To elucidate the transcriptomic regulation mechanisms that underlie the response of Ginkgo biloba to dehydration and rehydration, we used ginkgo saplings exposed to osmotically driven water stress and subsequent rewatering. When compared with a control group, 137, 1453, 1148, and 679 genes were differentially expressed in ginkgo leaves responding to 2, 6, 12, and 24 h of water deficit, and 796 and 1530 genes were differentially expressed responding to 24 and 48 h of rewatering. Upregulated genes participated in the biosynthesis of abscisic acid, eliminating reactive oxygen species (ROS), and biosynthesis of flavonoids and bilobalide, and downregulated genes were involved in water transport and cell wall enlargement in water stress-treated ginkgo leaves. Under rehydration conditions, the genes associated with water transport and cell wall enlargement were upregulated, and the genes that participated in eliminating ROS and the biosynthesis of flavonoids and bilobalide were downregulated in the leaves of G. biloba. Furthermore, the weighted gene coexpression networks were established and correlated with distinct water stress and rewatering time-point samples. Hub genes that act as key players in the networks were identified. Overall, these results indicate that the gene coexpression networks play essential roles in the transcriptional reconfiguration of ginkgo leaves in response to water stress and rewatering.

The Remorin (REM) gene family is a plant-specific, oligomeric, filamentous family protein located on the cell membrane, which is important for plant growth and stress responses. In this study, a total of 22 PtREMs were identified in the genome of Populus trichocarpa. Subcellular localization analysis showed that they were predictively distributed in the cell membrane and nucleus. Only five PtREMs members contain both Remorin_C- and Remorin_N-conserved domains, and most of them only contain the Remorin_C domain. A total of 20 gene duplication pairs were found, all of which belonged to fragment duplication. Molecular evolutionary analysis showed the PtREMs have undergone purified selection. Lots of cis-acting elements assigned into categories of plant growth and development, stress response, hormone response and light response were detected in the promoters of PtREMs. PtREMs showed distinct gene expression patterns in response to diverse stress conditions where the mRNA levels of PtREM4.1, PtREM4.2 and PtREM6.11 were induced in most cases. A co-expression network centered by PtREMs was constructed to uncover the possible functions of PtREMs in protein modification, microtube-based movement and hormone signaling. The obtained results shed new light on understanding the roles of PtREMs in coping with environmental stresses in poplar species.

The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 B3 genes were identified from the apricot genome. The apricot B3 superfamily can be divided into five subfamilies, i.e., REM, ARF, ABI3, RAV, and HSI, and genes in the same subfamily have similar structures. The distribution of B3 genes on chromosomes presents a clustering phenomenon. Tandem duplication is the main mode of apricot B3 family expansion, and gene duplication mainly occurs in the REM and ARF subfamilies. Many B3 genes originated from a common ancestor of Arabidopsis and apricot before lineage divergence, and ancestor genes expanded fewer times in apricot than in Arabidopsis. Gene ontology analysis showed that apricot B3 genes were closely related to vernalization, flower development, and shoot system development. PaABI3-1 and PaABI3-2 might play a positive regulation role in the transcription of PaOleosin, which encodes a lipid body protein. This study lays a foundation for the further study of the B3 superfamily function in apricot, especially the specific functions of the ABI3 subfamily in apricot kernel oil storage.

Introduction: Shikimic acid, as a critical precursor for oseltamivir synthesis in antiviral pharmaceuticals, faces escalating global demand. Although Ginkgo biloba leaves have emerged as a promising natural source of shikimic acid owing to their exceptional content of this valuable compound and substantial biomass production capacity, the molecular mechanisms underlying its biosynthesis and downstream metabolic regulation in G. biloba leaves remain largely unknown.Methods: Here, the concentration of shikimic acid in 33 clones were assessed, and 1# (referred as HS) had the highest level. The shikimic acid content in HS was 119% higher than that in 24# (referred as LS), which possessed the lowest shikimic acid level. Concurrently, we analyzed downstream metabolites including flavonoids, phenylalanine, tryptophan and tyrosine, along with transcriptomic and metabolomic profiles in HS and LS.Results: The concentrations of flavonoids, phenylalanine, tryptophan and tyrosine in HS were markedly lower than those in LS. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) analyses revealed clear differences in metabolites between HS and LS. Numerous metabolites and genes related to biosynthesis and downstream metabolic partitioning of shikimic acid were significantly differentially regulated. For instance, the transcript levels of malate dehydrogenase (MDH) and ribose-5-phosphate isomerase (RPI), that are involved in shikimic acid biosynthesis, were more upregulated in HS compared to LS. The abundances of tyrosine, tryptophan, luteolin and dihydromyricetin and the mRNA levels of chorismate synthase (CS), chalcone synthase (CHS), chalcone isomerase (CHI) and flavanone-3b-hydroxylase (F3H), that are implicated in downstream metabolism of shikimic acid were downregulated in HS compared to LS. Additionally, the abundances of abscisic acid and auxin in HS were lower than those in LS. Through association analysis, 27 metabolites, 33 structural genes and 28 transcription factors, such as ERFs, C2H2s and MYBs that play roles in shikimic acid accumulation were identified.Conclusion: These results suggest that metabolites and structural genes participating in biosynthesis and downstream metabolism of shikimic acids, and phytohormones and transcript factors play essential roles in shikimic acid accumulation in G. biloba leaves.

Background: Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcriptome, resequencing, and phenotype data have been increasely generated. However, with the emergence of new information, the data are expected to integrate, and disseminate. Results: To better manage the continuous addition of new data and increase convenience, we constructed the apricot genomic and phenotypic database (AprGPD, http://apricotgpd.com). At present, AprGPD contains three reference genomes, 1692 germplasms, 306 genome resequencing data, 90 RNA sequencing data. A set of user-friendly query, analysis, and visualization tools have been implemented in AprGPD. We have also performed a detailed analysis of 59 transcription factor families for the three genomes of apricot. Conclusion: Six modules are displayed in AprGPD, including species, germplasm, genome, variation, product, tools. The data integrated by AprGPD will be helpful for the molecular breeding of apricot.

MicroRNAs (miRNAs) play essential roles in regulating various development processes in plants. However, their role in regulating rubber biosynthesis in Eucommia ulmoides is largely unknown. Rubber is mainly distributed in the tissue covering the seed (GZ) rather than the periphery (GB) of the pericarp of E. ulmoides during accumulation in May. To investigate the roles of miRNAs in rubber biosynthesis, we conducted high-throughput small RNA sequencing using GZ and GB collected on 11 May (rapid accumulation) and 11 June (reduced accumulation). In total, 12 and 25 miRNAs were either up- or downregulated in GZ in May (GZ511) compared to GB (GB511) in May, while 27 and 38 miRNAs were either up- or downregulated in GZ in May compared to GZ in June (GZ611), respectively. Functional analyses of differentially expressed (DE−) genes targeted by DE-miRNAs revealed that miRNAs may regulate genes involved in rubber biosynthesis. For instance, when Eu-miR45 expression declined, the expression of its predicted target, small rubber particle protein 1 (EuSRPP1), increased in GZ511 vs. GB511 and GZ511 vs. GZ611, possibly resulting in higher rubber accumulation in GZ511. Additionally, we identified potential lncRNA−miRNA−mRNA networks in rubber biosynthesis. Overall, these results indicate that miRNAs play pivotal roles in regulating rubber biosynthesis via miRNA-target gene pairs and lncRNA−miRNA−mRNA networks in E. ulmoides. Our findings will enhance research on the mechanisms of rubber biosynthesis in plants.