Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Abstract

Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.

A Transcriptomic and Metabolomic Study on the Biosynthesis of Iridoids in Phlomoides rotata from the Qinghai–Tibet Plateau

“…Based on the transcriptome sequences of P. rotata from four different regions, we screened the sole gene sequences of nineteen genes ( DXS1 , DXS2 , G10H1 , G10H2 , GPPS1 , GPPS2 , AACT1 , CMK , DXR , HDR1 , HDS1 , HMGS , IDI1 , MCS , MVK , MVD , PMK , HMGR2 , and 8-HGO1 ) involved in the metabolism of iridoids in P. rotata ( Table S6 ). The CYP22 gene was selected as an internal reference based on a previous screening study [ 72 ]. Online Primer Premier software (version 5.0) was used to design the gene-specific primers synthesized by Aoke Dingsheng Biotechnology Co., Ltd. (Xian, China).…”

Identification and validation of qRT-PCR reference genes for analyzing grape infection with gray mold

“…Nevertheless, under drought stress, 18S rRNA CL5051. Contig1 was chosen as the reference gene [8] ; Similarly, in apple peel, genes like WD40, ACT and GAPDH are utilized, while for apple esh EF-1α, CKL and WD40 are found to be the most stable, and MDH was the least stable reference gene for both samples [4]; This variability is observed across many species, including Taxus spp [9], switchgrass [10], and Lamiophlomis rotata [11], indicating that different environmental factors, developmental stages, and individual differences affect the stability of potential reference genes. Consequently, a universally applicable internal reference gene does not exist, necessitating the selection of speci c reference genes tailored to the experimental conditions and the biological system.…”