Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses.

BACKGROUND: AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. RESULTS: A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. CONCLUSION: A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

[Identification and analysis of NAC family in ginger(Zingiber officinale) based on RNA-seq data].

The NAC family is an important transcription factor which regulate plant growth and development， signal transduction， and stress response.In this study， the protein identification， subfamily classification， the determination of physical and chemical properties， protein structure， and expression pattern of NAC family were performed using bioinformatic methods based on the RNA-seq data of ginger. The results showed that a total of 72 NAC transcription factors were identified in 271.1 Mb total nucleotides， and they could be clustered into 13 subfamilies according to the phylogenetic tree.The physical and chemical properties， structure analysis revealed that the amino acid number and isoelectric point were different among 13 NAC subfamilies; the secondary structure of NACs transcription factors mainly consist of random coil， and the tertiary structure is similar.In addition，the expression patterns of genes under different soil moisture and Ralstonia solanacearum infection showed that 23 NACs were differentially expressed， which were mainly distributed in Ⅷ，Ⅶ， and ⅩⅤ subfamilies related to plant senescence， hormone metabolism and cell wall metabolism.The results provide some valuable information for the research and development of NAC transcription factors in ginger.

Characterization and expression of Rubisco activase genes in Ipomoea batatas.

Two-dimensional electrophoresis, coupled with MALDI-TOF-MS, was used to identify differentially expressed proteins between young and mature leaves of sweet potato [Ipomoea batatas (L.) Lam]. The results showed that there were 25 differential proteins between young and mature leaves. The Rubisco activase (RCA) that catalyzes the activation of Rubisco in vivo and plays a crucial role in photosynthesis was among these 25 proteins. So far, little was known about the molecular biology of RCA in sweet potato. Here, this research reports the cloning and characterization of two genes encoding the short isoform and the long isoform of sweet potato RCAs. Analysis of DNA sequences of RCA suggested that the corresponding mRNAs were transcribed from two different genes. To study the roles of these two RCA isoforms in photosynthesis, we investigated the expression patterns of these RCA genes at the mRNA and protein levels every 2 h in a photoperiod and under different temperatures conditions. The results indicated that these two RCA isoforms may play different roles in regulating photosynthesis and they may be regulated by light, heat or both. In addition, there were interactions between Rubisco large subunit (RBCl) and short isoform RCA (RCAs) as well as RCAs and long isoform RCA (RCAl), but no interaction between RBCl and RCAl, implying they might form a sandwich-like structure (RBCl-RCAs-RCAl), at least in yeast cells. These results provided new information on the modulation of RCA genes in sweet potato, which could be useful in improving photosynthesis and plant growth in sweet potato.

Transcriptome analysis to identify putative floral-specific genes and flowering regulatory-related genes of sweet potato.

Sweet potato flowers were collected for a transcriptome analysis to identify the putative floral-specific and flowering regulatory-related genes by using the RNA-sequencing technique. Pair-end short reads were de novo assembled by an integrated strategy, and then the floral transcriptome was carefully compared with several published vegetative transcriptomes. A total of 2595 putative floral-specific and 2928 putative vegetative-specific transcripts were detected. We also identified a large number of transcripts similar to the key genes in the flowering regulation network of Arabidopsis thaliana.

Transcriptome profiles reveal gene regulation of ginger flowering induced by photoperiod and light quality.

