De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

Transcriptomic and Physiological Studies Unveil that Brassinolide Maintains the Balance of Maize's Multiple Metabolisms under Low-Temperature Stress

Low-temperature (LT) is one of the major abiotic stresses that restrict the growth and development of maize seedlings. Brassinolides (BRs) have been shown to enhance LT tolerance in several plant species; the physiological and molecular mechanisms by which BRs enhance maize tolerance are still unclear. Here, we characterized changes in the physiology and transcriptome of N192 and Ji853 seedlings at the three-leaf stage with or without 2 μM 2,4-epibrassinolide (EBR) application at 25 and 15 °C environments via high-performance liquid chromatography and RNA-Sequencing. Physiological analyses revealed that EBR increased the antioxidant enzyme activities, enhanced the cell membrane stability, decreased the malondialdehyde formation, and inhibited the reactive oxygen species (ROS) accumulation in maize seedlings under 15 °C stress; meanwhile, EBR also maintained hormone balance by increasing indole-3-acetic acid and gibberellin 3 contents and decreasing the abscisic acid level under stress. Transcriptome analysis revealed 332 differentially expressed genes (DEGs) enriched in ROS homeostasis, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) cascade. These DEGs exhibited synergistic and antagonistic interactions, forming a complex LT tolerance network in maize. Additionally, weighted gene co-expression network analysis (WGCNA) revealed that 109 hub genes involved in LT stress regulation pathways were discovered from the four modules with the highest correlation with target traits. In conclusion, our findings provide new insights into the molecular mechanisms of exogenous BRs in enhancing LT tolerance of maize at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to LT stress.

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using a sample integrating the plant's bark, leaves, and flowers. De novo transcriptome assembly yielded 177,046 transcripts and 42,518 coding sequences. Notably, we identified 796 species-specific genes enriched in organelle gene regulation and defense responses. A codon usage bias analysis revealed that mutation bias appears to be the primary driver of selection in shaping the species' genetic architecture. An evolutionary analysis based on dN/dS values of paralogous and orthologous gene pairs indicated a predominance of purifying selection, suggesting strong evolutionary constraints on most genes. A comparative transcriptomic analysis with Magnolia sinica identified approximately 1000 ultra-conserved genes, enriched in essential cellular processes such as transcriptional regulation, protein synthesis, and genome stability. Interestingly, only a limited number of 511 rapidly evolving genes under positive selection were detected compared to M. sinica and Magnolia kuangsiensis. These genes were enriched in metabolic processes associated with adaptation to specific environments, potentially limiting the species' ability to expand its range. Our findings contribute to understanding the genetic architecture of M. lotungensis and suggest that an insufficient number of adaptive genes contribute to its endangered status.

Integrated transcriptomic and metabolomic analysis provides insights into cold tolerance in lettuce (Lactuca sativa L.)

The popular leafy vegetable lettuce (Lactuca sativa L.) is susceptible to cold stress during the growing season, which slows growth rate, causes leaf yellowing and necrosis, and reduced yield and quality. In this study, transcriptomic and metabolomic analyses of two cold-resistant lettuce cultivars (GWAS-W42 and F11) and two cold-sensitive lettuce cultivars (S13K079 and S15K058) were performed to identify the mechanisms involved in the cold response of lettuce. Overall, transcriptome analysis identified 605 differentially expressed genes (DEGs), including significant enrichment of genes involved in the flavonoid and flavonol (CHS, CHI, F3H, FLS, CYP75B1, HCT, etc.) biosynthetic pathways related to oxidation-reduction and catalytic activity. Untargeted metabolomic analysis identified fifteen flavonoid metabolites and 28 other metabolites potentially involved in the response to cold stress; genistein, quercitrin, quercetin derivatives, kaempferol derivatives, luteolin derivatives, apigenin and their derivatives accumulate at higher levels in cold-resistant cultivars. Moreover, MYBs, bHLHs, WRKYs and Dofs also play positive role in the low temperature response, which affected the expression of structural genes contributing to the variation of metabolites between the resistant and sensitive. These results provide valuable evidence that the metabolites and genes involved in the flavonoid biosynthetic pathway play important roles in the response of lettuce to cold stress.

Comparative analysis of POD genes and their expression under multiple hormones in Pyrus bretschenedri

BACKGROUND

Class III peroxidase (POD) enzymes play vital roles in plant development, hormone signaling, and stress responses. Despite extensive research on POD families in various plant species, the knowledge regarding the POD family in Chinese pear (Pyrus bretschenedri) is notably limited.

RESULTS

We systematically characterized 113 POD family genes, designated as PbPOD1 to PbPOD113 based on their chromosomal locations. Phylogenetic analysis categorized these genes into seven distinct subfamilies (I to VII). The segmental duplication events were identified as a prevalent mechanism driving the expansion of the POD gene family. Microsynteny analysis, involving comparisons with Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume and Prunus persica, highlighted the conservation of duplicated POD regions and their persistence through purifying selection during the evolutionary process. The expression patterns of PbPOD genes were performed across various plant organs and diverse fruit development stages using transcriptomic data. Furthermore, we identified stress-related cis-acting elements within the promoters of PbPOD genes, underscoring their involvement in hormonal and environmental stress responses. Notably, qRT-PCR analyses revealed distinctive expression patterns of PbPOD genes in response to melatonin (MEL), salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA), reflecting their responsiveness to abiotic stress and their role in fruit growth and development.

