Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

Expressions and annotations of the 1502 differentially expressed unigenes in sesame. (XLSX 338 kb

Light and Potassium Improve the Quality of <i>Dendrobium officinale</i> through Optimizing Transcriptomic and Metabolomic Alteration

Background: Dendrobium officinale is a perennial epiphytic herb in Orchidaceae. Cultivated products are the main alternative for clinical application due to the shortage of wild resources. However, the phenotype and quality of D. officinale have changed post-artificial cultivation, and environmental cues such as light, temperature, water, and nutrition supply are the major influencing factors. This study aims to unveil the mechanisms beneath the cultivation-induced variation by analyzing the changes of the metabolome and transcriptome of D. officinale seedlings treated with red- blue LED light and potassium fertilizer. Results: After light- and K-treatment, the D. officinale pseudobulbs turned purple and the anthocyanin content increased significantly. Through wide-target metabolome analysis, compared with pseudobulbs in the control group (P), the proportion of flavonoids in differentially-accumulated metabolites (DAMs) was 22.4% and 33.5% post light- and K-treatment, respectively. The gene modules coupled to flavonoids were obtained through the coexpression analysis of the light- and K-treated D. officinale transcriptome by WGCNA. The KEGG enrichment results of the key modules showed that the DEGs of the D. officinale pseudobulb were enriched in phenylpropane biosynthesis, flavonoid biosynthesis, and jasmonic acid (JA) synthesis post-light- and K-treatment. In addition, anthocyanin accumulation was the main contribution to the purple color of pseudobulbs, and the plant hormone JA induced the accumulation of anthocyanins in D. officinale. Conclusions: These results suggested that light and potassium affected the accumulation of active compounds in D. officinale, and the gene-flavone network analysis emphasizes the key functional genes and regulatory factors for quality improvement in the cultivation of this medicinal plant

Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress

Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20&#8211;22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

Abstract Background Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress. Results To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress. Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize. Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves. Conclusions These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes

Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize

In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants

Le Courrier

12 février 18391839/02/12 (N43)

Additional file 4: Figure S1. of Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

Quantitative RT-PCR of 8 randomly selected DEGs expression in in rice roots exposed to Cd for 1 h. Actin-1 (LOC4333919) was used to standardize transcript levels in each sample. The primers used in the qRT-PCR experiments are listed in additional Table S3. (PPT 75 kb