BACKGROUND: Under natural conditions, ginger (Zingiber officinale Rosc.) rarely blossom and has seed, which limits new variety breeding of ginger and industry development. In this study, the effects of different photoperiods and light quality on flowering induction in ginger were performed, followed by gene expression analysis of flower buds differentiation under induced treatment using RNA-seq technology. RESULTS: First, both red light and long light condition (18 h light/6 h dark) could effectively induce differentiation of flower buds in ginger. Second, a total of 3395 differentially expressed genes were identified from several different comparisons, among which nine genes, including CDF1, COP1, GHD7, RAV2-like, CO, FT, SOC1, AP1 and LFY, were identified to be associated with flowering in induced flower buds and natural leaf buds. Aside from four down-regulated genes (CDF1, COP1, GHD7 and RAV2-like), other five genes were all up-regulated expression. These differentially expressed genes were mainly classified into 2604 GO categories, which were further enriched into 120 KEGG metabolic pathways. Third, expression change of flowering-related genes in ginger indicated that the induction may negatively regulated expression of CDF1, COP1, GHD7 and RAV2-like, and subsequently positively regulated expression of CO, FT, SOC1, LFY and AP1, which finally led to ginger flowering. In addition, the RNA-seq results were verified by qRT-PCR analysis of 18 randomly selected genes, which further demonstrated the reliability of transcriptome analysis. CONCLUSION: This study revealed the ginger flowering mechanism induced by light treatment and provided abundant gene information, which contribute to the development of hybrid breeding of ginger.

Molecular Mechanism of miR160d in Regulating Kiwifruit Resistance to Botrytis cinerea.

Gray mold caused by Botrytis cinerea leads to huge economic losses to the kiwifruit (Actinidia chinensis) industry. Elucidating the molecular mechanism responding to B. cinerea is the theoretical basis for the resistance to molecular breeding of kiwifruit. Previous studies have shown that miR160 regulates plant disease resistance through the indole-3-acetic acid (IAA) signaling pathway. In this study, kiwifruit "Hongyang" was used as the material, and Ac-miR160d and its target genes were identified and cloned. Overexpression and virus-induced gene silencing (VIGS) technology combined with RNA-seq were adopted to analyze the regulatory role of Ac-miR160d in kiwifruit resistance to B. cinerea. Silencing Ac-miR160d (AcMIR160d-KN) increased kiwifruit sensitivity to B. cinerea, whereas overexpression of Ac-miR160d (AcMIR160d-OE) increased kiwifruit resistance to B. cinerea, suggesting that Ac-miR160d positively regulates kiwifruit resistance to B. cinerea. In addition, overexpression of Ac-miR160d in kiwifruit increased antioxidant enzyme activities, such as catalase (CAT) and superoxide dismutase (SOD), and endogenous phytohormone IAA and salicylic acid (SA) content, in response to B. cinerea-induced stress. RNA-seq identified 480 and 858 unique differentially expressed genes in the AcMIR160d-KN vs CK and AcMIR160d-OE vs CK groups, respectively, with fold change ≥2 and false discovery rate <0.01. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that families associated with "biosynthesis of secondary metabolites" are possibly regulated by Ac-miR160d. "Phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "terpenoid backbone biosynthesis" were further activated in the two comparison groups upon B. cinerea infection. Our results may reveal the molecular mechanism by which miR160d regulates kiwifruit resistance to B. cinerea and may provide gene resources for molecular breeding in kiwifruit resistance.

Nitroglycerin improves the visibility of fibula-free flap perforators on computed tomography angiography in patients with oral or maxillofacial lesion.

PURPOSE: To investigate the improvement of image quality and visualization of fibula-free flap (FFF) perforators on computed tomography angiography (CTA) after administration of sublingual nitroglycerin (NTG) tablets. METHODS: A total of 60 patients with oral or maxillofacial lesions before CTA of the lower extremity were randomly divided into two groups (NTG group and non-NTG group). The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), overall image quality and grading of vessels were evaluated and compared. The lumen diameters of the major arteries and the proximal and distal peroneal perforators were measured. The number of visible perforators in muscular clearance and muscular layer was also counted and compared between the two groups. RESULTS: The CNR of posterior tibial artery and overall image quality of CTA images in the NTG group was significantly higher than that in the non-NTG group (p < 0.05), although the SNR and CNR of other arteries did not show significant differences (p > 0.05). The lumen diameters of the peroneal artery and its perforators, anterior tibial artery, and posterior tibial artery were significantly larger in the NTG group (p < 0.001), while no significant difference prevailed in the diameter of the popliteal artery between the two groups (p = 0.298). Compared with the non-NTG group, a significant increase in the number of visible perforators was noted in the NTG group (p < 0.001). CONCLUSIONS: The administration of sublingual NTG in CTA of the lower extremity can improve the image quality and visualization of perforators, which aids to surgeons select the optimum FFF.

