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Panax notoginseng (Burk.) F. H. Chen, a species of the genus Panax, radix has been traditionally used to deal with various hematological diseases and cardiovascular diseases since ancient times in East Asia. P. notoginseng produces recalcitrant seeds which are sensitive to desiccation and difficult to store for a long time. However, few data are available on the mechanism of the desiccation sensitivity of P. notoginseng seeds. To gain a comprehensive perspective of the genes associated with desiccation sensitivity, cDNA libraries from seeds under control and desiccation processes were prepared independently for Illumina sequencing. The data generated a total of 70,189,896 reads that were integrated and assembled into 55,097 unigenes with a mean length of 783 bp. In total, 12,025 differentially expressed genes (DEGs) were identified during the desiccation process. Among these DEGs, a number of central metabolism, hormonal network-, fatty acid-, and ascorbate-glutathione-related genes were included. Our data provide a comprehensive resource for identifying the genes associated with the desiccation sensitivity of P. notoginseng seeds. [ABSTRACT FROM AUTHOR]

SUMMARY: Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little is known about the precise distribution of taxoids and the transcriptional regulation of taxoid biosynthesis across Taxus stems. Here, we used MALDI‐IMS analysis to visualize the taxoid distribution across Taxus mairei stems and single‐cell RNA sequencing to generate expression profiles. A single‐cell T. mairei stem atlas was created, providing a spatial distribution pattern of Taxus stem cells. Cells were reordered using a main developmental pseudotime trajectory which provided temporal distribution patterns in Taxus stem cells. Most known taxol biosynthesis‐related genes were primarily expressed in epidermal, endodermal, and xylem parenchyma cells, which caused an uneven taxoid distribution across T. mairei stems. We developed a single‐cell strategy to screen novel transcription factors (TFs) involved in taxol biosynthesis regulation. Several TF genes, such as endodermal cell‐specific MYB47 and xylem parenchyma cell‐specific NAC2 and bHLH68, were implicated as potential regulators of taxol biosynthesis. Furthermore, an ATP‐binding cassette family transporter gene, ABCG2, was proposed as a potential taxoid transporter candidate. In summary, we generated a single‐cell Taxus stem metabolic atlas and identified molecular mechanisms underpinning the cell‐specific transcriptional regulation of the taxol biosynthesis pathway. Significance Statement: Integrating mass spectrometry imaging and single‐cell transcriptome atlas strategies, we created a single‐cell T. mairei stem atlas and provided a spatial distribution pattern of Taxus stem cells. Screening for novel transcription factors helped us to reveal the molecular mechanisms underpinning the cell‐specific transcriptional regulation of the taxol biosynthesis pathway. [ABSTRACT FROM AUTHOR]

Noccaea caerulescens (J. Presl & C. Presl) F. K. Mey. is a heavy metal hyperaccumulator exhibiting extreme tolerance to various environmental stresses. To date, the functional role of Ca2+-binding protein in this plant is largely unknown. To investigate the function of calmodulins (CaMs) in N. caerulescens , CaM2 , a Ca2+ sensor encoding gene, was identified and functionally characterised. Protein structure analysis showed that NcCaM2 contains four classic exchange factor (EF)-hand motifs with high sequence similarity to the CaM proteins from model plant Arabidopsis thaliana L. Tissue specific expression analysis showed that NcCaM2 is constitutively expressed in stems, leaves, and roots. Expression level of NcCaM2 was significantly upregulated under various environmental stimulus, indicating a potential involvement of NcCaM2 in the tolerance to abiotic stresses. The heterologous expression of NcCaM2 in a yeast mutant strain increased the heavy metal tolerance in yeast cells. Furthermore, the constitutive expression of NcCaM2 enhanced the heavy metal tolerance capability of transgenic tobacco (Nicotiana tabacum L.) plants. Our data suggested an important role of NcCaM2 in the responses to environmental stresses and provided a potential target gene to enhance of the ability to hyperaccumulate metals. Noccaea caerulescens (J. Presl & C. Presl) F. K. Mey. is a heavy metal hyperaccumulator exhibiting extreme tolerance to various heavy metal stresses. A Ca2+-binding protein in N. caerulescens has been cloned and functional identified. Our data provides a clue to reveal the adaptation strategy of plants to metalliferous soils. [ABSTRACT FROM AUTHOR]

Engineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases. [ABSTRACT FROM AUTHOR]

