ArticleScientific reports2020
Selection and Validation of Reference Genes for Gene Expression Studies in Codonopsis pilosula Based on Transcriptome Sequence Data.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 32 citations in OpenAlex.
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- Transcriptome-based analysis of key functional genes in the triterpenoid saponin synthesis pathway of Platycodon grandiflorum.BMC genomic data · 2024Article
- RNA-seq validation: software for selection of reference and variable candidate genes for RT-qPCR.BMC genomics · 2024Article
- Transcriptome-based identification and validation of reference genes for corm growth stages, different tissues, and drought stress in Taro (Colocasia esculenta).BMC plant biology · 2024Article
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- A protocol for identifying universal reference genes within a genus based on RNA-Seq data: a case study of poplar stem gene expression.Forestry research · 2024Article
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- Identification and validation of reference genes in vetiver (Physiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Identification and validation of reference genes for qRT-PCR based studies in horse gram (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction ineLife · 2021Article
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- Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling.Scientific reports · 2021Article
- Validation of reference genes for quantitative gene expression in the Lippia alba polyploid complex (Verbenaceae).Molecular biology reports · 2021Article
- Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus).BMC genomics · 2020Article
Corrections and comments
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Authors and funding
8 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Relative gene expression analyses by RT-qPCR (reverse transcription-quantitative PCR) are highly dependent on the reference genes in normalizing the expression data of target genes. Therefore, inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, and the selection and validation of suitable internal reference genes becomes essential. In this study, we retrieved the commonly used reference genes in transcriptome datasets of Codonopsis pilosula by RNA-Seq (unpublished data), and selected 15 candidate reference genes according to the coefficient of variation (CV) and fold change (FC) value of gene expression. The expression levels of candidate reference genes, which is at different growth stages, undergoing cold stress and drought stress, was determined by RT-qPCR. The expression stability of these genes was evaluated using software packages and algorithms including ΔCt, geNorm, NormFinder and Bestkeeper. Then appropriate reference genes were screened and validated by target gene-UDGPase (UDP glucose pyrophosphorylase). The optimal RGs combinations of C. pilosula, including PP2A59γ, CPY20-1, UBCE32, RPL5B and UBC18 for developmental stage, RPL5B, RPL13 and PP2A59γ for cold treatment, RPL13 and PP2A59γ for drought treatment, were found and proposed as reference genes for future work. This paper laid foundations for both the selection of reference genes and exploration in metabolic mechanism of C. pilosula.
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