scholarly journals Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5642 ◽  
Author(s):  
Chenhua Zhang ◽  
Hongying Zheng ◽  
Xinyang Wu ◽  
Heng Xu ◽  
Kelei Han ◽  
...  
Keyword(s):  
Reference Genes ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Rna Seq ◽  
Isopentenyl Transferase ◽  
Genome Wide ◽  
Transcriptome Database ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Selection Of

Lagenaria siceraria is an economically important cucurbitaceous crop, but suitable reference genes (RGs) to use when the plants are infected by cucumber green mottle mosaic virus (CGMMV) have not been determined. Sixteen candidate RGs of both leaf and fruit and 18 candidate RGs mostly from separate RNA-Seq datasets of bottle gourd leaf or fruit were screened and assessed by RT-qPCR. The expression stability of these genes was determined and ranked using geNorm, NormFinder, BestKeeper and RefFinder. Comprehensive analysis resulted in the selection of LsCYP, LsH3, and LsTBP as the optimal RGs for bottle gourd leaves, and LsP4H, LsADP, and LsTBP for fruits. LsWD, LsGAPDH, and LsH3 were optimal for use in both leaves and fruits under the infection of CGMMV. Isopentenyl transferase (IPT) and DNA-directed RNA polymerase (DdRP) were used to validate the applicability of the most stable identified RGs from bottle gourd in response to CGMMV. All the candidate RGs performed in RT-qPCR consistently with the data from the transcriptome database. The results demonstrated that LsWD, LsGAPDH and LsH3 were the most suitable internal RGs for the leaf, and LsH3, LsGAPDH, LsP4H and LsCYP for the fruit.

scholarly journals Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Katerina Jureckova ◽  
Hana Raschmanova ◽  
Jan Kolek ◽  
Maryna Vasylkivska ◽  
Barbora Branska ◽  
...  
Keyword(s):  
Reference Genes ◽  
Enrichment Analysis ◽  
Clostridium Beijerinckii ◽  
Stable Expression ◽  
Rna Seq ◽  
Go Enrichment ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Go Enrichment Analysis ◽  
Selection Of

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.

scholarly journals Selection of Suitable Reference Genes for qPCR Normalization under Abiotic Stresses in Oenanthe javanica (BI.) DC

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e92262 ◽  
Author(s):  
Qian Jiang ◽  
Feng Wang ◽  
Meng-Yao Li ◽  
Jing Ma ◽  
Guo-Fei Tan ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Reference Genes ◽  
Oenanthe Javanica ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Selection Of

scholarly journals Selection of Suitable Reference Genes for qPCR Normalization under Abiotic Stresses and Hormone Stimuli in Carrot Leaves

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0117569 ◽  
Author(s):  
Chang Tian ◽  
Qian Jiang ◽  
Feng Wang ◽  
Guang-Long Wang ◽  
Zhi-Sheng Xu ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Reference Genes ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Selection Of

scholarly journals Appropriate Reference Genes for RT-qPCR Normalization in Various Organs of Anemone Flaccida Fr. Schmidt at Different Growing Stages

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 459
Author(s):  
Zeying Zhao ◽  
Hanwen Zhou ◽  
Zhongnan Nie ◽  
Xuekui Wang ◽  
Biaobiao Luo ◽  
...  
Keyword(s):  
Reference Genes ◽  
Gene Selection ◽  
Quantitative Polymerase Chain Reaction ◽  
Cultivated Plants ◽  
Gene Expressions ◽  
Natural Habitats ◽  
Triterpenoid Saponins ◽  
Qpcr Normalization ◽  
Suitable Reference

Anemone flaccida Fr. Schmidt is a traditional medicinal herb in southwestern China and has multiple pharmacological effects on bruise injuries and rheumatoid arthritis (RA). A new drug with a good curative effect on RA has recently been developed from the extract of A. flaccida rhizomes, of which the main medicinal ingredients are triterpenoid saponins. Due to excessive exploitation, the wild population has been scarce and endangered in a few of its natural habitats and research on the cultivation of the plant commenced. Studies on the gene expressions related to the biosynthesis of triterpenoid saponins are not only helpful for understanding the effects of environmental factors on the medicinal ingredient accumulations but also necessary for monitoring the herb quality of the cultivated plants. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) as a sensitive and powerful technique has been widely used to detect gene expression across tissues in plants at different stages; however, its accuracy and reliability depend largely on the reference gene selection. In this study, the expressions of 10 candidate reference genes were evaluated in various organs of the wild and cultivated plants at different stages, using the algorithms of geNorm, NormFinder and BestKeeper, respectively. The purpose of this study was to identify the suitable reference genes for RT-qPCR detection in A. flaccida. The results showed that two reference genes were sufficient for RT-qPCR data normalization in A. flaccida. PUBQ and ETIF1a can be used as suitable reference genes in most organs at various stages because of their expression stabilitywhereas the PUBQ and EF1Α genes were desirable in the rhizomes of the plant at the vegetative stage.

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