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The emergence of environmental endocrine disruptor chlorobenzene (CB) in surface water and its potential environmental impacts have attracted serious global attention. It is still very difficult to achieve effective degradation of it by catalytic oxidation process under mild conditions. Here, an optimized method for degrading CB in aqueous solution using Trametes versicolor laccase and surfactant-assisted laccase-mediator (SALM) system was investigated. The use of a Tween 80 surfactant enhanced the solubility of CB and promoted its efficient degradation. Under favorable conditions, the SALM system yielded a degradation efficiency of 43.5% and a dechlorination efficiency of 41.55% for CB (25 mg/L) within 24 h. The possible degradation pathway of CB by this system was speculated by detecting the intermediates produced during the reaction. The outcome of the proliferation assays on MCF-7 human breast cancer cells demonstrated a reduction in the estrogenic activity of the CB solution following treatment with the SALM system. Furthermore, the influence of the quantity and positional variation of chlorine substituents on the degradation process was methodically investigated. Moreover, molecular analyses were employed to study the detailed interaction mechanism between laccase and CB, which revealed that the hydrophobic interaction contributed dominantly to binding process. These findings provide an efficient and environmentally friendly degradation system for the development of purification strategies for halogenated pollutants.

Summary: Apocynum species have great application prospects in textile and phytoremediation of saline soil, are rich in flavonoids, and possess medicinal significance. Here, we report the draft genomes of Apocynum venetum and Apocynum hendersonii, and elucidate their evolutionary relationship. The high synteny and collinearity between the two suggested that they have experienced the same WGD event. Comparative analysis revealed that flavone 3-hydroxylase (ApF3H) and differentially evolved flavonoid 3-O-glucosyl transferase (ApUFGT) genes are critical for determining natural variation in flavonoid biosynthesis between the species. Overexpression of ApF3H-1 enhanced the total flavonoid content and promoted the antioxidant capacity of transformed plants compared to the wild-type. ApUFGT5 and 6 explained the diversification of flavonoids or their derivatives. These data provide biochemical insight and knowledge on the genetic regulation of flavonoid biosynthesis, supporting the adoption of these genes in breeding programs aimed at the multipurpose utilization of the plants.

Ramie (Boehmeria nivea L.) bast fiber is one of the most ancient natural fibers, which is used for textile only after degumming. Hemicellulose, pectin, and hydrotrope are the main colloidal matters in ramie fiber, which are removed when degumming. However, the genetic variation and control loci are poorly understood. Here, we analyzed the genetic variation of the colloidal matters and discovered the favorable single nucleotide poly morphisms (SNP) by genome-wide association study using 319 ramie core germplasms. In total, 21, 5, and 10 SNPs were found to be the significantly key control loci associated with hemicellulose, pectin, and hydrotrope, respectively, which changed the amino acid sequences of the reference genes. Fourteen key genes involved in various sugars biosynthesis and metabolism pathways were identified to regulate the hemicellulose content in ramie. Meanwhile, 7 calcium transporting or binding related genes were identified to involve in the biosynthesis of calcium magnesium pectinate-the main component of pectin. Moreover, 306 genes related to hydrotrope were identified and their function were also discussed. Our study first reveals the genetic variation and candidate genes related to the colloidal matters of ramie bast fiber, and provides tools for marker-assisted selection in improvement of agricultural traits.

To provide a theoretical and practical foundation for the genetic analysis of Apocynum species, SSRs were identified based on the transcriptomic data of A.hendersonii leaves. A total of 50,957 unigenes containing 5 660 SSR motifs with an average of 1 SSR locus per 9.09 Kb were identified. The dinucleotide repeat motifs were the most prevalent, having 48.23% of the total repeat, with the dominant repeats being AG/CT (1,703) followed by A/T (1,222). Furthermore, the results of genetic relationship analsyis based on the allele polymorphism of the selected SSR primer showed that A. hendersonii and A.venetum grouped into various clades, and those from different regions clusted into different subgroups.These identified SSR markers may provide a foundation for genetic identification, diversity analysis and marker-assisted genetic breeding in Apocynum species.