CONCLUSIONS

In this study, we investigated the potential functions and evolutionary dynamics of PbPOD genes in Pyrus bretschenedri, positioning them as promising candidates for further research and valuable indicators for enhancing fruit quality through molecular breeding strategies.

Metabolomics combined with physiology and transcriptomics reveal how Nicotiana tabacum leaves respond to cold stress

Low temperature-induced cold stress is a major threat to plant growth, development and distribution. Unraveling the responses of temperature-sensitive crops to cold stress and the mechanisms of cold acclimation are critical for food demand. In this study, combined physiological, transcriptomic, and metabolomic analyses were conducted on Nicotiana tabacum suffering short-term 4 °C cold stress. Our results showed that cold stress destroyed cellular membrane stability, decreased the chlorophyll (Chl) and carotenoid contents, and closed stomata, resulting in lipid peroxidation and photosynthesis restriction. Chl fluorescence measurements revealed that primary photochemistry, photoelectrochemical quenching and photosynthetic electron transport in Nicotiana tabacum leaves were seriously suppressed upon exposer to cold stress. Enzymatic and nonenzymatic antioxidants, including superoxide dismutase, catalase, peroxidase, reduced glutathione, proline, and soluble sugar, were all profoundly increased to trigger the cold acclimation defense against oxidative damage. A total of 178 metabolites and 16,204 genes were differentially expressed in cold-stressed Nicotiana tabacum leaves. MEturquoise and MEblue modules identified by WGCNA were highly correlated with physiological indices, and the corresponding hub genes were significantly enriched in pathways related to photosynthesis - antenna proteins and flavonoid biosynthesis. Untargeted metabolomic analysis identified specific metabolites, including sucrose, phenylalanine, glutamine, glutamate, and proline, that enhance plant cold acclimation. Combined transcriptomics and metabolomic analysis highlight the vital roles of carbohydrate and amino acid metabolism in enhancing the cold tolerance of Nicotiana tabacum. Our comprehensive investigation provides novel insights for efforts to alleviate low temperature-induced oxidative damage to Nicotiana tabacum plants and proposes a breeding target for cold stress-tolerant cultivars.

Transcriptomic and physiological analysis of the response of Spirodela polyrrhiza to sodium nitroprusside

BACKGROUND

Spirodela polyrrhiza is a simple floating aquatic plant with great potential in synthetic biology. Sodium nitroprusside (SNP) stimulates plant development and increases the biomass and flavonoid content in some plants. However, the molecular mechanism of SNP action is still unclear.

RESULTS

To determine the effect of SNP on growth and metabolic flux in S. polyrrhiza, the plants were treated with different concentrations of SNP. Our results showed an inhibition of growth, an increase in starch, soluble protein, and flavonoid contents, and enhanced antioxidant enzyme activity in plants after 0.025 mM SNP treatment. Differentially expressed transcripts were analysed in S. polyrrhiza after 0.025 mM SNP treatment. A total of 2776 differentially expressed genes (1425 upregulated and 1351 downregulated) were identified. The expression of some genes related to flavonoid biosynthesis and NO biosynthesis was upregulated, while the expression of some photosynthesis-related genes was downregulated. Moreover, SNP stress also significantly influenced the expression of transcription factors (TFs), such as ERF, BHLH, NAC, and WRKY TFs.

CONCLUSIONS

Taken together, these findings provide novel insights into the mechanisms of underlying the SNP stress response in S. polyrrhiza and show that the metabolic flux of fixed CO2 is redirected into the starch synthesis and flavonoid biosynthesis pathways after SNP treatment.

Comparative Transcriptomic Analysis of the Metabolism of Betalains and Flavonoids in Red Amaranth Hypocotyl under Blue Light and Dark Conditions

Amaranth plants contain abundant betalains and flavonoids. Anthocyanins are important flavonoids; however, they cannot coexist in the same plant with betalains. Blue light influences metabolite synthesis and hypocotyl elongation; accordingly, analyses of its effects on betalain and flavonoid biosynthesis in Amaranthus tricolor may provide insight into the distribution of these plant pigments. We analyzed the betalain and flavonoid content and transcriptome profiles in amaranth hypocotyls under blue light and dark conditions. Furthermore, we analyzed the expression patterns of key genes related to betalains and flavonoids. Amaranth hypocotyls were shorter and redder and showed higher betalain and flavonoid content under blue light than in dark conditions. Key genes involved in the synthesis of betalains and flavonoids were upregulated under blue light. The gene encoding DELLA was also upregulated. These results suggest that blue light favors the synthesis of both betalains and flavonoids via the suppression of bioactive gibberellin and the promotion of DELLA protein accumulation, which also suppresses hypocotyl elongation. The metabolite profiles differed between plants under blue light and dark conditions. These findings improve our understanding of the environmental cues and molecular mechanisms underlying pigment variation in Amaranthus.