Improving visualization of free fibula flap perforators and reducing radiation dose in dual-energy CT angiography.

Background: The precise assessment of the perforators of the fibula free flap (FFF) is crucial for minimizing procedure-related complications when harvesting the FFF in patients with maxillofacial lesions. This study aims to investigate the utility of virtual noncontrast (VNC) images for radiation dose saving and to determine the optimal energy level of virtual monoenergetic imaging (VMI) reconstructions in dual-energy computed tomography (DECT) for visualization of the perforators of the fibula free flap (FFF). Methods: Data from 40 patients with maxillofacial lesions who received lower extremity DECT examinations in the noncontrast and arterial phase were collected in this retrospective, cross-sectional study. To compare VNC images from the arterial phase with true non-contrast images in a DECT protocol (M_0.5-TNC) and to compare VMI images with 0.5 linear images blending from the arterial phase (M_0.5-C), the attenuation, noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and subjective image quality were assessed in different arteries, muscles, and fat tissues. Two readers evaluated the image quality and visualization of the perforators. The dose-length product (DLP) and CT volume dose index (CTDIvol) were used to determine the radiation dose. Results: Objective and subjective analyses showed no significant difference between the M_0.5-TNC and VNC images in the arteries and muscles (P>0.09 to P>0.99), and VNC imaging could reduce 50% of the radiation dose (P<0.001). Compared with those of the M_0.5-C images, the attenuation and CNR of VMI reconstructions at 40 kiloelectron volt (keV) and 60 keV were higher (P<0.001 to P=0.04). Noise was similar at 60 keV (all P>0.99) and increased at 40 keV (all P<0.001), and the SNR in arteries was increased at 60 keV (P<0.001 to P=0.02) in VMI reconstructions compared with those in the M_0.5-C images. The subjective scores in VMI reconstructions at 40 and 60 keV was higher than those in M_0.5-C images (all P<0.001). The image quality at 60 keV was superior to that at 40 keV (P<0.001), and there was no difference in the visualization of the perforators between 40 and 60 keV (P=0.31). Conclusions: VNC imaging is a reliable technique for replacing M_0.5-TNC and provides radiation dose saving. The image quality of the 40-keV and 60-keV VMI reconstructions was higher than that of the M_0.5-C images, and 60 keV provided the best assessment of perforators in the tibia.

Evaluation of Quantitative Dual-Energy Computed Tomography Parameters for Differentiation of Parotid Gland Tumors.

RATIONALE AND OBJECTIVES: To assess the diagnostic performance of quantitative parameters from dual-energy CT (DECT) in differentiating parotid gland tumors (PGTs). MATERIALS AND METHODS: 101 patients with 108 pathologically proved PGTs were enrolled and classified into four groups: pleomorphic adenomas (PAs), warthin tumors (WTs), other benign tumors (OBTs), and malignant tumors (MTs). Conventional CT attenuation and DECT quantitative parameters, including iodine concentration (IC), normalized iodine concentration (NIC), effective atomic number (Zeff), electron density (Rho), double energy index (DEI), and the slope of the spectral Hounsfield unit curve (λHU), were obtained and compared between benign tumors (BTs) and MTs, and further compared among the four subgroups. Logistic regression analysis was used to assess the independent parameters and the receiver operating characteristic (ROC) curves were used to analyze the diagnostic performance. RESULTS: Attenuation, Zeff, DEI, IC, NIC, and λHU in the arterial phase (AP) and venous phase (VP) were higher in MTs than in BTs (p < 0.001-0.047). λHU in VP and Zeff in AP were independent predictors with an area under the curve (AUC) of 0.84 after the combination. Furthermore, attenuation, Zeff, DEI, IC, NIC, and λHU in the AP and VP of MTs were higher than those of PAs (p < 0.001-0.047). Zeff and NIC in AP and λHU in VP were independent predictors with an AUC of 0.93 after the combination. Attenuation and Rho in the precontrast phase; attenuation, Rho, Zeff, DEI, IC, NIC, and λHU in AP; and the Rho in the VP of PAs were lower than those of WTs (p < 0.001-0.03). Rho in the precontrast phase and attenuation in AP were independent predictors with an AUC of 0.89 after the combination. MTs demonstrated higher Zeff, DEI, IC, NIC, and λHU in VP and lower Rho in the precontrast phase compared with WTs (p < 0.001-0.04); but no independent predictors were found. CONCLUSION: DECT quantitative parameters can help to differentiate PGTs.