Ramie (Boehmeria nivea L.), belonging to Urticaceae, is principally used for fabric production. It is a well-known natural fiber material for ancient clothing. Despite its important position and application value, the understanding on genetic regulation mechanism of fiber quality is limited. Here, we generate a chromosome-scale, high-quality reference genome of ramie, in which, approximately 90.2% of the assembled sequences have been anchored to 14 pseudochromosomes. Totally 27,664 protein-coding genes are predicted which cover 268.24 Mb region of the genome. Comparative genomic analysis reveals that 2,047 and 796 gene clusters expand and contract, respectively, underlying significant genes in plant hormone signal transduction and cellulose/lignin biosynthesis pathways. An integrative analysis combining quantitative trait loci (QTL), comparative transcriptomic data, and cytological experiments unravels the molecular regulatory mechanism of ramie fiber fineness, especially the critical regulating role of ethylene. This study would lay a solid foundation for the research of molecular biology in ramie and provide valuable reference for the improvement of high-quality fiber varieties.

Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.

Abstract Abscisic acid (ABA) is known as an important hormone regulating plant stress resistance, such as salt, drought and heavy metal resistance. However, the relationship between ABA and cadmium (Cd) enrichment in ramie (Boehmeria nivea L.) is still unclear to date. This study aimed to reveal the effect of ABA on Cd enrichment in ramie, and we received the following results: (1) Under Cd treatment, the Cd uptake of ramie increased with the increase of Cd concentration, but the chlorophyll content decreased. Under Cd treatment, the ABA content was highest in roots of ramie, followed by that in old leaves, and lowest in new leaves. Long-time treatment of high Cd concentration reduced the ability of endogenous ABA biosynthesis. (2) Spraying ABA on ramie plants (SORP) and adding ABA directly to the culture solution (ADCS) with low concentration can promote the growth of ramie and increase the amount of Cd uptake, and the effect of SORP is better. (3) The molecular reason for the decrease of chlorophyll content due to Cd stress, may be resulted from the down-regulated expression of the chlorophyll synthesis genes (BnPAO and BnNYC1) and the up-regulated expression of the chlorophyll degradation genes (BnCHLH, BnCHLG, BnHAP3A and BnPPR1). The elevated ABA content in ramie plants may due to the up-regulated expression of the ABA synthesis related genes (BnABA1, BnNCED3, and BnNCED5) and the genes (BnABCG40, BnNFXL2, BnPYL9, BnGCR2, BnGTG1, BnBGLU1, BnUTG1, BnVHAG1 and BnABI5) that encoding ABA transport and response proteins, which was consistent with the enhance the Cd uptake in ramie. Our study revealed the relationship between ABA and Cd uptake in ramie, which provided a reference for improving the enrichment of Cd in ramie.

Abstract Background The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie variety with a light reddish brown leaf color, which is obviously different from elite cultivar, Zhongzhu No.1 (ZZ_1, green leaf). While, the regulatory mechanism of color difference or secondary metaboliates synthesis between these two varieties have not been studied. Results In this study, phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 were conducted to elucidate the mechanism of leaf color formation. Chromaticity value and pigment content measuring showed that anthocyanin was the main metabolites imparting the different leaf color phenotype between the two varieties. Based on LC/MS, at least 14 anthocyanins were identified in leaves of HX_1 and ZZ_1, and the HX_1 showed the higher relative content of malvidin-, pelargonidin-,and cyanidin-based anthocyanins. Transcriptome and metabolome co-analysis revealed that the up-regulated expression of flavonoids synthesis gene was positively correlated with total anthocyanins accumulation in ramie leaf, and the differentfially expression of “blue gene” (F3’5’H) and the “red gene” (F3’H) in leaves bring out HX_1 metabolic flow more input into the cyanidin branch. Furthermore, the enrichment of glycosylated modification pathway (UGT and AT) and the expression of flavonoid 3-O-glucosyl transferase (UFGT), anthocyanidin reductase (ANR), in leaves were significantly influenced the diversity of anthocyanins between HX_1 and ZZ_1. Conclusions Phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 indicated that the expression levels of genes related to anthocyanin metabolism contribute to the color formation of ramie variety. Anthocyanins are important plant secandary metabilates with many physiological functions, the results of this study will deepened our understanding of ramie leaf color formation, and provided basis for molecular breeding of functional forage ramie.