Transcriptome Analysis Reveals Brassinolide Signaling Pathway Control of Foxtail Millet Seedling Starch and Sucrose Metabolism under Freezing Stress, with Implications for Growth and Development

Low-temperature stress limits the growth and development of foxtail millet. Freezing stress caused by sudden temperature drops, such as late-spring coldness, often occurs in the seedling stage of foxtail millet. However, the ability and coping strategies of foxtail millet to cope with such stress are not clear. In the present study, we analyzed the self-regulatory mechanisms of freezing stress in foxtail millet. We conducted a physiological study on foxtail millet leaves at -4 °C for seven different durations (0, 2, 4, 6, 8, 10, and 12 h). Longer freezing time increased cell-membrane damage, relative conductance, and malondialdehyde content. This led to osmotic stress in the leaves, which triggered an increase in free proline, soluble sugar, and soluble protein contents. The increases in these substances helped to reduce the damage caused by stress. The activities of superoxide dismutase, peroxidase, and catalase increased reactive oxygen species (ROS) content. The optimal time point for the response to freezing stress was 8 h after exposure. The transcriptome analysis of samples held for 8 h at -4 °C revealed 6862 differentially expressed genes (DEGs), among which the majority are implicated in various pathways, including the starch and sucrose metabolic pathways, antioxidant enzyme pathways, brassinolide (BR) signaling pathway, and transcription factors, according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We investigated possible crosstalk between BR signals and other pathways and found that BR signaling molecules were induced in response to freezing stress. The beta-amylase (BAM) starch hydrolase signal was enhanced by the BR signal, resulting in the accelerated degradation of starch and the formation of sugars, which served as emerging ROS scavengers and osmoregulators to resist freezing stress. In conclusion, crosstalk between BR signal transduction, and both starch and sucrose metabolism under freezing stress provides a new perspective for improving freezing resistance in foxtail millet.

Transcriptomic Analysis of Liver Tissue of Black Sea Bass (Centropristis striata) Exposed to High Nitrogen Environment

The black sea bass, Centropristis striata, is a potential candidate for commercial aquaculture. Due to inadequate removal of nitrogen in its breeding environment, C. striata exhibits increased nitrate concentration, which can cause acute toxicity, including energy metabolism damage and tissue damage. Therefore, RNA-seq technology was applied to characterize genes associated with toxicity tolerance under nitrate stress. The nitrate treatment caused significant changes in a total of 8920 genes, of which 2949 genes were up-regulated and 5971 genes were down-regulated. It was found that significantly enriched GO terms and KEGG were associated with blood microparticles, inhibitors of enzyme activity, and complement and coagulation cascade pathways. Furthermore, through bioinformatics analysis, it was found that these different pathways obtained in GO and KEGG enrichment analysis were mostly related to the immune and inflammatory response of fish. This study expands our understanding of the mechanism of nitrate stress affecting the liver function of C. striata.

Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant (Camellia sinensis (L.) Kuntze)

Introduction

Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement.

Methods

In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought.

Results

The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6).

Discussion

Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.

Transcriptome analysis revealed molecular basis of cold response in Prunus mume

Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional woody flower and fruit tree restrictedly cultivated in northern area due to its inability to survive harsh winters and early springs. In the current study, RNA-seq and physiological assay were used to study the cold response of P. mume 'Xuemei'. A total of 4705 genes were identified as differentially expressed genes (DEGs) in the 21 pairwise comparisons among seven time points under 0 °C cold treatment, and 3678 of them showed differential levels compared with control at normal temperature. The gene expression profiles indicated that the number of upregulated genes increased with prolongation of treatment time throughout the whole 48 h. Hierarchical clustering suggested three obvious phases of the gene expression profiles. Gene ontology (GO) analysis of the 4705 DEGs resulted in 102 significantly enriched GO items in which the transcription activity was dominant. 225 DEGs were predicted to encode transcription factor (TF) genes. Some important TFs (ERF, CBF, WRKY, NAC, MYB, bHLH) were strongly induced during the whole cold treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that plant signal transduction pathways such as plant hormone and calcium (Ca2+) were notable. Metabolic pathways such as sugar metabolism, especially RFOs (raffinose family oligosaccharides) were activated, which was accompanied by the accumulation of soluble sugars. SOD and POD enzyme activities coupled with reactive oxygen species (ROS)-related gene expression profile implied a gradually induced ROS scavenging system under cold treatment. These results might shed light on the sensitivity to cold stress in Japanese apricot and provide new insights into hardiness studies in P. mume and its related species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01376-2.

Comparative transcriptome analysis reveals the regulatory mechanisms of two tropical water lilies in response to cold stress

BACKGROUND

Tropical water lily is an aquatic plant with high ornamental value, but it cannot overwinter naturally at high latitudes. The temperature drop has become a key factor restricting the development and promotion of the industry.

RESULTS

The responses of Nymphaea lotus and Nymphaea rubra to cold stress were analyzed from the perspective of physiology and transcriptomics. Under the cold stress, Nymphaea rubra had obvious leaf edge curling and chlorosis. The degree of peroxidation of its membrane was higher than that of Nymphaea lotus, and the content of photosynthetic pigments also decreased more than that of Nymphaea lotus. The soluble sugar content, SOD enzyme activity and CAT enzyme activity of Nymphaea lotus were higher than those of Nymphaea rubra. This indicated that there were significant differences in the cold sensitivity of the two varieties. GO enrichment and KEGG pathway analysis showed that many stress response genes and pathways were affected and enriched to varying degrees under the cold stress, especially plant hormone signal transduction, metabolic pathways and some transcription factor genes were from ZAT gene family or WKRY gene family. The key transcription factor ZAT12 protein in the cold stress response process has a C₂H₂ conserved domain, and the protein is localized in the nucleus. Under the cold stress, overexpression of the NlZAT12 gene in Arabidopsis thaliana increased the expression of some cold-responsive protein genes. The content of reactive oxygen species and MDA in transgenic Arabidopsis thaliana was lower, and the content of soluble sugar was higher, indicating that overexpression of NlZAT12 can improve the cold tolerance of Arabidopsis thaliana.