A proteomic analysis of storage stress responses in Ipomoea batatas (L.) Lam. tuberous root.

During post-harvest storage, tuberous roots of sweet potato (Ipomoea batatas L. Lam.) usually undergo a biotic and abiotic stress influencing protein expression pattern and substance contents. This research compared the change of total proteins and carbohydrate content in tuberous roots of sweet potato during the storage period. The result of the two-dimensional electrophoresis analysis demonstrated that there were 25 differentially expressed proteins between day 0 and day 75 during the storage. Among these proteins, 11 proteins were down-regulated and the other 14 were up-regulated. The results from MALDI-TOF-TOF/MS analyses and mascot database searching showed that 11 of the 25 differentially expressed proteins were identified as store-stress regulated proteins. It was also found that the proteins involved in the energy metabolism and the stress-response were drastically up-regulated, whereas those in biomacromolecule synthesis were markedly down-regulated. Meanwhile, under the experimental conditions, the content of the starch and the cellulose was decreased by more than a quarter and the amylase activity was increased moderately.

Dual RNA Sequencing Reveals the Genome-Wide Expression Profiles During the Compatible and Incompatible Interactions Between Solanum tuberosum and Phytophthora infestans.

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating plant disease. P. infestans genome encodes hundreds of effectors, complicating the interaction between the pathogen and its host and making it difficult to understand the interaction mechanisms. In this study, the late blight-resistant potato cultivar Ziyun No.1 and the susceptible potato cultivar Favorita were infected with P. infestans isolate SCPZ16-3-1 to investigate the global expression profiles during the compatible and incompatible interactions using dual RNA sequencing (RNA-seq). Most of the expressed Arg-X-Leu-Arg (RXLR) effector genes were suppressed during the first 24 h of infection, but upregulated after 24 h. Moreover, P. infestans induced more specifically expressed genes (SEGs), including RXLR effectors and cell wall-degrading enzymes (CWDEs)-encoding genes, in the compatible interaction. The resistant potato activated a set of biotic stimulus responses and phenylpropanoid biosynthesis SEGs, including kirola-like protein, nucleotide-binding site-leucine-rich repeat (NBS-LRR), disease resistance, and kinase genes. Conversely, the susceptible potato cultivar upregulated more kinase, pathogenesis-related genes than the resistant cultivar. This study is the first study to characterize the compatible and incompatible interactions between P. infestans and different potato cultivars and provides the genome-wide expression profiles for RXLR effector, CWDEs, NBS-LRR protein, and kinase-encoding genes.

Comparative Metabolomic Profiling of Compatible and Incompatible Interactions Between Potato and Phytophthora infestans.

