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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.

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

Background: 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 RNA-Seq under water culture (treatment, T) and non-water culture conditions (control, CK) to reveal the regulatory mechanism of rooting. Results: Characterization of the cuttings of two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had high adventitious rooting rate but H4 had low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26723 genes were identified. In non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in 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 DEGs were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After water culture, more DEGs were up-regulated in Z2, but more DEGs were down-regulated in H4. Gene Ontology (GO) Gene functional analysis of the DEGs indicated that polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctive 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 identified in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) can interact with ethylene to regulate the occurrence and number of AR in Z2.Conclusions: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 adventitious root 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&mdash, 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.

Flavonoids contained in ramie (Boehmeria nivea) root are important resources for officinal use. The plant seedling can grow optimally and develop an easy-harvesting adventitious root system in a hydroponic system. This research was carried out to unravel the regulation mechanism of flavonoid biosynthesis under hydroponic culturing condition, which hitherto remained unknown. Root samples of the ramie plants grown in soil and hydroponic conditions at different developmental stages were collected and pooled for transcriptome sequencing, and the expression levels of flavonoid biosynthesis-related genes and total flavonoid content were quantified. A total of 43,541 unigenes were finally annotated and the expression of 9 key unigenes were confirmed by qRT-PCR. The flavonoid biosynthesis-related gene BnF3H was significantly up-regulated in the roots of hydroponic ramie, and higher total flavonoids content in the hydroponic ramie roots was also observed. The large dataset of transcripts and unigenes provided abundant genetic information for identifying flavonoid biosynthesis genes in ramie roots. Our results suggest flavonoid biosynthesis in ramie roots is positively affected in aquatic environment, and hydroponic culturing could have a potential for enhancing total flavonoids content in ramie roots.

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.

Apocynum plants, especially A. venetum and A. hendersonii, are rich in flavonoids. In the present study, a whole genome survey of the two species was initially carried out to optimize the flavonoid biosynthesis-correlated gene mining. Then, the metabolome and transcriptome analyses were combined to elucidate the flavonoid biosynthesis pathways. Both species have small genome sizes of 232.80 Mb (A. venetum) and 233.74 Mb (A. hendersonii) and showed similar metabolite profiles with flavonols being the main differentiated flavonoids between the two specie. Positive correlation of gene expression levels (flavonone-3 hydroxylase, anthocyanidin reductase, and flavonoid 3-O-glucosyltransferase) and total flavonoid content were observed. The contents of quercitrin, hyperoside, and total anthocyanin in A. venetum were found to be much higher than in A. hendersonii, and such was thought to be the reason for the morphological difference in color of A. venetum and A. hendersonii. This study provides valuable genomic and metabolome information for understanding of A. venetum and A. hendersonii, and lays a foundation for elucidating Apocynum genus plant flavonoid biosynthesis.

Ramie (Boehmeria nivea (L.) Gaudich) is widely used in the manufacture of garments and industrial fabrics. In the present study, 1151 ramie germplasm resources from 13 regions within China, Brazil, Indonesia, India, and Cuba were analyzed for genetic diversity and population structure using 23 simple sequence repeat (SSR) markers and three phenotypic markers to provide baseline information for ramie’s breeding and conservation plans. Overall, 117 loci were identified and Shannon’s diversity index ranged from 0.3201 to 1.6773 (average, 0.8272). The polymorphism information content varied from 0.1578 to 0.7603 (average, 0.5017), expected heterozygosity from 0.1694 to 0.7815 (average, 0.5282), and genetic diversity from 0.1722 to 0.7884 (average, 0.5228). Genetic diversity was higher in Sichuan, Yunnan, and Guizhou than in the other regions studied. Cluster analysis based on unweighted pair group method with arithmetic mean and genetic distance revealed marked differences between domestic (Chinese) and foreign (other regions) germplasm resources. Population structure analysis also evidenced two groups. Genetic diversity was higher in wild than in domesticated germplasms. Overall, results obtained here will be useful for selecting parents for breeding and performing association analyses in ramie.

Ramie is an important natural fibre crop and a perennial herbaceous plant of the nettle family Urticaceae. In 2013, brown root rot disease was observed on ramie plants in Yuangjiang, Hunan Province, China. Symptoms included stunted plants, reduced number of ramets per plant, and brown to purple-black discolouration of the root. The pathogen was identified as Pythium vexans according to morphological features and sequence identity (99–100%) to the published data for internal transcribed spacer (ITS), 18S and 28S rDNA sequences. The pathogenicity was confirmed on healthy fibrous roots of seedlings and on detached storage roots under greenhouse conditions. To our knowledge, this is the first report of brown root rot disease caused by Pythium vexans on ramie.

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.

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. Electronic supplementary material The online version of this article (10.1186/s12870-018-1561-5) contains supplementary material, which is available to authorized users.

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.

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.