CONCLUSION

We demonstrate that ethylene signalling and reactive oxygen species signalling play critical roles in the response of the two cultivars to cold stress. The key gene NlZAT12 for improving cold tolerance was identified. Our study provides a theoretical basis for revealing the molecular mechanism of tropical water lily in response to cold stress.

Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia

Identifying cold-related genes can provide insights into the cold adaptation mechanism of weeping forsythia. In this study, we compared the changes in gene expressions and physiological and biochemical indices under short-term cold stimulation with the changes in gene sequences under a long-term heterogeneous environment to investigate the cold adaptation mechanism in weeping forsythia. The data of adaptive gene sequence changes, e.g., single nucleotide polymorphisms, were obtained from previous landscape genomics studies. The physiological and biochemical indicators and transcriptome results showed that weeping forsythia initiated a series of programs, including increasing cell osmotic pressures, scavenging ROS, activating the defense mechanism that crosses with pathogen infection, and upregulating CBF/DREB1 transcription factor 1, to cope with short-term cold stress. A reanalysis of landscape genomic data suggested that weeping forsythia responded to long-term heterogeneous cold stress by the differentiation of genes related to synthesis of aromatic substances and adenosine triphosphate. Our results supported the hypothesis that the adaptation mechanisms of species to short-term environmental stimulation and long-term stress in heterogeneous environments are different. The differences in cold tolerance among populations are not necessarily obtained by changing cold-responsive gene sequences. This study provides new insights into the cold adaptation mechanisms of plants.

De-novo transcriptome assembly and analysis of lettuce plants grown under red, blue or white light

Lettuce (Lactuca sativa) is grown in various parts of the world for use as a leafy vegetable. Although the use of light-emitting diode (LED) in controlled plant production systems has been successfully used to enhance nutritional quality and plant growth efficiently, the molecular basis of lettuce's response to varying light spectra is not studied. Using next-generation sequencing, we have analyzed the transcriptomes of leaf lettuce (Lactuca sativa var. 'New Red Fire') grown hydroponically in a modular agricultural production system under three different types of LED lighting: red, blue, and white light. Illumina HiSeq sequencing platform was used to generate paired-end sequence reads (58 Gb raw and 54 Gb clean data) of the transcriptome of lettuce leaves exposed to varying light spectra. The de novo assembled final transcriptome contained 74,096 transcripts. Around 53% and 39% of the assembled transcripts matched to the UniProt and RefSeq RNA sequences, respectively. The validation of the differentially expressed transcripts using RT-qPCR showed complete agreement with RNA-Seq data for 27 transcripts. A comparison of the blue versus red light treatments showed the highest number of significantly differentially expressed transcripts. Among the transcripts significantly up-regulated in blue-light-exposed leaves compared to white-light-exposed leaves, ~ 26% were involved in the 'response to stress'. Among the transcripts significantly upregulated under red light compared to white light, ~ 6% were associated with 'nucleosome assembly' and other processes, such as 'oxidation-reduction process' and 'response to water deprivation' were significantly enriched. Thus, the result from the current study provides deeper insights into differential gene expression patterns and associated functional aspects under varying light qualities.

Genome-wide transcriptome profiling revealed biological macromolecules respond to low temperature stress in Brassica napus L

Brassica napus L. (B. napus) is a vital oilseed crop cultivated worldwide; low temperature (LT) is one of the major stress factors that limit its growth, development, distribution, and production. Even though processes have been developed to characterize LT-responsive genes, only limited studies have exploited the molecular response mechanisms in B. napus. Here the transcriptome data of an elite B. napus variety with LT adaptability was acquired and applied to investigate the gene expression profiles of B. napus in response to LT stress. The bioinformatics study revealed a total of 79,061 unigenes, of which 3,703 genes were differentially expressed genes (DEGs), with 2,129 upregulated and 1,574 downregulated. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis pinpointed that the DEGs were enriched in LT-stress-responsive biological functions and metabolic pathways, which included sugar metabolism, antioxidant defense system, plant hormone signal transduction, and photosynthesis. Moreover, a group of LT-stress-responsive transcription factors with divergent expression patterns under LT was summarized. A combined protein interaction suggested that a complex interconnected regulatory network existed in all detected pathways. RNA-seq data was verified using real-time quantitative polymerase chain reaction analysis. Based on these findings, we presented a hypothesis model illustrating valuable information for understanding the LT response mechanisms in B. napus.

Transcriptional Memory in Taraxacum mongolicum in Response to Long-Term Different Grazing Intensities

Grazing, as an important land use method in grassland, has a significant impact on the morphological and physiological traits of plants. However, little is known about how the molecular mechanism of plant responds to different grazing intensities. Here, we investigated the response of Taraxacum mongolicum to light grazing and heavy grazing intensities in comparison with a non-grazing control. Using de novo transcriptome assembly, T. mongolicum leaves were compared for the expression of the different genes under different grazing intensities in natural grassland. In total, 194,253 transcripts were de novo assembled and comprised in nine leaf tissues. Among them, 11,134 and 9058 genes were differentially expressed in light grazing and heavy grazing grassland separately, with 5867 genes that were identified as co-expression genes in two grazing treatments. The Nr, SwissProt, String, GO, KEGG, and COG analyses by BLASTx searches were performed to determine and further understand the biological functions of those differentially expressed genes (DEGs). Analysis of the expression patterns of 10 DEGs by quantitative real-time RT-PCR (qRT-PCR) confirmed the accuracy of the RNA-Seq results. Based on a comparative transcriptome analysis, the most significant transcriptomic changes that were observed under grazing intensity were related to plant hormone and signal transduction pathways, carbohydrate and secondary metabolism, and photosynthesis. In addition, heavy grazing resulted in a stronger transcriptomic response compared with light grazing through increasing the of the secondary metabolism- and photosynthesis-related genes. These changes in key pathways and related genes suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of T. mongolicum. Our findings provide important clues for improving grassland use and protection and understanding the molecular mechanisms of plant response to grazing.

