2020
DOI: 10.1371/journal.pone.0227927
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Selection and validation of reference genes for gene expression studies in Pseudomonas brassicacearum GS20 using real-time quantitative reverse transcription PCR

Abstract: Pseudomonas brassicacearum GS20 is an antagonistic strain of bacteria recently isolated from the rhizosphere of Codonopsis pilosula. No validated reference gene has been indentified from P. brassicacearum to use in the normalization of real-time quantitative reverse transcription-PCR data. Therefore, in this study, nine candidate reference genes (recA, gyrA, rpoD, proC, gmk, rho, 16S, ftsz, and secA) were assessed at different growth phases and under various growth conditions. The expression stability of the… Show more

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Cited by 23 publications
(18 citation statements)
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“…Identical observations were demonstrated by DeLorenzo and Moon 41 . Unfortunately, according to the literature, there were some discrepancies in the results obtained by BestKeeper, geNorm and NormFinder software 36,39,40 . It should be emphasized that such calculation differences may be a result of these three programs being based on different algorithms.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…Identical observations were demonstrated by DeLorenzo and Moon 41 . Unfortunately, according to the literature, there were some discrepancies in the results obtained by BestKeeper, geNorm and NormFinder software 36,39,40 . It should be emphasized that such calculation differences may be a result of these three programs being based on different algorithms.…”
Section: Discussionmentioning
confidence: 99%
“…proved that the 16S rRNA-coding gene was characterized by poor expression stability in Ochrobactrum quorumnocens (Cp value = 10.26) and was one of the most unstable candidate reference genes under 10 different tested culture conditions 39 . The 16S rRNA gene has also been proven unsuitable for the analysis of iron-regulated gene expression in Pseudomonas brassicacearum (it ranked sixth of the eight genes tested) 40 . On the other hand, based on mathematical models (BestKeeper, geNorm and NormFinder software), 16S rRNA was classified as one of the best reference genes to evaluate expression levels in Rhodococcus opacus under different growth conditions 41 .…”
Section: Discussionmentioning
confidence: 99%
“…The rat primer sequences of Col2a1, Aggrecan, Sox9, and GAPDH used were as follows: Col2a1: 5′-GGAGCAGCAAGAGCAAGGAGAAG-3′ (Forward) and 5′-GGAGCCCTCAGTGGACAGTAGAC-3′ (Reverse), Aggrecan: 5′-GCTACGACGCCATCTGCTACAC-3′ (Forward) and 5′- ATGTCCTCTTCACCACCCACTCC-3′ (Reverse), Sox9: 5′-TGGCAGAGGGTGGCAGACAG-3′ (Forward) and 5′-CGTTGGGCGGCAGGTATTGG-3′ (Reverse), and GAPDH: 5′- ATGGTGAAGGTCGGTGTGAA-3′ (Forward) and 5′-CACCACCCTGTTGCTGTAGC-3′ (Reverse). Relative amounts of mRNA were standardized and calculated as previously described [ 25 , 26 ].…”
Section: Methodsmentioning
confidence: 99%
“…The mouse primer sequences of the Col2a1, Col10a1, Sox9, Runx2 and GAPDH used were as follows: Col2a1: 5'-TACTGGAGTGACTGGTCCTAAG-3' (Reverse). Relative amounts of mRNA were standardized and calculated as previously described (25,26) .…”
Section: Immunohistochemistry He/safranin-o Fast Green Staining and mentioning
confidence: 99%