Identification of Accurate Reference Genes for qRT-PCR Analysis of Gene Expression in Eremochloa ophiuroides under Multiple Stresses of Phosphorus Deficiency and/or Aluminum Toxicity

Genome-Wide Identification and Characterization of the TIFY Gene Family and Their Expression Patterns in Response to MeJA and Aluminum Stress in Centipedegrass (Eremochloa ophiuroides)

The TIFY family is a group of novel plant-specific transcription factors involved in plant development, signal transduction, and responses to stress and hormones. TIFY genes have been found and functionally characterized in a number of plant species. However, there is no information about this family in warm-season grass plants. The current study identified 24 TIFY genes in Eremochloa ophiuroides, a well-known perennial warm-season grass species with a high tolerance to aluminum toxicity and good adaptability to the barren acidic soils. All of the 24 EoTIFYs were unevenly located on six out of nine chromosomes and could be classified into two subfamilies (ZIM/ZML and JAZ), consisting of 3 and 21 genes, respectively, with the JAZ subfamily being further divided into five subgroups (JAZ I to JAZ V). The amino acids of 24 EoTIFYs showed apparent differences between the two subfamilies based on the analysis of gene structures and conserved motifs. MCScanX analysis revealed the tandem duplication and segmental duplication of several EoTIFY genes occurred during E. ophiuroides genome evolution. Syntenic analyses of TIFY genes between E. ophiuroides and other five plant species (including A. thaliana, O. sativa, B. distachyon, S. biocolor, and S. italica) provided valuable clues for understanding the potential evolution of the EoTIFY family. qRT-PCR analysis revealed that EoTIFY genes exhibited different spatial expression patterns in different tissues. In addition, the expressions of EoTIFY genes were highly induced by MeJA and all of the EoTIFY family members except for EoJAZ2 displayed upregulated expression by MeJA. Ten EoTIFY genes (EoZML1, EoZML1, EoJAZ1, EoJAZ3, EoJAZ5, EoJAZ6, EoJAZ8, EoJAZ9, EoJAZ10, and EoJAZ21) were observed to be highly expressed under both exogenous MeJA treatment and aluminum stress, respectively. These results suggest that EoTIFY genes play a role in the JA-regulated pathway of plant growth and aluminum resistance as well. The results of this study laid a foundation for further understanding the function of TIFY genes in E. ophiuroides, and provided useful information for future aluminum tolerance related breeding and gene function research in warm-season grass plants.

Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing

Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.