De Novo Transcriptome Analysis of R. nigrum cv. Aldoniai in Response to Blackcurrant Reversion Virus Infection

The most damaging pathogen in blackcurrant plantations is mite-transmitted blackcurrant reversion virus (BRV). Some Ribes species have an encoded genetic resistance to BRV. We performed RNA sequencing analysis of BRV-resistant blackcurrant cv. Aldoniai to evaluate the molecular mechanisms related to the BRV infection response. The RNA of virus-inoculated and mock-inoculated microshoots was sequenced, and the transcriptional changes at 2- and 4-days post inoculation (dpi) were analyzed. The accumulation and expression of BRV RNA1 were detected in infected plants. In total, 159,701 transcripts were obtained and 30.7% were unigenes, annotated in 7 databases. More than 25,000 differentially expressed genes (DEGs) according to FPKM were upregulated or downregulated. We observed 221 and 850 DEGs at 2 and 4 dpi, respectively, in BRV-infected microshoots related to the stress response. The proportion of upregulated DEGs at 4 dpi was about 3.5 times higher than at 2 dpi. Pathways of the virus defense response were activated, and key candidate genes were identified. The phenylpropanoid and the cutin, suberine, and wax biosynthesis pathways were activated in infected plants. Our comparative de novo analysis of the R. nigrum transcriptome provides clues not only for understanding the molecular BRV resistance mechanisms but also for breeding BRV-tolerant genotypes.

A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds of Taxillus chinensis (DC.) Danser

Taxillus chinensis (DC.) Danser, a parasitic plant of the Loranthaceae family, grows by attacking other plants. It has a long history of being used in Chinese medicine to treat multiple chronic diseases. We previously observed that T. chinensis seeds are sensitive to cold. In this study, we performed transcriptome sequencing for T. chinensis seeds treated by cold (0°C) for 0 h, 12 h, 24 h, and 36 h. TRINITY assembled 257,870 transcripts from 223,512 genes. The GC content and N50 were calculated as 42.29% and 1,368, respectively. Then, we identified 42,183 CDSs and 35,268 likely proteins in the assembled transcriptome, which contained 1,622 signal peptides and 6,795 transmembrane domains. Next, we identified 17,217 genes (FPKM > 5) and 2,333 differentially expressed genes (DEGs) in T. chinensis seeds under cold stress. The MAPK pathway, as an early cold response, was significantly enriched by the DEGs in the T. chinensis seeds after 24 h of cold treatment. Known cold-responsive genes encoding abscisic acid-associated, aquaporin, C-repeat binding factor (CBF), cold-regulated protein, heat shock protein, protein kinase, ribosomal protein, transcription factor (TF), zinc finger protein, and ubiquitin were deregulated in the T. chinensis seeds under cold stress. Notably, the upregulation of CBF gene might be the consequences of the downregulation of MYB and GATA TFs. Additionally, we identified that genes encoding CDC20, YLS9, EXORDIUM, and AUX1 and wound-responsive family protein might be related to novel mechanisms of T. chinensis seeds exposed to cold. This study is first to report the differential transcriptional induction in T. chinensis seeds under cold stress. It will improve our understanding of parasitic plants in response to cold and provide a valuable resource for future studies.

Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads

Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.

Transcriptomic Analysis Reveals the Positive Role of Abscisic Acid in Endodormancy Maintenance of Leaf Buds of Magnolia wufengensis

Magnolia wufengensis (Magnoliaceae) is a deciduous landscape species, known for its ornamental value with uniquely shaped and coloured tepals. The species has been introduced to many cities in south China, but low temperatures limit the expansion of this species in cold regions. Bud dormancy is critical for plants to survive in cold environments during the winter. In this study, we performed transcriptomic analysis of leaf buds using RNA sequencing and compared their gene expression during endodormancy, endodormancy release, and ecodormancy. A total of 187,406 unigenes were generated with an average length of 621.82 bp (N50 = 895 bp). In the transcriptomic analysis, differentially expressed genes involved in metabolism and signal transduction of hormones especially abscisic acid (ABA) were substantially annotated during dormancy transition. Our results showed that ABA at a concentration of 100 μM promoted dormancy maintenance in buds of M. wufengensis. Furthermore, the expression of genes related to ABA biosynthesis, catabolism, and signalling pathway was analysed by qPCR. We found that the expression of MwCYP707A-1-2 was consistent with ABA content and the dormancy transition phase, indicating that MwCYP707A-1-2 played a role in endodormancy release. In addition, the upregulation of MwCBF1 during dormancy release highlighted the enhancement of cold resistance. This study provides new insights into the cold tolerance of M. wufengensis in the winter from bud dormancy based on RNA-sequencing and offers fundamental data for further research on breeding improvement of M. wufengensis.

Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress

Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of 'NL-6' treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.

Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated

Background

Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in wild apple trees.

