Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

Comparative Phenotypic and Transcriptomic Analyses Provide Novel Insights into the Molecular Mechanism of Seed Germination in Response to Low Temperature Stress in Alfalfa

Low temperature is the most common abiotic factor that usually occurs during the seed germination of alfalfa (Medicago sativa L.). However, the potential regulatory mechanisms involved in alfalfa seed germination under low temperature stress are still ambiguous. Therefore, to determine the relevant key genes and pathways, the phenotypic and transcriptomic analyses of low-temperature sensitive (Instict) and low-temperature tolerant (Sardi10) alfalfa were conducted at 6 and 15 h of seed germination under normal (20 °C) and low (10 °C) temperature conditions. Germination phenotypic results showed that Sardi10 had the strongest germination ability under low temperatures, which was manifested by the higher germination-related indicators. Further transcriptome analysis indicated that differentially expressed genes were mainly enriched in galactose metabolism and carbon metabolism pathways, which were the most commonly enriched in two alfalfa genotypes. Additionally, fatty acid metabolism and glutathione metabolism pathways were preferably enriched in Sardi10 alfalfa. The Weighted Gene Co-Expression Network Analysis (WGCNA) suggested that genes were closely related to galactose metabolism, fatty acid metabolism, and glutathione metabolism in Sardi10 alfalfa at the module with the highest correlation (6 h of germination under low temperature). Finally, qRT-PCR analysis further validated the related genes involved in the above pathways, which might play crucial roles in regulating seed germination of alfalfa under low temperature conditions. These findings provide new insights into the molecular mechanisms of seed germination underlying the low temperature stress in alfalfa.

Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions

Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress

BACKGROUND

NIN-like protein (NLP) transcription factors (TFs) compose a plant-specific gene family whose members play vital roles in plant physiological processes, especially in the regulation of plant growth and the response to nitrate-nitrogen. However, no systematic identification or analysis of the NLP gene family has been reported in alfalfa. The recently completed whole-genome sequence of alfalfa has allowed us to investigate genome-wide characteristics and expression profiles.

RESULTS

53 MsNLP genes were identified from alfalfa and renamed according to their respective chromosome distributions. Phylogenetic analysis demonstrated that these MsNLPs can be classified into three groups on the basis of their conserved domains. Gene structure and protein motif analyses showed that closely clustered MsNLP genes were relatively conserved within each subgroup. Synteny analysis revealed four fragment duplication events of MsNLPs in alfalfa. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of gene pairs indicated that the MsNLP genes underwent purifying selection during evolution. Examination of the expression patterns of different tissues revealed specific expression patterns of the MsNLP genes in the leaves, indicating that these genes are involved in plant functional development. Prediction of cis-acting regulatory elements and expression profiles further demonstrated that the MsNLP genes might play important roles in the response to abiotic stress and in phytohormone signal transduction processes.

CONCLUSION

This study represents the first genome-wide characterization of MsNLP in alfalfa. Most MsNLPs are expressed mainly in leaves and respond positively to abiotic stresses and hormonal treatments. These results provide a valuable resource for an improved understanding of the characteristics and biological roles of the MsNLP genes in alfalfa.

Uncovering early transcriptional regulation during adventitious root formation in Medicago sativa

BACKGROUND

Alfalfa (Medicago sativa L.) as an important legume plant can quickly produce adventitious roots (ARs) to form new plants by cutting. But the regulatory mechanism of AR formation in alfalfa remains unclear.

RESULTS

To better understand the rooting process of alfalfa cuttings, plant materials from four stages, including initial separation stage (C stage), induction stage (Y stage), AR primordium formation stage (P stage) and AR maturation stage (S stage) were collected and used for RNA-Seq. Meanwhile, three candidate genes (SAUR, VAN3 and EGLC) were selected to explore their roles in AR formation. The numbers of differentially expressed genes (DEGs) of Y-vs-C (9,724) and P-vs-Y groups (6,836) were larger than that of S-vs-P group (150), indicating highly active in the early AR formation during the complicated development process. Pathways related to cell wall and sugar metabolism, root development, cell cycle, stem cell, and protease were identified, indicating that these genes were involved in AR production. A large number of hormone-related genes associated with the formation of alfalfa ARs have also been identified, in which auxin, ABA and brassinosteroids are thought to play key regulatory roles. Comparing with TF database, it was found that AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, C2H2, bZIP, GRAS played a major regulatory role in the production of ARs of alfalfa. Furthermore, three identified genes showed significant promotion effect on AR formation.

