiudan; Yuan, Shuli; Dai, Liuye; Dong, Shenghua; Liu, Jinhui; Peng, Liangyue; Wang, Minmeng; Tang, Yi; Xiao, Yamei

doi:10.1186/s12863-020-00915-6

Cited by 6 publications

(4 citation statements)

References 60 publications

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“…Using such an index we obtained quantification of individual transcripts (-l "IU" -validateMappings). To validate both the methodology and (and most importantly) the quality of individual data samples, we also utilized four marker genes with virtually stable and predictable behavior throughout individual tissues [62]. These reference markers are 40S (acc.…”

Section: Transcriptomic Analysis In the Common Carp Tissuesmentioning

confidence: 99%

Evolution of the Parvalbumin Genes in Teleost Fishes after the Whole-Genome Duplication

Mukherjee

Bartoš²,

Zdeňková

et al. 2021

Fishes

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Parvalbumin is considered a major fish allergen. Here, we report the molecular evolution of the parvalbumin genes in bony fishes based on 19 whole genomes and 70 transcriptomes. We found unexpectedly high parvalbumin diversity in teleosts; three main gene types (pvalb-α, pvalb-β1, and pvalb-β2, including oncomodulins) originated at the onset of vertebrates. Teleosts have further multiplied the parvalbumin gene repertoire up to nine ancestral copies—two copies of pvalb-α, two copies of pvalb-β1, and five copies of pvalb-β2. This gene diversity is a result of teleost-specific whole-genome duplication. Two conserved parvalbumin genomic clusters carry pvalb-β1 and β2 copies, whereas pvalb-α genes are located separately in different linkage groups. Further, we investigated parvalbumin gene expression in 17 tissues of the common carp (Cyprinus carpio), a species with 21 parvalbumin genes in its genome. Two pvalb-α and eight pvalb-β2 copies are highly expressed in the muscle, while two alternative pvalb-α copies show expression in the brain and the testes, and pvalb-β1 is dominant in the retina and the kidney. The recent pairs of muscular pvalb-β2 genes show differential expression in this species. We provide robust genomic evidence of the complex evolution of the parvalbumin genes in fishes.

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Section: Transcriptomic Analysis In the Common Carp Tissuesmentioning

confidence: 99%

Evolution of the Parvalbumin Genes in Teleost Fishes after the Whole-Genome Duplication

Mukherjee

Bartoš²,

Zdeňková

et al. 2021

Fishes

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“…However, it is yet to be determined whether the expression stability of reference genes has been tested in plant protein-based diet experiments. In the present study, six candidate genes that cover multiple physiological activities of cells involved in cytoskeleton formation ( β-actin ), protein synthesis ( EF1a ), glycolysis canalization ( GAPDH ), purine nucleotide cycle ( HPRT1 ), protein translation ( 18S rRNA ), immune response, and structural protein ( B2M ) were chosen based on previous studies on fish [ 4 , 28 , 31 ]. The expression variations in different tissues reflected by violin maps or the interquartile range of Ct values of each gene indicated the tissue-dependent expression of these reference genes in hybrid yellow catfish fed with different SBM levels.…”

Section: Discussionmentioning

confidence: 99%

“…When the V value of V n /V n + 1 was <0.15, the number of optimal reference genes was “ n ”. When the V value of V n /V n + 1 was >0.15, the optimal number of reference genes was “ n + 1” [ 28 ]. The Delta Ct method first computes the Δ Ct value between each reference gene and other reference genes in each sample, then computes the standard deviation (SD) of all sample Δ Ct values, and finally computes the average SD of each reference gene compared to other reference genes.…”

Section: Methodsmentioning

confidence: 99%

Screening and Stability Analysis of Reference Genes for Gene Expression Normalization in Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) Fed Diets Containing Different Soybean Meal Levels

Guo,

Zhang,

Zhang

et al. 2023

Aquaculture Nutrition

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In this study, we screened the expression stability of six reference genes (18S rRNA, β-actin, GAPDH, EF1a, B2M, and HPRT1) in hybrid yellow catfish (n = 6), considering the SBM levels, sampling time points, and different tissues. Four different statistical programs, BestKeeper, NormFinder, Genorm, and Delta Ct, combined with a method that comprehensively considered all results, were used to evaluate the expression stability of these reference genes systematically. The results showed that SBM levels significantly impacted the expression stability of most of the reference genes studied and that this impact was time-, dose-, and tissue-dependent. The expression stability of these six reference genes varied depending on tissue, sampling time point, and SBM dosage. Additionally, more variations were found among different tissues than among different SBM levels or sampling time points. Due to its high expression, 18S rRNA was excluded from the list of candidate reference genes. β-actin and GAPDH in the liver and β-actin, HPRT1 and EF1a in the intestine were the most stable reference genes when SBM levels were considered. HPRT1, and EF1a in tissues sampled at 2 W and EF1a and β-actin in tissues sampled at 4 and 6 W were proposed as two stable reference genes when different tissues were considered. When the sampling time points were considered, β-actin, EF1a, and HPRT1 were the top three stable reference genes in the intestine. In contrast, β-actin and B2M are the most stable reference genes in the liver. In summary, β-actin, EF1a, and HPRT1 were the more stable reference genes in this study. The stability of reference genes depends on the tissues, sampling time points, and SBM diet levels in hybrid yellow catfish. Therefore, attention should be paid to these factors before selecting suitable reference genes for normalizing the target genes.

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“…Reference genes (RGs), also known as housekeeping genes, are stably expressed in various cells, and are less affected by external factors [ 1 , 2 ]. RGs are widely used in molecular biology research, such as RT-qPCR, ribonuclease protection assay (RPA), northern blotting, gene chips, Western blotting, etc.…”

Section: Introductionmentioning

confidence: 99%

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum

Zhang

Zhou

et al. 2022

Genes

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Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.

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Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Cited by 6 publications

References 60 publications

Evolution of the Parvalbumin Genes in Teleost Fishes after the Whole-Genome Duplication

Evolution of the Parvalbumin Genes in Teleost Fishes after the Whole-Genome Duplication

Screening and Stability Analysis of Reference Genes for Gene Expression Normalization in Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) Fed Diets Containing Different Soybean Meal Levels

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum

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