Results

Phytohormone and physiology profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that JA, IAA, and ABA accumulated in the cold acclimation stage and decreased during freezing stress in response to freezing stress. To elucidate the molecular mechanisms of freezing stress after cold acclimation, we employed single molecular real-time (SMRT) and RNA-seq technologies to study genome-wide expression profiles in wild apple. Using the PacBio and Illumina platform, we obtained 20.79G subreads. These reads were assembled into 61,908 transcripts, and 24,716 differentially expressed transcripts were obtained. Among them, 4410 transcripts were differentially expressed during the whole process of freezing stress, and these were examined for enrichment via GO and KEGG analyses. Pathway analysis indicated that “plant hormone signal transduction”, “starch and sucrose metabolism”, “peroxisome” and “photosynthesis” might play a vital role in wild apple responses to freezing stress. Furthermore, the transcription factors DREB1/CBF, MYC2, WRKY70, WRKY71, MYB4 and MYB88 were strongly induced during the whole stress period.

Conclusions

Our study presents a global survey of the transcriptome profiles of wild apple trees in dynamic response to freezing stress after two days cold acclimation and provides insights into the molecular mechanisms of freezing adaptation of wild apple plants for the first time. The study also provides valuable information for further research on the antifreezing reaction mechanism and genetic improvement of M. sieversii after cold acclimation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07998-0.

Transcriptomic responses and physiological changes to cold stress among natural populations provide insights into local adaptation of weeping forsythia

Genetic mechanisms of species local adaptation are an emerging topic of great interest in evolutionary biology and molecular ecology. In this study, we compared the changes of physiological and phenotypic indexes and gene expression of four weeping forsythia populations under cold stress through a common garden experiment. Physiological and phenotypic results showed that there were differences in cold tolerance among populations. cold tolerance of high the latitude population (HBWZ) was the strongest, followed by the middle latitude population (SXWL), while the low latitude populations (SXHM) and (SXLJ) expressed the weakest cold tolerance. We identified significant differences in gene expression of cold tolerance related pathways and ontologies, including genes of oxylipin and isoquinoline alkaloid biosynthetic process, galactose, tyrosine and unsaturated fatty acids metabolism, among these populations under the same experimental temperature treatments. Even under the same degree of stress, there were notable differences in gene expression among natural populations. In this study, we present a working model of weeping forsythia populations which evolved in the context of different intensities of cold stress. Our study provides new insights for comprehending the genetic mechanisms of local adaptation for non-model species.

Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis 'Old Blush' After Exposure to a Gradual Drought Stress Followed by Recovery

Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

Transcriptome analysis of Sonneratia caseolaris seedlings under chilling stress

Sonneratia caseolaris is a native mangrove species found in China. It is fast growing and highly adaptable for mangrove afforestation, but suffered great damage by chilling event once introduced to high latitude area. To understand the response mechanisms under chilling stress, physiological and transcriptomic analyses were conducted. The relative electrolyte conductivity, malondialdehyde (MDA) content, soluble sugar content and soluble protein content increased significantly under chilling stress. This indicated that S. caseolaris suffered great damage and increased the levels of osmoprotectants in response to the chilling stress. Gene expression comparison analysis of S. caseolaris leaves after 6 h of chilling stress was performed at the transcriptional scale using RNA-Seq. A total of 168,473 unigenes and 3,706 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that the DEGs were mainly involved in carbohydrate metabolism, antioxidant enzyme, plant hormone signal transduction, and transcription factors (TFs). Sixteen genes associated with carbohydrate metabolism, antioxidant enzyme, phytohormones and TFs were selected for qRT-PCR verification, and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the chilling response of S. caseolaris at both physiological and transcriptomic levels, which will prove useful for further studies on stress-responses in mangrove plants.

Leveraging Methylation Alterations to Discover Potential Causal Genes Associated With the Survival Risk of Cervical Cancer in TCGA Through a Two-Stage Inference Approach

BACKGROUND

Multiple genes were previously identified to be associated with cervical cancer; however, the genetic architecture of cervical cancer remains unknown and many potential causal genes are yet to be discovered.

METHODS

To explore potential causal genes related to cervical cancer, a two-stage causal inference approach was proposed within the framework of Mendelian randomization, where the gene expression was treated as exposure, with methylations located within the promoter regions of genes serving as instrumental variables. Five prediction models were first utilized to characterize the relationship between the expression and methylations for each gene; then, the methylation-regulated gene expression (MReX) was obtained and the association was evaluated via Cox mixed-effect model based on MReX. We further implemented the aggregated Cauchy association test (ACAT) combination to take advantage of respective strengths of these prediction models while accounting for dependency among the p-values.

RESULTS

A total of 14 potential causal genes were discovered to be associated with the survival risk of cervical cancer in TCGA when the five prediction models were separately employed. The total number of potential causal genes was brought to 23 when conducting ACAT. Some of the newly discovered genes may be novel (e.g., YJEFN3, SPATA5L1, IMMP1L, C5orf55, PPIP5K2, ZNF330, CRYZL1, PPM1A, ESCO2, ZNF605, ZNF225, ZNF266, FICD, and OSTC). Functional analyses showed that these genes were enriched in tumor-associated pathways. Additionally, four genes (i.e., COL6A1, SYDE1, ESCO2, and GIPC1) were differentially expressed between tumor and normal tissues.

CONCLUSION

Our study discovered promising candidate genes that were causally associated with the survival risk of cervical cancer and thus provided new insights into the genetic etiology of cervical cancer.

Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

BACKGROUND

Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.

RESULTS

The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results.