CONCLUSIONS

Stimulation of stem basal cells in alfalfa by cutting induced AR production through the regulation of various hormones, transcription factors and kinases. This study provides new insights of AR formation in alfalfa and enriches gene resources in crop planting and cultivation.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Illumina RNA and SMRT Sequencing Reveals the Mechanism of Uptake and Transformation of Selenium Nanoparticles in Soybean Seedlings

Selenium (Se) is an essential element for mammals, and its deficiency in the diet is a global problem. Agronomic biofortification through exogenous Se provides a valuable strategy to enhance human Se intake. Selenium nanoparticles (SeNPs) have been regarded to be higher bioavailability and less toxicity in comparison with selenite and selenate. Still, little has been known about the mechanism of their metabolism in plants. Soybean (Glycine max L.) can enrich Se, providing an ideal carrier for Se biofortification. In this study, soybean sprouts were treated with SeNPs, and a combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing was applied to clarify the underlying molecular mechanism of SeNPs metabolism. A total of 74,662 nonredundant transcripts were obtained, and 2109 transcription factors, 9687 alternative splice events, and 3309 long non-coding RNAs (lncRNAs) were predicted, respectively. KEGG enrichment analysis of the DEGs revealed that metabolic pathways, biosynthesis of secondary metabolites, and peroxisome were most enriched both in roots and leaves after exposure to SeNPs. A total of 117 transcripts were identified to be putatively involved in SeNPs transport and biotransformation in soybean. The top six hub genes and their closely coexpressed Se metabolism-related genes, such as adenylylsulfate reductase (APR3), methionine-tRNA ligase (SYM), and chloroplastic Nifs-like cysteine desulfurases (CNIF1), were screened by WGCNA and identified to play crucial roles in SeNPs accumulation and tolerance in soybean. Finally, a putative metabolism pathway of SeNPs in soybean was proposed. These findings have provided a theoretical foundation for future elucidation of the mechanism of SeNPs metabolism in plants.

Integrated transcriptomics and metabolomics analysis reveals key regulatory network that response to cold stress in common Bean (Phaseolus vulgaris L.)

Cold temperatures can be detrimental to crop survival and productivity. Breeding progress can be improved by understanding the molecular basis of low temperature tolerance. We investigated the key routes and critical metabolites related to low temperature resistance in cold-tolerant and -sensitive common bean cultivars 120 and 093, respectively. Many potential genes and metabolites implicated in major metabolic pathways during the chilling stress response were identified through transcriptomics and metabolomics research. Under chilling stress, the expression of many genes involved in lipid, amino acid, and flavonoid metabolism, as well as metabolite accumulation increased in the two bean types. Malondialdehyde (MDA) content was lower in 120 than in 093. Regarding amino acid metabolism, 120 had a higher concentration of acidic amino acids than 093, whereas 093 had a higher concentration of basic amino acids. Methionine accumulation was clearly higher in 120 than in 093. In addition, 120 had a higher concentration of many types of flavonoids than 093. Flavonoids, methionine and malondialdehyde could be used as biomarkers of plant chilling injury. Transcriptome analysis of hormone metabolism revealed considerably greater, expression of abscisic acid (ABA), gibberellin (GA), and jasmonic acid (JA) in 093 than in 120 during chilling stress, indicating that hormone regulation modes in 093 and 120 were different. Thus, chilling stress tolerance is different between 093 and 120 possibly due to transcriptional and metabolic regulation.

