L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (), β-tubulin (), actin (), cyclophilin (), elongation factor-1α (), the B family of regulatory subunits of protein phosphatase (, , and ), and phosphoglycerate kinase (), to determine the most appropriate reference genes in the leaf, stem, and root tissues of . A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were and in leaves, and in stems, and and in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in . They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
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http://dx.doi.org/10.3390/genes15020231 | DOI Listing |
Curr Gene Ther
January 2025
Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
Dementia is a comprehensive term that refers to illnesses characterized by a decline in cognitive memory and other cognitive functions, affecting a person's overall ability to operate. The exact causes of dementia are unknown to this day. The heterogeneity of Alzheimer's indicates the contribution of genetic polymorphism to this disease.
View Article and Find Full Text PDFNAR Genom Bioinform
March 2025
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Evaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there is no broadly applicable solution. In this manuscript, we introduce PSAURON (Protein Sequence Assessment Using a Reference ORF Network), a novel software tool developed to help assess the quality of protein-coding gene annotations. Utilizing a machine learning model trained on a diverse dataset from over 1000 plant and animal genomes, PSAURON assigns a score to coding DNA or protein sequence that reflects the likelihood that the sequence is a genuine protein-coding region.
View Article and Find Full Text PDFNAR Genom Bioinform
March 2025
Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
Recent advancements in viral metagenomics and single-virus genomics have improved our ability to obtain the draft genomes of environmental viruses. However, these methods can introduce virus sequence contaminations into viral genomes when short, fragmented partial sequences are present in the assembled contigs. These contaminations can lead to incorrect analyses; however, practical detection tools are lacking.
View Article and Find Full Text PDFAdvancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree-building efforts, yet the impacts of backbone tree completeness and species composition remain under-explored.
View Article and Find Full Text PDFJ Transl Med
January 2025
Medical College of YiChun University, Xuefu Road No 576, Yichun, 336000, Jiangxi, People's Republic of China.
Background: Artificial sweeteners (AS) have been widely utilized in the food, beverage, and pharmaceutical industries for decades. While numerous publications have suggested a potential link between AS and diseases, particularly cancer, controversy still surrounds this issue. This study aims to investigate the association between AS consumption and cancer risk.
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