Late blight is one of the main biological stresses limiting the potato yield; however, the biochemical mechanisms underlying the infection process of Phytophthora infestans remain unrevealed. In this study, the late blight-resistant potato cultivar Ziyun No.1 (R) and the susceptible cultivar Favorita (S) were inoculated with P. infestans. Untargeted metabolomics was used to study the changes of metabolites in the compatible and incompatible interactions of the two cultivars and the pathogen at 0, 48, and 96 h postinoculation (hpi). A total of 819 metabolites were identified, and the metabolic differences mainly emerged after 48 hpi. There were 198 and 115 differentially expressed metabolites (DEMs) in the compatible and incompatible interactions. These included 147 and 100 upregulated metabolites during the compatible and incompatible interactions, respectively. Among them, 73 metabolites were identified as the P. infestans-responsive DEMs. Furthermore, the comparisons between the two cultivars identified 57 resistance-related metabolites. Resistant potato cultivar had higher levels of salicylic acid and several upstream phenylpropanoid biosynthesis metabolites, triterpenoids, and hydroxycinnamic acids and their derivatives, such as sakuranetin, ferulic acid, ganoderic acid Mi, lucidenic acid D2, and caffeoylmalic acid. These metabolites play crucial roles in cell wall thickening and have antibacterial and antifungal activities. This study reports the time-course metabolomic responses of potatoes to P. infestans. The findings reveal the responses involved in the compatible and incompatible interactions of potatoes and P. infestans.

Preoperative Prediction of the Aggressiveness of Oral Tongue Squamous Cell Carcinoma with Quantitative Parameters from Dual-Energy Computed Tomography.

Objectives: To determine whether quantitative parameters derived from dual-energy computed tomography (DECT) were predictive of the aggressiveness of oral tongue squamous cell carcinoma (OTSCC) including the pathologic stages, histologic differentiation, lymph node status, and perineural invasion (PNI). Methods: Between August 2019 and March 2021, 93 patients (mean age, 54.6 ± 13.8 years; 66 men) with pathologically diagnosed OTSCC were enrolled in this prospective study. Preoperative DECT was performed and quantitative parameters (e.g., slope of the spectral Hounsfield unit curve [λHu], normalized iodine concentration [nIC], normalized effective atomic number [nZeff], and normalized electron density [nRho]) were measured on arterial phase (AP) and venous phase (VP) DECT imaging. Quantitative parameters from DECT were compared between patients with different pathologic stages, histologic differentiation, lymph node statuses, and perineural invasion statuses. Logistic regression analysis was utilized to assess independent parameters and the diagnostic performance was analyzed by the receiver operating characteristic curves (ROC). Results: λHu and nIC in AP and λHu, nZeff, and nIC in VP were significantly lower in stage III-IV lesions than in stage I-II lesions (p < 0.001 to 0.024). λHu in VP was an independent predictor of tumor stage with an odds ratio (OR) of 0.29, and area under the curve (AUC) of 0.80. λHu and nIC were higher in well-differentiated lesions than in poorly differentiated lesions (p < 0.001 to 0.021). The nIC in VP was an independent predictor of histologic differentiation with OR of 0.31, and AUC of 0.78. λHu and nIC in VP were lower in OTSCCs with lymph node metastasis than those without metastasis (p < 0.001 to 0.005). λHu in VP was the independent predictor of lymph node status with OR of 0.42, and AUC of 0.74. No significant difference was found between OTSCCs without PNI and those with PNI in terms of the quantitative DECT parameters. Conclusion: DECT can be a complementary means for the preoperative prediction of the aggressiveness of OTSCC.

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale).

BACKGROUND: Cytochrome P450s play crucial roles in various biosynthetic reactions. Ginger (Zingiber officinale), which is often threatened by Ralstonia solanacearum, is the most economically important crop in the family Zingiberaceae. Whether the cytochrome P450 complement (CYPome) significantly responds to this pathogen has remained unclear. METHODS: Transcriptomic responses to R. solanacearum and soil moisture were analyzed in ginger, and expression profiles of the CYPome were determined based on transcriptome data. RESULTS: A total of 821 P450 unigenes with ORFs ≥ 300 bp were identified. Forty percent soil moisture suppressed several key P450 unigenes involved in the biosynthesis of flavonoids, gingerols, and jasmonates, including unigenes encoding flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, steroid 22-alpha-hydroxylase, cytochrome P450 family 724 subfamily B polypeptide 1, and allene oxide synthase. Conversely, the expression of P450 unigenes involved in gibberellin biosynthesis and abscisic acid catabolism, encoding ent-kaurene oxidase and abscisic acid 8'-hydroxylase, respectively, were promoted by 40% soil moisture. Under R. solanacearum infection, the expression of P450 unigenes involved in the biosynthesis of the above secondary metabolites were changed, but divergent expression patterns were observed under different soil moisture treatments. High moisture repressed expression of genes involved in flavonoid, brassinosteroid, gingerol, and jasmonate biosynthesis, but promoted expression of genes involved in GA anabolism and ABA catabolism. These results suggest possible mechanisms for how high moisture causes elevated susceptibility to R. solanacearum infection.

Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway.

Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger 'Zhugen', a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3'H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

Transcriptome analysis provides novel insights into high-soil-moisture-elevated susceptibility to Ralstonia solanacearum infection in ginger (Zingiber officinale Roscoe cv. Southwest).

Ginger (Zingiber officinale Roscoe), one of the most economically valuable plants in the Zingiberaceae family, is widely used as a spice and flavoring agent for beverages, bakery, confectionary, and pharmaceutics. Bacterial wilt disease, caused by Ralstonia solanacearum, is one of the most detrimental production constraints in ginger cultivation. Field cultivation experiments indicated that soil moisture affects the incidence of bacterial wilt disease. However, the relationship between soil moisture and bacterial wilt incidence as well as the mechanism that underlie this infection remain unclear. This study confirms that high soil moisture elevates the susceptibility to R. solanacearum infection; transcriptome sequencing was performed to elucidate the underlying mechanisms. Differential expression indicates that a small number of genes is involved in both the response to high soil moisture as well as post successful R. solanacearum infection; furthermore, a large number of genes is involved in the defense of the infection. In response to high soil moisture, higher ABA contents, and higher expression levels of ABF4 may be related to higher tiller density in ginger. More importantly, WAK16 and WAK3-2 may be determinative genes that weaken the resistance to R. solanacearum in ginger under high soil moisture. The down-regulated expression levels of PRX, CPY, and XET genes indicate that in response to successful R. solanacearum infection, the normal cell wall metabolism may be disturbed and the hypersensitive response may be inhibited. In summary, our study deepens our understanding of the molecular mechanisms of the soil moisture dependent wilt susceptibility of ginger.

Transcriptome Analysis Provides Insights into Gingerol Biosynthesis in Ginger (Zingiber officinale).

Ginger ( Roscoe), a perennial herb, is one of the most economically valuable plants in the Zingiberaceae family. Gingerol, as the major constituents of ginger essential oil, contributes to the unique flavor and pharmaceutical value of ginger. However, the pathway of gingerol biosynthesis has not been verified and described in ginger to help understand the biosynthesis of secondary metabolites in nonmodel species. In this study, the concentrations of gingerols were quantified at different stages of rhizome development and in different tissues. The results confirmed that rhizomes are the major source of gingerols and that accumulation of gingerols in the rhizome starts at an early developmental stage. We also assembled a reference ginger transcriptome, which is composed of 219,479 unigenes consisting of 330,568 transcripts and provides a high-quality genetic resource for further research. An analysis of differentially expressed genes (DEGs) identified 12,935 DEGs among several different comparisons. Five genes [ (), (), p (), O (), and ()] associated with gingerol biosynthesis were identified as being significantly differentially expressed in the rhizome at an early developmental stage and all five genes were upregulated. Expression analysis revealed that different loci of these genes have become functionally specialized in different tissues and different developmental stages of the rhizome (subfunctionalization). Among the DEGs, and may act as gatekeepers and rate-limiting enzymes in the gingerol biosynthesis pathway and thus play an important role in regulating the biosynthesis of gingerol.

Transcriptome analysis reveals the genetic basis underlying the biosynthesis of volatile oil, gingerols, and diarylheptanoids in ginger (Zingiber officinale Rosc.).