Research progress on plant noncoding RNAs in response to low-temperature stress

Low temperature (LT) is an important factor limiting plant growth and distribution. Plants have evolved sophisticated adaptive mechanisms to cope with hypothermia. RNA silencing is the orchestrator of these cellular responses. RNA silencing, which modifies gene expression through noncoding RNAs (ncRNAs), is a strategy used by plants to combat environmental stress. ncRNAs, which have very little protein-coding capacity, work by binding reverse complementary endogenous transcripts. In plants, ncRNAs include small non-coding RNAs (sncRNAs), medium-sized non-coding RNAs (mncRNAs), and long non-coding RNAs (lncRNAs). Apart from describing the biogenesis of different ncRNAs (miRNAs, siRNAs, and lncRNAs), we thoroughly discuss the functions of these ncRNAs during cold acclimation. Two major classes of sncRNAs, microRNAs and siRNAs, play essential regulatory roles in cold response processes through the posttranscriptional gene silencing (PTGS) pathway or transcriptional gene silencing (TGS) pathway. Microarray or transcriptome sequencing analysis can reveal a large number of cold-responsive miRNAs in plants. In this review, the cold-response patterns of miRNAs verified by Northern blotting or quantitative PCR in Arabidopsis thaliana, rice, and many other important crops are discussed. The detailed molecular mechanisms of several miRNAs in Arabidopsis (miR397, miR408, miR402, and miR394) and rice (Osa-miR156, Osa-miR319, and Osa-miR528) that regulate plant cold resistance are elucidated. In addition, the regulatory mechanism of the lncRNA SVALKA in the cold signaling pathway is explained in detail. Finally, we present the challenges for understanding the roles of small ncRNAs in cold signal transduction.

Identification of long non-coding RNAs involved in floral scent of Rosa hybrida

Long non-coding RNAs (lncRNAs) were found to play important roles in transcriptional, post-transcriptional, and epigenetic gene regulation in various biological processes. However, lncRNAs and their regulatory roles remain poorly studied in horticultural plants. Rose is economically important not only for their wide use as garden and cut flowers but also as important sources of natural fragrance for perfume and cosmetics industry, but presently little was known about the regulatory mechanism of the floral scent production. In this paper, a RNA-Seq analysis with strand-specific libraries, was performed to rose flowers in different flowering stages. The scented variety 'Tianmidemeng' (Rosa hybrida) was used as plant material. A total of 13,957 lncRNAs were identified by mining the RNA-Seq data, including 10,887 annotated lncRNAs and 3070 novel lncRNAs. Among them, 10,075 lncRNAs were predicted to possess a total of 29,622 target genes, including 54 synthase genes and 24 transcription factors related to floral scent synthesis. 425 lncRNAs were differentially expressed during the flowering process, among which 19 were differentially expressed among all the three flowering stages. Using weighted correlation network analysis (WGCNA), we correlate the differentially-expressed lncRNAs to synthesis of individual floral scent compounds. Furthermore, regulatory function of one of candidate lncRNAs for floral scent synthesis was verified using VIGS method in the rose. In this study, we were able to show that lncRNAs may play important roles in floral scent production in the rose. This study also improves our understanding of how plants regulate their secondary metabolism by lncRNAs.

Overexpression of an NF-YC2 gene confers alkali tolerance to transgenic alfalfa (Medicago sativa L.)

Alkaline stress severely limits plant growth and yield worldwide. NF-YC transcription factors (TFs) respond to abiotic stress by activating gene expression. However, the biological function of NF-YC TFs in alfalfa (Medicago sativa L.) is not clear. In our study, an NF-YC2 gene was identified and transgenic plants were obtained by constructing overexpression vector and cotyledon node transformation system in alfalfa. The open reading frame of MsNF-YC2 is 879 bp with 32.4 kDa molecular mass. MsNF-YC2 showed tissue expression specificity and was induced by a variety of abiotic stresses including drought, salt, and alkali stress in alfalfa. Under alkali stress treatment, transgenic plants exhibited higher levels of antioxidant enzyme activities and proline (Pro), correlating with a lower levels of hydrogen peroxide (H₂O₂), superoxide anion (O₂ ^-) compared with wild-type (WT) plants. Transcriptomic results showed that overexpression of MsNF-YC2 regulated the expression of phytohormone signal transduction and photosynthesis-related genes under normal and alkaline stress treatments. These results suggest that the MsNF-YC2 gene plays crucial role enhance alkali adaptation abilities in alfalfa.

Exploring epitranscriptomics for crop improvement and environmental stress tolerance

Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m⁵C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.