CONCLUSIONS

We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

Physiological analysis and transcriptome sequencing reveal the effects of drier air humidity stress on Pterocarya stenoptera

Identifying physiological and transcriptomic changes can provide insights into the effects of drier air humidity stress on plants. In this study, we selected 6-month-old seedlings of Pterocarya stenoptera as study materials and used physiological index detection and transcriptome sequencing to investigate the adaptation mechanism of P. stenoptera in response to drier air humidity stress. Proline content, and superoxide dismutase and peroxidase activities did not increase significantly under drier air humidity stress. The physiological results showed that the drier air humidity stress only had slight effects on P. stenoptera. However, transcriptome sequencing showed that P. stenoptera initiated a series of metabolic pathways including L-phenylalanine catabolic process, NAD biosynthetic process, ATP biosynthetic process, and thiamine metabolism under drier air humidity stress. The enriched Kyoto Encyclopedia of Genes and Genomes results at 2 and 4 weeks under the drier air humidity stress showed that the genes THI1 and THIC in thiamine metabolism exhibited significantly differential expression. Previous studies confirmed that the two genes can improve drought tolerance. Our results implicitly indicated that exogenous thiamine might improve drought tolerance and alleviate the yellowing of the P. stenoptera leaves. Our study provides insights into the adaptation mechanism of P. stenoptera in response to drier air humidity stress and important clues into the cultivation and management of P. stenoptera in northern cities in China.

Exogenous abscisic acid induces the lipid and flavonoid metabolism of tea plants under drought stress

Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance, but the regulation mechanism of exogenous ABA on tea plants under drought stress was rarely reported. Here, we analyzed the effects of exogenous ABA on genes and metabolites of tea leaves under drought stress using transcriptomic and metabolomic analysis. The results showed that the exogenous ABA significantly induced the metabolic pathways of tea leaves under drought stress, including energy metabolism, amino acid metabolism, lipid metabolism and flavonoids biosynthesis. In which, the exogenous ABA could clearly affect the expression of genes involved in lipid metabolism and flavonoid biosynthesis. Meanwhile, it also increased the contents of flavone, anthocyanins, flavonol, isoflavone of tea leaves under drought stress, including, kaempferitrin, sakuranetin, kaempferol, and decreased the contents of glycerophospholipids, glycerolipids and fatty acids of tea leaves under drought stress. The results suggested that the exogenous ABA could alleviate the damages of tea leaves under drought stress through inducing the expression of the genes and altering the contents of metabolites in response to drought stress. This study will be helpful to understand the mechanism of resilience to abiotic stress in tea plant and provide novel insights into enhancing drought tolerance in the future.

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage

Young cotyledons of cotton seedlings are most susceptible to chilling stress. To gain insight into the potential mechanism of cold tolerance of young cotton cotyledons, we conducted physiological and comparative transcriptome analysis of two varieties with contrasting phenotypes. The evaluation of chilling injury of young cotyledons among 74 cotton varieties revealed that H559 was the most tolerant and YM21 was the most sensitive. The physiological analysis found that the ROS scavenging ability was lower, and cell membrane damage was more severe in the cotyledons of YM21 than that of H559 under chilling stress. RNA-seq analysis identified a total of 44,998 expressed genes and 19,982 differentially expressed genes (DEGs) in young cotyledons of the two varieties under chilling stress. Weighted gene coexpression network analysis (WGCNA) of all DEGs revealed four significant modules with close correlation with specific samples. The GO-term enrichment analysis found that lots of genes in H559-specific modules were involved in plant resistance to abiotic stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that pathways such as plant hormone signal transduction, MAPK signaling, and plant–pathogen interaction were related to chilling stress response. A total of 574 transcription factors and 936 hub genes in these modules were identified. Twenty hub genes were selected for qRT-PCR verification, revealing the reliability and accuracy of transcriptome data. These findings will lay a foundation for future research on the molecular mechanism of cold tolerance in cotyledons of cotton.

Volatile Organic Compounds of Endophytic Burkholderia pyrrocinia Strain JK-SH007 Promote Disease Resistance in Poplar

Volatile organic compounds (VOCs) play important roles in the regulation of plant growth and pathogen resistance. However, little is known about the influence of VOCs released from endophytic strains (Burkholderia pyrrocinia strain JK-SH007) on controlling pathogens or inducing systemic resistance in poplar. In this study, we found that VOCs produced by strain JK-SH007 inhibit three poplar canker pathogens (Cytospora chrysosperma, Phomopsis macrospora, and Fusicoccum aesculi) and promote defense enzyme activity and malondialdehyde (MDA) and total phenol (TP) accumulation. Thirteen kinds of VOC components were identified using the solid-phase microextraction combined with gas chromatography-mass spectrometry method. Dimethyl disulfide (DMDS) accounted for the largest proportion of these VOCs. Treatments of poplar seedlings with different volumes of VOC standards (DMDS, benzothiazole, dimethylthiomethane, and phenylacetone) showed that DMDS had the greatest effects on various defense enzyme activities and MDA and TP accumulation. We also found that the inhibitory effect of the VOCs on the three pathogens was gradually enhanced with increasing standard volume. Moreover, the treatment of samples with DMDS significantly reduced the severity and development of the disease caused by three poplar canker pathogens. Comparative transcriptomics analysis of poplar seedlings treated with DMDS showed that there were 1,586 differentially expressed genes in the leaves and stems, and quantitative PCR showed that the gene expression trends were highly consistent with the transcriptome sequencing results. The most significant transcriptomic changes induced by VOCs were related to hormone signal transduction, transcriptional regulation of plant-pathogen interactions, and energy metabolism. Moreover, 137 transcription factors, including members of the ethylene response factor, NAC, WRKY, G2-like, and basic helix-loop-helix protein families, were identified to be involved in the VOC-induced process. This study elucidates the resistance induced by Burkholderia pyrrocinia strain JK-SH007 to poplar canker at the molecular level and can make possible a new method for the comprehensive prevention and control of poplar disease.