BACKGROUND: Ginger (Zingiber officinale Rosc.) is a popular flavoring that widely used in Asian, and the volatile oil in ginger rhizomes adds a special fragrance and taste to foods. The bioactive compounds in ginger, such as gingerols, diarylheptanoids, and flavonoids, are of significant value to human health because of their anticancer, anti-oxidant, and anti-inflammatory properties. However, as a non-model plant, knowledge about the genome sequences of ginger is extremely limited, and this limits molecular studies on this plant. In this study, de novo transcriptome sequencing was performed to investigate the expression of genes associated with the biosynthesis of major bioactive compounds in matured ginger rhizome (MG), young ginger rhizome (YG), and fibrous roots of ginger (FR). RESULTS: A total of 361,876 unigenes were generated by de novo assembly. The expression of genes involved in the pathways responsible for the biosynthesis of major bioactive compounds differed between tissues (MG, YG, and FR). Two pathways that give rise to volatile oil, gingerols, and diarylheptanoids, the "terpenoid backbone biosynthesis" and "stilbenoid, diarylheptanoid and gingerol biosynthesis" pathways, were significantly enriched (adjusted P value < 0.05) for differentially expressed genes (DEGs) (FDR < 0.005) both between the FR and YG libraries, and the FR and MG libraries. Most of the unigenes mapped in these two pathways, including curcumin synthase, phenylpropanoylacetyl-CoA synthase, trans-cinnamate 4-monooxygenase, and 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, were expressed to a significantly higher level (log2 (fold-change) ≥ 1) in FR than in YG or MG. CONCLUSION: This study provides the first insight into the biosynthesis of bioactive compounds in ginger at a molecular level and provides valuable genome resources for future molecular studies on ginger. Moreover, our results establish that bioactive compounds in ginger may predominantly synthesized in the root and then transported to rhizomes, where they accumulate.

Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians' skin.

Skin as the first barrier against external invasions plays an essential role for the survival of amphibians on land. Understanding the genetic basis of skin function is significant in revealing the mechanisms underlying immunity of amphibians. In this study, we de novo sequenced and comparatively analyzed skin transcriptomes from three different amphibian species, Andrias davidianus, Bufo gargarizans, and Rana nigromaculata Hallowell. Functional classification of unigenes in each amphibian showed high accordance, with the most represented GO terms and KEGG pathways related to basic biological processes, such as binding and metabolism and immune system. As for the unigenes, GO and KEGG distributions of conserved orthologs in each species were similar, with the predominantly enriched pathways including RNA polymerase, nucleotide metabolism, and defense. The positively selected orthologs in each amphibian were also similar, which were primarily involved in stimulus response, cell metabolic, membrane, and catalytic activity. Furthermore, a total of 50 antimicrobial peptides from 26 different categories were identified in the three amphibians, and one of these showed high efficiency in inhibiting the growth of different bacteria. Our understanding of innate immune function of amphibian skin has increased basis on the immune-related unigenes, pathways, and antimicrobial peptides in amphibians.

Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene from Ipomoea batatas (L.) Lam.

As an indicator of the antioxidant capability of plants, catalase can detoxify reactive oxygen species (ROS) generated by environmental stresses. Sweet potato is one of the top six most important crops in the world. However, its catalases remain largely unknown. In this study, a catalase encoding gene, IbCAT2 (accession number: KY615708), was identified and cloned from sweet potato cv. Xushu 18. It contained a 1479 nucleotides' open reading frame (ORF). S-R-L, Q-K-L, and a putative calmodulin binding domain were located at the C-terminus of IbCAT2, which suggests that IbCAT2 could be a peroxisomal catalase. Next-generation sequencing (NGS) based quantitative analyses showed that IbCAT2 was mainly expressed in young leaves and expanding tuberous roots under normal conditions. When exposed to 10% PEG6000 or 200 mmol/L NaCl solutions, IbCAT2 was upregulated rapidly in the first 11 days and then downregulated, although different tissues showed different degree of change. Overexpression of IbCAT2 conferred salt and drought tolerance in Escherichia coli and Saccharomyces cerevisiae. The positive response of IbCAT2 to abiotic stresses suggested that IbCAT2 might play an important role in stress responses.