Identification and Characterization of Regulatory Pathways Controlling Dormancy Under Lower Temperature in Alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.), a kind of high-quality perennial legume forage, is widely distributed in the northern regions of China. In recent years, low temperatures have frequently occurred and limited alfalfa productivity and survival in early spring and late fall. However, the underlying molecular mechanisms of alfalfa response to cold tolerance are not well-documented. In this study, dormancy and non-dormancy alfalfa standard varieties were characterized under low-temperature stress. Our analysis revealed that plant height of the dormancy genotype was strongly inhibited by low temperature; flavonoids content, and higher expression of flavonoids biosynthesis genes (chalcone synthase, leucoanthocyanidin dioxygenase, and flavonoid 3'-monooxygenase) may play essential roles in response to low-temperature stress in dormancy genotype alfalfa. Further analyses revealed that receptor-like kinase family genes (such as cysteine-rich RLK10, lectin protein kinase, and S-locus glycoprotein like kinase), RNA and protein synthesis genes (RNA polymerases, ribosomal protein, and protein phosphatase 2C family protein), and proteasome degradation pathway genes (such as F-box family protein, RING/U-box superfamily protein, and zinc finger family protein) also highly upregulated and contributed to cold tolerance phenotype in dormancy genotype alfalfa. This will provide new insights into future studies for cold tolerance in alfalfa and offer new target genes for further functional characterization and genetic improvement of alfalfa.

Full-Length Transcriptome Sequencing Reveals the Impact of Cold Stress on Alternative Splicing in Quinoa

Quinoa is a cold-resistant and nutrient-rich crop. To decipher the cold stress response of quinoa, the full-length transcriptomes of the cold-resistant quinoa variety CRQ64 and the cold-sensitive quinoa variety CSQ5 were compared. We identified 55,389 novel isoforms and 6432 novel genes in these transcriptomes. Under cold stress, CRQ64 had more differentially expressed genes (DEGs) and differentially alternative splicing events compared to non-stress conditions than CSQ5. DEGs that were specifically present only in CRQ64 were significantly enriched in processes which contribute to osmoregulation and ROS homeostasis in plants, such as sucrose metabolism and phenylpropanoid biosynthesis. More genes with differential alternative splicing under cold stress were enriched in peroxidase functions in CRQ64. In total, 5988 transcription factors and 2956 long non-coding RNAs (LncRNAs) were detected in this dataset. Many of these had altered expression patterns under cold stress compared to non-stress conditions. Our transcriptome results demonstrate that CRQ64 undergoes a wider stress response than CSQ5 under cold stress. Our results improved the annotation of the quinoa genome and provide new insight into the mechanisms of cold resistance in quinoa.

Integrative Comparative Assessment of Cold Acclimation in Evergreen and Deciduous Iris Species

Cold acclimation (CA) is a strategy which plants have evolved to increase freezing tolerance. Global climate change could obstruct CA and raise the probability of winter injury, especially for evergreens. Hence, understanding the regulatory mechanism of CA is crucial to improve freezing tolerance in evergreen plants. A comparative study on a pair of closely related evergreen and deciduous iris species in response to cold through CA was conducive to uncovering and complementing the knowledge of CA. We investigated morphological, physiological and biochemical changes, as well as the expression of associated genes in the functional leaves of both iris species from natural CA to deacclimation. Briefly, fast and strong CA in the evergreen iris might cause early expressions of BAM1, NCED3, GPX6, etc., which leads to strong enzyme activity of starch degradation, abscisic acid biosynthesis and reactive oxygen species scavenging. Additionally, genes belonging to the antioxidant system were mainly induced during deacclimation. These results suggest that interspecies differences in the leaf freezing tolerance of irises are associated with the rate and degree of CA, which activates multiple signaling networks with complex interactions and induces the transcription of cold-responsive genes. Moreover, the ICE–CBF–COR signaling cascade may integrate and initiate diverse cold-responsive pathways during CA of the evergreen iris. The findings of this study provide valuable insight to further research on CA mechanisms and implicate genes which could support breeding strategies in herbaceous perennials under climate changes.

Integration of full-length transcriptomes and anthocyanin metabolite analysis for understanding fruit coloration mechanism in Schisandra chinensis