A total of 60 WRKY family genes of ramie were identified in the ramie. The genes were unevenly distributed across 14 chromosomes in the specie and highly concentrated (72%) in the distal telomeric region. Phylogenetic analysis placed these genes into seven distinct subfamilies groups: I, II (a, b, c, d, e), and III, with group IIc containing only the variant of heptapetide sequence (WRKYGKK). Segmental duplication events (41.7%) was found to be the main driver of BnGWRKY evolution. Thirty eight from among the genes showed collinear relationships with WRKY genes from Arabidopsis thaliana, Cannabis sativa, Oryza sativa, and Zea mays. The number and density of stress and hormone responsives cis-acting elements were comparably higher than other elements, with abundant ARE and rare LTR cis-acting elements indicating the long-standing adaptability of ramie to its natural environment. GO and KEGG enrichment analysis of the WRKY target genes revealed their involvement in response to stimuli, immune system processes, transporter protein activity and antioxidant activity. Expression analysis show that most WRKYs were activated by the cadmium stress, more especially the BnGWRKY2, BnGWRKY15, BnGWRKY20, BnGWRKY50 and BnGWRKY58. Combining transcriptome, orthologous gene relationships and qPCR result, we established the possible involvement of BnGWRKY50 and BnGWRKY58 in crosstalk mechanism between secondary cell wall thickening and Cd2+ stress. This provided information into the role of BnGWRKY proteins in ramie secondary wall development and cadmium stress response to, and could serve as basis for improvement of the ramie.

NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the most prominent plant-specific TF families and play essential roles in plant growth, development and adaptation to abiotic stress. Although the NAC gene family has been extensively characterized in many species, systematic analysis is still relatively lacking in Apocynum venetum (A. venetum). In this study, 74 AvNAC proteins were identified from the A. venetum genome and were classified into 16 subgroups. This classification was consistently supported by their gene structures, conserved motifs and subcellular localizations. Nucleotide substitution analysis (Ka/Ks) showed the AvNACs to be under the influence of strong purifying selection, and segmental duplication events were found to play the dominant roles in the AvNAC TF family expansion. Cis-elements analysis demonstrated that the light-, stress-, and phytohormone-responsive elements being dominant in the AvNAC promoters, and potential TFs including Dof, BBR-BPC, ERF and MIKC_MADS were visualized in the TF regulatory network. Among these AvNACs, AvNAC58 and AvNAC69 exhibited significant differential expression in response to drought and salt stresses. The protein interaction prediction further confirmed their potential roles in the trehalose metabolism pathway with respect to drought and salt resistance. This study provides a reference for further understanding the functional characteristics of NAC genes in the stress-response mechanism and development of A. venetum.

AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

In the current study, the total content from two Apocynum species leaves (Apocynum venetum and Apocynum hendersonii) collected from the Ili River Valley Region were extracted, and their bioactivities were investigated. The results showed a significant variation in the total flavonoid contents in the leaf samples collected at different periods (June, July, August, and September), with the highest content in August (60.11 ± 0.38 mg RE/g DW for A. venetum and 56.56 ± 0.24 mg RE/g DW for A. hendersonii), and the lowest in June (22.36 ± 0.05 mg RE/g DW for A. venetum and 20.79 ± 0.02 mg RE/g DW for A. hendersonii). The total flavonoid content was comparably higher in A. venetum than in A. hendersonii. Leaves extracts from the two species demonstrated strong bioactivity, which positively correlated with the total flavonoid contents. The anti-oxidative activity of A. venetum was higher than that of A. hendersonii in tandem with its higher flavonoid contents; the antibacterial activity, however, was conversely opposite. Furthermore, a total of 83 flavonoid metabolites were identified in the two species based on UPLC-ESI-MS/MS, out of which 24 metabolites were differentially accumulated. The variability in these metabolites might be the reason for the different bioactivities displayed by the two species. The present study provides insight into the optimal harvest time for Apocynum species planted in the major distribution area of the Ili River Valley and the specific utilization of A. venetum and A. hendersonii.

Ramie (Boehmeria nivea) is a perennial herb that is highly tolerant of heavy metals. In the present study, we cloned a novel metallothionein‐like gene from ramie; this gene, termed BnMTL, encodes a putative 46 amino acid protein with a molecular mass of 4.38 kDa. Analysis using quantitative RT‐PCR revealed that cadmium (Cd2+) treatment results in elevated expression of BnMTL in the roots. We heterologously overexpressed BnMTL in Escherichia coli cells to examine its binding to Cd2+ and its possible role in homeostasis. Recombinant E. coli cells expressing BnMTL exhibited a high tolerance of Cd2+ stress up to a concentration of 1 mm, and the observed accumulation of Cd2+ was almost eight‐fold higher than the control. These results demonstrate that BnMTL (i) is highly expressed in the root following exposure to Cd2+ and (ii) encodes a typical metallothionein‐like protein with high cadmium‐binding activity.

Apocynum hendersonii is a traditional medicinal plant used primarily as tea. It has a potential health benefit from its rich bioactive substances. This study investigated the reactivity of solvents of different polarities (ethanol, ethyl acetate, n-hexane, methanol, and water) extracts of the A. hendersonii leaf. The phytochemical composition of the extracts was evaluated using a Fourier Transform Infrared spectrophotometer (FT-IR), Gas Chromatography-Mass Spectrometry (GC-MS), UHPLC-MS, and Higher Performance Liquid Chromatography (HPLC). The result revealed the presence of medicinally important bioactive constituents, including phenols, flavonoids, and polysaccharides. Methanol extracts exhibited the highest flavonoid contents (20.11 ± 0.85 mg QE/g DW) and the second-highest in terms of phenolic (9.25 ± 0.03 mg GAE/g DW) and polysaccharide (119.66 ± 2.65 mg GE/g DW). It also had the highest antioxidant capacity with 60.30 ± 0.52% and 4.60 ± 0.02 µmol Fe2+ per g DW based on a 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and ferric reducing antioxidant power (FRAP), respectively. Ethanol extract displayed the maximum antibacterial action against Gram-negative and Gram-positive bacteria and the highest inhibition activity against the enzymes tyrosinase and acetylcholinesterase, followed by methanol extract. The principal component analysis revealed a positive correlation between the constituents, bioactivities, and extracts. The overall result showed A. hendersonii as a rich natural source of antimicrobial and antioxidant bioactive compounds and may be used for future applications in pharmaceuticals and food industries.

Abstract Background Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. Results A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P

Abstract Background MicroRNAs (miRNAs) regulate numerous crucial abiotic stress processes in plants. However, information is limited on their involvement in cadmium (Cd) stress response and tolerance mechanisms in plants, including ramie (Boehmeria nivea L.) that produces a number of economic valuable as an important natural fibre crop and an ideal crop for Cd pollution remediation. Results Four small RNA libraries of Cd-stressed and non-stressed leaves and roots of ramie were constructed. Using small RNA-sequencing, 73 novel miRNAs were identified. Genome-wide expression analysis revealed that a set of miRNAs was differentially regulated in response to Cd stress. In silico target prediction identified 426 potential miRNA targets that include several uptake or transport factors for heavy metal ions. The reliability of small RNA sequencing and the relationship between the expression levels of miRNAs and their target genes were confirmed by quantitative PCR (q-PCR). We showed that the expression patterns of miRNAs obtained by q-PCR were consistent with those obtained from small RNA sequencing. Moreover, we demonstrated that the expression of six randomly selected target genes was inversely related to that of their corresponding miRNAs, indicating that the miRNAs regulate Cd stress response in ramie. Conclusions This study enriches the number of Cd-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in ramie during Cd stress.

