Selection and validation of reference genes for quantitative real-time PCR of Quercus mongolica Fisch. ex Ledeb under abiotic stresses

Selection and verification of reference genes for real-time quantitative PCR in endangered mangrove species Acanthus ebracteatus under different abiotic stress conditions

Acanthus ebracteatus is an endangered true mangrove species with great ecological and medicinal values. Real-time quantitative PCR (RT-qPCR) has been widely used to investigate transcriptional responses in A. ebracteatus, which can facilitate its protection and medicinal usage. However, lack of prior knowledge on the optimal reference genes for RT-qPCR data normalization of A. ebracteatus, especially under stress scenarios, restricts gene expression investigations of this species. To address this issue, we evaluated the expression stability of seven candidate reference genes (ACT, PP2A, TUB, TUA, UBQ, EF-1α and RPS13) in leaves of A. ebracteatus upon heat, cadmium (Cd), drought, cold, flood and salt stress, respectively, using four state-of-the-art methods, GeNorm, NormFinder, BestKeeper and RefFinder. The results indicated that ACT was the most stably expressed in most scenarios, while EF-1α, PP2A and TUB ranked first under Cd, flood and salt stress, respectively. TUB was also the suboptimal reference gene for the samples exposed to drought and cold stress, and ACT was the second-best for Cd stress. For all the examined stress conditions, a combination of two reference genes was considered to be adequate enough for accurate expression standardization. A functional gene FLA17 was further employed to validate the performance of the candidate reference genes. The expression profiles of FLA17 displayed similar trends when using the top two stable reference genes, but were under- or overestimated when normalized by less stable genes, indicative of the importance of choosing the optimal reference genes for RT-qPCR normalization. Our findings provide a foundation for future gene expression studies of A. ebracteatus.

Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family and Its Response to Abiotic Stress in Mongolian Oak (Quercus mongolica)

The basic helix-loop-helix (bHLH) family, one of the largest families of transcription factors in plants, is extensively involved in the growth, development, and stress response of several woody plants. However, no systematic analysis of the bHLH gene family in Quercus mongolica has been reported. We characterize QmbHLH genes and identify the functions of QmbHLH proteins in Q. mongolica. We used bioinformatics approaches, qRT-PCR analysis, and RNA sequencing data to examine chromosomal distributions, gene structures, and conserved patterns, and identified 89 QmbHLH genes, which were divided into 21 subgroups based on the phylogenetic analysis of bHLH genes in Arabidopsis thaliana. Segmental replication played a more prominent role than tandem duplication in the expansion of the QmbHLH gene family. Based on patterns of tissue-specific expression, protein interactions, and cis-element analysis, QmbHLH genes may be extensively involved in the growth and development of Q. mongolica. In leaves, stems, and roots, 12 selected QmbHLH genes exhibited responsiveness to abiotic stresses (salt, cold, weak light, and drought). Our study facilitates follow-up functional investigations of the bHLH gene family in Q. mongolica and provides novel insights into bHLH superfamilies in woody plants.