Coloration directly affects the commercial value of Schisandra chinensis fruits. The composition and content of anthocyanin determine the S. chinensis fruit coloration. However, the molecular mechanism of anthocyanin biosynthesis and regulation in this fruit remains unknown. In this study, we performed integrative full-length transcriptomics and targeted metabolomics analyses in S. chinensis fruits at four different developmental stages to elucidate the coloration mechanism. Cyanidin3-O-xyl-rutinoside is the key anthocyanin, which is responsible for the reddening of S. chinensis fruits, and its accumulation gradually accelerated from the 80th day after fluorescence. Overall, 122,289 unigenes with an average length of 2592 bp and an N50 of 4232 bp were obtained through single-molecule real-time sequencing; a total of 16,456 differentially expressed genes were identified. Moreover, 10 full-length structural genes related to anthocyanin biosynthesis were found to be significantly differentially expressed with fruit ripening. Moreover, 10 glycosyltransferases (GTs) that may possess the activities of anthocyanidin 3-O-glucosyltransferase, anthocyanidin 3-O-glucoside rhamnosyltransferase, and xylosyltransferases, which are involved in the final three steps for cyanidin3-O-xyl-rutinoside synthesis, were identified through phylogenetic analysis. Based on these findings, we constructed the complete anthocyanin biosynthetic pathway in S. chinensis fruits; five ScMYBs, three ScbHLHs, and two ScWD40s potentially involved in regulating anthocyanin biosynthesis in S. chinensis fruits were also selected. Our study provides the foundation for further research on the molecular mechanism of anthocyanin biosynthesis and regulation for improving the quality of S. chinensis fruits. The results of full-length transcriptomes would provide researchers with novel insights into the molecular cloning of enzymes and their activity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01179-3.

Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance

Salt stress negatively impacts crop production worldwide. Genetic diversity among barley (Hordeum vulgare) landraces adapted to adverse conditions should provide a valuable reservoir of tolerance genes for breeding programs. To identify molecular and biochemical differences between barley genotypes, transcriptomic and antioxidant enzyme profiles along with several morpho-physiological features were compared between salt-tolerant (Boulifa) and salt-sensitive (Testour) genotypes subjected to salt stress. Decreases in biomass, photosynthetic parameters, and relative water content were low in Boulifa compared to Testour. Boulifa had better antioxidant protection against salt stress than Testour, with greater antioxidant enzymes activities including catalase, superoxide dismutase, and guaiacol peroxidase. Transcriptome assembly for both genotypes revealed greater accumulation of differentially expressed transcripts in Testour compared to Boulifa, emphasizing the elevated transcriptional response in Testour following salt exposure. Various salt-responsive genes, including the antioxidant catalase 3, the osmoprotectant betaine aldehyde dehydrogenase 2, and the transcription factors MYB20 and MYB41, were induced only in Boulifa. By contrast, several genes associated with photosystems I and II, and light receptor chlorophylls A and B, were more repressed in Testour. Co-expression network analysis identified specific gene modules correlating with differences in genotypes and morpho-physiological traits. Overall, salinity-induced differential transcript accumulation underlies the differential morpho-physiological response in both genotypes and could be important for breeding salt tolerance in barley.

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

BACKGROUND

Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance.

RESULTS

In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress.

CONCLUSIONS

Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure-function genetic and comparative genomics studies of this important crop.

Full-Length Transcriptome and RNA-Seq Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Kiwifruit (Actinidia valvata)

Actinidia valvata possesses waterlogging tolerance; however, the mechanisms underlying this trait are poorly characterized. Here, we performed a transcriptome analysis by combining single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing and investigated the physiological responses of the roots of KR5 (A. valvata, a tolerant genotype) after 0, 12, 24 and 72 h of waterlogging stress. KR5 roots responded to waterlogging stress mainly via carbohydrate and free amino acids metabolism and reactive oxygen species (ROS) scavenging pathways. Trehalose-6-phosphate synthase (TPS) activity, alcohol dehydrogenase (ADH) activity and the total free amino acid content increased significantly under waterlogging stress. The nicotinamide adenine dinucleotide-dependent glutamate synthase/alanine aminotransferase (NADH-GOGAT/AlaAT) cycle was correlated with alanine accumulation. Levels of genes encoding peroxidase (POD) and catalase (CAT) decreased and enzyme activity increased under waterlogging stress. Members of the LATERAL ORGAN BOUNDARIES (LOB), AP2/ERF-ERF, Trihelix and C3H transcription factor families were identified as potential regulators of the transcriptional response. Several hub genes were identified as key factors in the response to waterlogging stress by a weighted gene co-expression network analysis (WGCNA). Our results provide insights into the factors contributing to waterlogging tolerance in kiwifruit, providing a basis for further studies of interspecific differences in an important plant trait and for molecular breeding.