In this paper, we present the transcriptome profiles of the A. venetum L. by RNA-Seq approach. A total of 6.57 Gb raw data were obtained, and 52,983 unigenes with an average length of 1009 bp and N50 of 1632 bp were annotated with the 7 databases. The unigenes annotated to KEGG database were divided into 21 categories from 6 main groups. Among these, 4952 (22.21%) unigenes were clustered to “Global and overview maps”, and 1834 (8.23%) unigenes were clustered to “Carbohydrate metabolism”. In addition, 6340 unigenes containing 7579 SSRs were identified and the mononucleotide, dinucleotide, trinucleotide motifs were the most common motif type (95.59%), accounting for 39.62%, 36.02%, and 19.95%, respectively.

Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5 days, 30 days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. Gene expression levels of each samples were quantified using the BGISEQ500 platform to help understand the distribution of aquatic root development related genes at the macro level (GSE98903). Our data resources provided an opportunity to elucidate the adaptation mechanisms of ramie seedlings roots in aquatic environment.

In the current study, the active flavonoids from Apocynum venetum and Apocynum hendersonii leaf were efficiently characterized using UPLC-ESI-MS/MS, and yielding the highest content of 15.35 mg/g (A. venetum) and 13.28 mg/g (A. hendersonii) respectively. The antioxidant assay in vitro showed that the isolated flavonoid ingredient groups exhibited free radical scavenging activities to DPPH, ABTS and linoleic acid. The antimicrobial assay revealed the isolated flavonoid ingredient from both A. venetum and A. hendorsonii have exerted anti-MRSA and anti-P. aeruginosa effect through disrupting cell integrity and declining ATP. In vivo assay demonstrated that these flavonoid ingredients effectively accelerated MRSA-infected and P. aeruginosa-infected Balb/c mice wound healing. In summary, these results showed that the characterized flavonoid ingredients exhibited great potential as natural antioxidant and antimicrobial agents, and shed light into future potential applications of Apocynum spp.

The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

Nitrogen-use efficiency (NUE) has significant impacts on plant growth and development. NUE in plants differs substantially in physiological resilience to nitrogen stress; however, the molecular mechanisms underlying enhanced resilience of high-NUE plants to nitrogen deficiency remains unclear. We compared transcriptome-wide gene expression between high-NUE and low-NUE ramie (Boehmeria nivea (L.) Gaudich) genotypes under nitrogen (N)-deficient and normal conditions to identify the transcriptomic expression patterns that contribute to ramie resilience to nitrogen deficiency. Two ramie genotypes with contrasting NUE were used in the study, including T29 (NUE = 46.01%) and T13 (NUE = 15.81%). Our results showed that high-NUE genotypes had higher gene expression under the control condition across 94 genes, including frontloaded genes such as GDSL esterase and lipase, gibberellin, UDP-glycosyltransferase, and omega-6 fatty acid desaturase. Seventeen stress-tolerance genes showed lower expression levels and varied little in response to N-deficiency stress in high-NUE genotypes. In contrast, 170 genes were upregulated under N deficiency in high-NUE genotypes but downregulated in low-NUE genotypes compared with the controls. Furthermore, we identified the potential key genes that enable ramie to maintain physiological resilience under N-deficiency stress, and categorized these genes into three groups based on the transcriptome and their expression patterns. The transcriptomic and clustering analysis of these nitrogen-utilization-related genes could provide insight to better understand the mechanism of linking among the three gene classes that enhance resilience in high-NUE ramie genotypes.