De novo leaf transcriptome assembly of Bougainvillea spectabilis for the identification of genes involves in the secondary metabolite pathways

Bougainvillea spectabilis is known as a vital medicinal, ornamental as well as an essential oil producing plant. It is also a rich source of important secondary metabolites with several therapeutic properties. Various studies on its pharmacological and toxicological aspects have been published but there is no genomic or transcriptomic resource available in the public databases. To address this important issue, the de-novo transcriptome assembly of B. spectabilis leaf tissue has been done for the identification of genes involved in various important secondary metabolites, Single nucleotide polymorphism (SNPs) and Simple sequence repeats (SSRs). The transcriptome sequencing of B. spectabilis leaf tissue generated 79,811,024 raw reads with GC value 42.77%. The transcriptomic assembly was performed by Trinity software which generated 100,374 transcripts and 99,793 unigenes with minimum and maximum length of 201 bp and 13,237 bp and N50 value of 1470 and 1472 respectively. Annotation of these unigenes was performed using seven databases including NR, PFAM, GO and KEGG. Approximately, 44,302 unigenes were annotated in GO database. The KEGG pathway analysis revealed 23,102 unigenes in which 19,054 genes were assigned to five groups in KEGG and 130 biochemical pathways. The highest group among the five groups was Metabolism with 9230 unigenes. Moreover, about 63,226 SNPs and 30,333 SSRs in the leaf transcriptome of B. spectabilis were identified. To the best of my understanding it will be the first comprehensive transcriptome analysis of B. spectabilis from family Nyctaginaceae which will help as a reference line for further genomic and transcriptomic studies.

Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress

BACKGROUND

Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability.

RESULTS

Five cDNA libraries were prepared from the third true leaf of hexaploid sweetpotato at seedlings stage (Xuzi-8 cultivar) treated with 200 mM NaCl for 0, 1, 6, 12, 48 h. Using second and third generation technology, Illumina sequencing generated 170,344,392 clean high-quality long reads that were assembled into 15,998 unigenes with an average length 2178 base pair and 96.55% of these unigenes were functionally annotated in the NR protein database. A number of 537 unigenes failed to hit any homologs which may be considered as novel genes. The current results indicated that sweetpotato plants behavior during the first hour of salt stress was different than the other three time points. Furthermore, expression profiling analysis identified 4, 479, 281, 508 significantly expressed unigenes in salt stress treated samples at the different time points including 1, 6, 12, 48 h, respectively as compared to control. In addition, there were 4, 1202, 764 and 2195 transcription factors differentially regulated DEGs by salt stress at different time points including 1, 6, 12, 48 h of salt stress. Validation experiment was done using 6 randomly selected unigenes and the results was in agree with the DEG results. Protein kinases include many genes which were found to play a vital role in phosphorylation process and act as a signal transductor/ receptor proteins in membranes. These findings suggest that salt stress tolerance in hexaploid sweetpotato plants may be mainly affected by TFs, PKs, Protein Detox and hormones related genes which contribute to enhance salt tolerance.

CONCLUSION

These transcriptome sequencing data of hexaploid sweetpotato under salt stress conditions can provide a valuable resource for sweetpotato breeding research and focus on novel insights into hexaploid sweetpotato responses to salt stress. In addition, it offers new candidate genes or markers that can be used as a guide to the future studies attempting to breed salt tolerance sweetpotato cultivars.

Comprehensive Transcriptome Analysis Revealed the Effects of the Light Quality, Light Intensity, and Photoperiod on Phlorizin Accumulation in Lithocarpus polystachyus Rehd

Lithocarpus polystachyus Rehd. is an important medicinal plant species grown in southern China, with phlorizin as its main active substance. The effects of light conditions on phlorizin biosynthesis in L. polystachyus remain unclear. Thus, we analyzed the transcriptomes of L. polystachyus plants cultivated under diverse light qualities, light intensities, and photoperiods. The light treatments resulted in 5977–8027 differentially expressed genes (DEGs), which were functionally annotated based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Genes encoding transcription factors from 89 families were differentially expressed after the light treatments, implying these transcription factors are photoresponsive. Phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) are the key enzymes for the accumulation of phlorizin. The transcription levels of PAL2, PAL, 4CL1 (DN121614), 4CLL7, and 4CL1 (DN102161) were positively correlated with phlorizin accumulation, suggesting that these genes are important for phlorizin biosynthesis. An ultra-high-performance liquid chromatography method was used to quantify the phlorizin content. Phlorizin accumulated in response to the green light treatment and following appropriate decreases in the light intensity or appropriate increases in the duration of the light exposure. The green light, 2000 lx, and 3000 lx treatments increased the PAL activity of L. polystachyus, but the regulatory effects of the light intensity treatments on PAL activity were relatively weak. This study represents the first comprehensive analysis of the light-induced transcriptome of L. polystachyus. The study results may form the basis of future studies aimed at elucidating the molecular mechanism underlying phlorizin biosynthesis in L. polystachyus. Moreover, this study may be relevant for clarifying the regulatory effects of light on the abundance of bioactive components in medicinal plants.