Cold stress tolerance of the intertidal red alga Neoporphyra haitanensis

BACKGROUND

Red algae Porphyra sensu lato grow naturally in the unfavorable intertidal environment, in which they are exposed to substantial temperature fluctuations. The strategies of Porphyra to tolerate cold stress are poorly understood.

RESULTS

Herein, investigations revealed that chilling and freezing induced alterations in the physiological properties, gene transcriptional profiles and metabolite levels in the economically important red algae species, Neoporphyra haitanensis. Control samples (kept at 20 °C) were compared to chilled thalli (10 and 4 °C) and to thalli under - 4 °C conditions. Chilling stress did not affect the health or photosynthetic efficiency of gametophytes, but freezing conditions resulted in the arrest of growth, death of some cells and a decrease in photosynthetic activity as calculated by Fv/Fm. Transcriptome sequencing analysis revealed that the photosynthetic system was down-regulated along with genes associated with carbon fixation and primary metabolic biosynthesis. Adaptive mechanisms included an increase in unsaturated fatty acids levels to improve membrane fluidity, an increase in floridoside and isofloridoside content to enhance osmotic resistance, and an elevation in levels of some resistance-associated phytohormones (abscisic acid, salicylic acid, and methyl jasmonic acid). These physiochemical alterations occurred together with the upregulation of ribosome biogenesis.

CONCLUSIONS

N. haitanensis adopts multiple protective mechanisms to maintain homeostasis of cellular physiology in tolerance to cold stress.

Overexpression of a Voltage-Dependent Anion-Selective Channel (VDAC) Protein-Encoding Gene, MsVDAC, from Medicago sativa Confers Cold and Drought Tolerance to Transgenic Tobacco

Voltage-dependent anion channels (VDACs) are highly conserved proteins that are involved in the translocation of tRNA and play a key role in modulating plant senescence and multiple pathways. However, the functions of VDACs in plants are still poorly understood. Here, a novel VDAC gene was isolated and identified from alfalfa (Medicago sativa L.). MsVDAC localized to the mitochondria, and its expression was highest in alfalfa roots and was induced in response to cold, drought and salt treatment. Overexpression of MsVDAC in tobacco significantly increased MDA, GSH, soluble sugars, soluble protein and proline contents under cold and drought stress. However, the activities of SOD and POD decreased in transgenic tobacco under cold stress, while the O2- content increased. Stress-responsive genes including LTP1, ERD10B and Hxk3 were upregulated in the transgenic plants under cold and drought stress. However, GAPC, CBL1, BI-1, Cu/ZnSOD and MnSOD were upregulated only in the transgenic tobacco plants under cold stress, and GAPC, CBL1, and BI-1 were downregulated under drought stress. These results suggest that MsVDAC provides cold tolerance by regulating ROS scavenging, osmotic homeostasis and stress-responsive gene expression in plants, but the improved drought tolerance via MsVDAC may be mainly due to osmotic homeostasis and stress-responsive genes.

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)

Alfalfa is an important legume forage grown worldwide and its productivity is affected by environmental stresses such as drought and high salinity. In this work, three alfalfa germplasms with contrasting tolerances to drought and high salinity were used for unraveling the transcriptomic responses to drought and salt stresses. Twenty-one different RNA samples from different germplasm, stress conditions or tissue sources (leaf, stem and root) were extracted and sequenced using the PacBio (Iso-Seq) and the Illumina platforms to obtain full-length transcriptomic profiles. A total of 1,124,275 and 91,378 unique isoforms and genes were obtained, respectively. Comparative analysis of transcriptomes identified differentially expressed genes and isoforms as well as transcriptional and post-transcriptional modifications such as alternative splicing events, fusion genes and nonsense-mediated mRNA decay events and non-coding RNA such as circRNA and lncRNA. This is the first time to identify the diversity of circRNA and lncRNA in response to drought and high salinity in alfalfa. The analysis of weighted gene co-expression network allowed to identify master genes and isoforms that may play important roles on drought and salt stress tolerance in alfalfa. This work provides insight for understanding the mechanisms by which drought and salt stresses affect alfalfa growth at the whole genome level.

Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts

BACKGROUND

Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, no reference genome or full-length transcripts at the genome-wide scale have been reported for cigar tobacco. In particular, anion channels/transporters are of high interest for their potential application in regulating the chloride content of cigar tobacco growing on coastal lands, which usually results in relatively high Cl- accumulation, which is unfavorable. Here, the PacBio platform and NGS technology were combined to generate a full-length transcriptome of cigar tobacco used for cigar wrappers.

