Auxin plays an essential role in flowering, embryonic development, seed dormancy, and germination. Auxin response factors (ARFs) are plant-specific key transcriptional factors in mediating the gene expression network of auxin signaling. Although ARFs in model plants such as Arabidopsis had been well characterized, their identities and potential roles in non-model plants are less studied. Here, we performed genome-wide identification of ARFs in Magnolia sieboldii K. Koch, a primitive species with high taxonomic importance and medicinal values. We found 25 ARF genes in M. sieboldii, which were widely distributed across multiple chromosomes. Based on sequence similarity, the encoded proteins could be either transcriptional repressors or activators. Gene expression analysis showed a dynamic pattern for many ARFs including MsARF5 during seed germination. In addition, overexpressing of MsARF5 showed that it restores many developmental defects in the Arabidopsis mutant. Moreover, two phenotypically distinct transgenic Arabidopsis lines were obtained, indicating a link between gene expression levels and developmental phenotypes. Taken together, we provided a systematic investigation of the ARF gene family in M. sieboldii and revealed an important role of MsARF5 in mediating auxin signaling.

Under drought stress, plants can change their morphology, physiological characteristics, and carbon allocation to maintain survival and growth. Non-structural carbohydrates (NSC) are major substrates for plant metabolism and play an important role in seedling survival and growth under drought conditions. Mongolian oak (Quercus mongolica Fisch. ex Ledeb.), a constructive species distributed in northeast China, has a high drought tolerance. However, studies on seedling growth and the NSC dynamics of Mongolian oak under different drought intensities and durations are limited. To investigate this, our study measured photosynthetic characteristics, growth, biomass, and NSC concentrations for Mongolian oak seedlings on the 0, 15th, 30th, 45th, and 60th day of the experiment under three soil moisture conditions [75% ± 5% (CK), 50% ± 5% (W1), and 23% ± 5% (W2) of soil moisture field capacity (FC)]. Results showed that the growth and biomass gradually decreased as the soil moisture decreased, but the root: shoot ratio and root biomass allocation ratio gradually increased. In the W1 treatment (moderate drought), NSC content in the stems and taproots was 7.42% and 16.39% higher than those in CK at 60 days. However, in W2 treatment (severe drought), NSC content in the stems and taproots was significantly higher than those in CK during the whole period (p < 0.05), and they were 14.14% and 26.69% higher than those in CK at 60 days. We found that, under drought stress, Mongolian oak seedlings had lower growth but higher allocation to root biomass and higher NSC content in stems and roots. Furthermore, the root system became a vital carbon sink under drought stress and was beneficial for seedling survival.

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.

Magnolia sieboldii K. Koch (M. sieboldii) is a deciduous Chinese tree species of the Magnoliaceae family with high ornamental, medicinal, and economic benefits. The germination of M. sieboldii seeds under natural conditions is extremely difficult, thereby hindering the cultivation and breeding of this important species. The molecular mechanisms underlying M. sieboldii seed germination remain unclear due to the lack of genomic and transcriptomic resources. Here, we integrated both mRNA and miRNA sequencing to identify the genes and pathways related to M. sieboldii germination. A comprehensive full-length transcriptome containing 158,083 high-quality unigenes was obtained by single-molecule real-time (SMRT) sequencing technology. We identified a total of 13,877 genes that were differentially expressed between non-germinated and germinated seeds. These genes were mainly involved in plant hormone signal transduction and diverse metabolic pathways such as those involving lipids, sugars, and amino acids. Our results also identified a complex regulatory network between miRNAs and their target genes. Taken together, we present the first transcriptome of M. sieboldii and provide key genes and pathways associated with seed germination for further characterization. Future studies of the molecular basis of seed germination will facilitate the genetic improvement M. sieboldii.