Auxin plays a pivotal role in the regulation of plant growth and development by controlling the expression of auxin response genes rapidly. As one of the major auxin early response gene families, Gretchen Hagen 3 ( GH3) genes are involved in auxin homeostasis by conjugating excess auxins to amino acids. However, how GH3 genes function in environmental stresses and rhizobial infection responses in Medicago truncatula are largely unknown. Here, based on the latest updated M. truncatula genome, a comprehensive identification and expression profiling analysis of MtGH3 genes were performed. Our data showed that most of MtGH3 genes were expressed in tissue-specific manner and were responsive to environmental stress-related hormones. To understand the possible roles of MtGH3 genes involved in symbiosis establishment between M. truncatula and symbiotic bacteria, quantitative real-time polymerase chain reaction (qRT-PCR) was used to test the expressions of MtGH3 genes during the early phase of Sinorhizobium meliloti infection. The expression levels of most MtGH3 genes were upregulated in shoots and downregulated in roots by S. meliloti infection. The differences in expression responses to S. meliloti infection between roots and shoots were in agreement with the results of free indoleacetic acid (IAA) content measurements. The identification and expression analysis of MtGH3 genes at the early phase of S. meliloti infection may help us to understand the role of GH3-mediated IAA homeostasis in the regulation of nodule formation in model legumes M. truncatula. [ABSTRACT FROM AUTHOR]

Background: Auxin/indoleacetic acid (Aux/IAA) genes, coding a family of short-lived nuclear proteins, play key roles in wide variety of plant developmental processes, including root system regulation and responses to environmental stimulus. However, how they function in auxin signaling pathway and symbiosis with rhizobial in Medicago truncatula are largely unknown. The present study aims at gaining deeper insight on distinctive expression and function features of Aux/IAA family genes in Medicago truncatula during nodule formation. Principal Findings: Using the latest updated draft of the full Medicago truncatula genome, a comprehensive identification and analysis of IAA genes were performed. The data indicated that MtIAA family genes are distributed in all the M. truncatula chromosomes except chromosome 6. Most of MtIAA genes are responsive to exogenous auxin and express in tissues-specific manner. To understand the biological functions of MtIAA genes involved in nodule formation, quantitative real-time polymerase chain reaction (qRT-PCR) was used to test the expression profiling of MtIAA genes during the early phase of Sinorhizobium meliloti (S. meliloti) infection. The expression patterns of most MtIAA genes were down-regulated in roots and up-regulated in shoots by S. meliloti infection. The differences in expression responses between roots and shoots caused by S. meliloti infection were alleviated by 1-NOA application. Conclusion: The genome-wide identification, evolution and expression pattern analysis of MtIAA genes were performed in this study. The data helps us to understand the roles of MtIAA-mediated auxin signaling in nodule formation during the early phase of S. meliloti infection. [ABSTRACT FROM AUTHOR]

Taxol is a widely used anticancer drug; however, its accumulation pattern can vary largely among leaf tissues. Taxol biosynthesis is driven by a series of transcription factors (TFs), but the extent of chromatin changes that functionally regulate gene expression associated with taxol biosynthesis remain poorly understood. To assess the effects of tissue heterogeneity on taxol biosynthesis, we applied single-cell transposase-accessible chromatin sequencing to Taxus mairei leaves and identified differentially accessible regions. We captured 9488 independent cells with 42,192 fragment reads per cell. In total, 66.64% were confidently mapped onto the T. mairei genome. Projection analysis divided all the cells into nine clusters, which suggests a high degree of cell heterogeneity in T. mairei leaves. Based on the cell type markers, Clusters 2 and 7 were annotated as leaf mesophyll cells, and Clusters 5 and 6 were annotated as leaf epidermal cells. A differential accessibility analysis identified 9600 and 8538 leaf mesophyll and epidermal, respectively, cell-specific open chromatin regions. We predicted the genomic features of the genes involved in different stages of taxol biosynthesis, and there was a close correlation between chromatin open peaks and the expression levels of several taxol biosynthesis-related genes. We further identified a number of cell type-specific TF motifs and reference TFs that appeared to be involved in taxol biosynthesis. The study of T. mairei leaves at a single-cell resolution provides a valuable resource for determining the basic principles of the cell type-specific regulation of taxol biosynthesis. [Display omitted] • Our study revealed a high degree of cell heterogeneity in T. mairei leaves. • A number of cell type-specific open chromatin regions were identified. • A number of cell type-specific motifs were identified in T. mairei leaves. [ABSTRACT FROM AUTHOR]