RESULTS

High-quality RNA isolated from the roots, leaves and stems of cigar tobacco were subjected to both the PacBio platform and NGS. From PacBio, a total of 11,652,432 subreads (19-Gb) were generated, with an average read length of 1,608 bp. After corrections were performed in conjunction with the NGS reads, we ultimately identified 1,695,064 open reading frames including 21,486 full-length ORFs and 7,342 genes encoding transcription factors from 55 TF families, together with 2,230 genes encoding long non-coding RNAs. Members of gene families related to anion channels/transporters, including members of the SLAC and CLC families, were identified and characterized.

CONCLUSIONS

The full-length transcriptome of cigar tobacco was obtained, annotated, and analyzed, providing a valuable genetic resource for future studies in cigar tobacco.

Comparative transcriptome analysis of genes involved in the drought stress response of two peanut (Arachis hypogaea L.) varieties

BACKGROUND

The peanut is one of the most important oil crops worldwide. Qualities and yields of peanut can be dramatically diminished by abiotic stresses particularly by drought. Therefore, it would be beneficial to gain a comprehensive understanding on peanut drought-responsive transcriptional regulatory activities, and hopefully to extract critical drought-tolerance-related molecular mechanism from it.

RESULTS

In this study, two peanut Arachis hypogaea L. varieties, NH5 (tolerant) and FH18 (sensitive), which show significantly differential drought tolerance, were screened from 23 main commercial peanut cultivars and used for physiological characterization and transcriptomic analysis. NH5 leaves showed higher water and GSH contents, faster stomatal closure, and lower relative conductivity (REC) than FH18. Under the time-course of drought-treatments 0 h (CK), 4 h (DT1), 8 h (DT2) and 24 h (DT3), the number of down-regulated differential expressed genes (DEGs) increased with the progression of treatments indicating repressive impacts on transcriptomes by drought in both peanut varieties.

CONCLUSIONS

Nevertheless, NH5 maintained more stable transcriptomic dynamics than FH18. Furthermore, annotations of identified DEGs implicate signal transduction, the elimination of reactive oxygen species, and the maintenance of cell osmotic potential which are key drought-tolerance-related pathways. Finally, evidences from the examination of ABA and SA components suggested that the fast stomatal closure in NH5 was likely mediated through SA rather than ABA signaling. In all, these results have provided us a comprehensive overview of peanut drought-responsive transcriptomic changes, which could serve as solid foundation for further identification of the molecular drought-tolerance mechanism in peanut and other oil crops.

Changes in photosynthesis and respiratory metabolism of maize seedlings growing under low temperature stress may be regulated by arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi as an important soil microbe have been demonstrated to mitigate the harmful effects of stress on plants. However, little is known about the molecular mechanisms underlying the AM symbiotic response to low temperature. Here, differentially expressed genes (DEGs) in the maize seedlings were identified after inoculating AMF under low temperature conditions. A total of 10,400 DEGs were obtained among four treatments, including non-inoculated AMF under ambient temperature (NMA), inoculated AMF under ambient temperature (MA), non-inoculated with low temperature stress (NML), and inoculated with low temperature stress (ML). The relative expression of 858 genes increased and that of 497 genes decreased in AM plants under low temperature stress. 24 DEGs were identified related to photosynthesis and respiratory metabolism. Among these DEGs, 10 genes were upregulated, and 14 genes were downregulated. The results show that inoculating AMF might decrease the production and transmission of electrons under low temperature, and the cyclic electron flow process in chloroplasts was stimulated to protect plants against low temperature. The fungi also influenced transmission of electrons and production of phosphoric acid in mitochondria in response to low temperature. CO₂ assimilation capacity was affected and the tricarboxylic acid cycle was promoted by the adjustments in the glycolysis, pentose phosphate pathway, gamma-aminobutyric acid shunt pathway, and glyoxylic acid cycle to produce more adenosine triphosphate and raw materials for other metabolic pathways under low temperature. These findings provide new insight into low temperature tolerance induced by AMF, and help identify genes for further investigation and functional analyses.

Research Progress on Plant Long Non-Coding RNA

Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.