Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress

Study on remediation of cadmium contaminated paddy field by ramie (Boehmeria nivea L.) floating island and its supporting technology

Ramie (Boehmeria nivea L.) is an ideal crop for cadmium (Cd) pollution remediation due to its advantages of both remediating and utilizing, however, it is mainly carried out in dry land, whose restoration effect is relatively slow. Previously, we found that the ramie plants cultivated by hydroponics has several tens of times higher Cd absorption capacity than that planted in soil. However, the issue of how to use hydroponic ramie to remediate Cd contaminated paddy fields needs to be addressed. In this study, we innovatively developed the ramie floating island technology and studied its remediation model on simulated Cd contaminated paddy fields. Different ramie varieties were used to compare the remediation effects, and the results showed that there were differences in adaptability among different varieties on floating islands and the remediation ability of the tested ramie varieties was Z2 > Z1 > Z3. Different harvested times were set to analyze the effects of harvested model on remediation, and it was suggested that multiple harvests can be carried out according to the plant growth status of ramie floating island after 30 days of remediation to achieve better remediation effects. Low water level height (5 cm) of paddy field was beneficial for the accumulation of Cd in the roots, but considering the adaptability of various ramie varieties and the effect of long-term restoration, it was recommended that the water level height of 20 cm for the cultivation of ramie floating island was more suitable. Moreover, we found that low concentration of citric acid (≤2 g L-1) or polyaspartic acid (≤3 g L-1) can improve the remediation effects for ramie floating island. Our study opens up a novel approach for ramie to remediate heavy metal pollution and provides a technical reference for water body Cd remediation by plants.

Transcriptomic, epigenomic and physiological comparisons reveal key factors for different manganese tolerances in three Chenopodium ambrosioides L. populations

Chenopodium ambrosioides is a manganese (Mn) hyperaccumulator that can be used for Mn-polluted soil phytoremediation. However, the mechanism of Mn tolerance of C. ambrosioides remains largely unknown. In this study, the key factors for Mn tolerance of C. ambrosioides was investigated from the aspects of DNA methylation pattern, gene expression regulation and physiological function. We found that the two genotypes of C. ambrosioides populations have differentiated tolerance to Mn stress (Mn-tolerant: CS and XC, Mn-sensitive: WH). Although there was no difference in Mn accumulation between two types under excess Mn, the biomass and photosynthetic systems were more severely inhibited in Mn-sensitive type, as well as suffering more serious oxidative damage. More differentially expressed genes (DEGs) were downregulated in the Mn-tolerant type, indicating that the Mn-tolerant type tends to inhibit gene expression to cope with Mn stress. DEGs related to metal transport, antioxidant system, phytohormone and transcription factors contribute to the tolerance of C. ambrosioides to Mn, and account for difference in Mn stress sensitivities between the Mn-sensitive and tolerant types. We also found that DNA methylation variation may help to cope with Mn stress. The global DNA methylation level in C. ambrosioides increased under Mn stress, especially in the Mn-sensitive type. Dozens of methylated loci were significantly associated with the Mn accumulation trait of C. ambrosioides, and some critical DEGs were regulated by DNA methylation. Our study comprehensively demonstrated the Mn tolerance mechanism of C. ambrosioides for the first time, and highlighted the roles of epigenetic modification in C. ambrosioides response to Mn stress. Our findings may contribute to elucidating the adaptation mechanism of hyperaccumulator to the heavy metal toxicity.

Overexpression of LaGRAS enhances phosphorus acquisition via increased root growth of phosphorus-deficient white lupin

The GRAS transcription factors play an indispensable role in plant growth and responses to environmental stresses. The GRAS gene family has extensively been explored in various plant species; however, the comprehensive investigation of GRAS genes in white lupin remains insufficient. In this study, bioinformatics analysis of white lupin genome revealed 51 LaGRAS genes distributed into 10 distinct phylogenetic clades. Gene structure analyses revealed that LaGRAS proteins were considerably conserved among the same subfamilies. Notably, 25 segmental duplications and a single tandem duplication showed that segmental duplication was the major driving force for the expansion of GRAS genes in white lupin. Moreover, LaGRAS genes exhibited preferential expression in young cluster root and mature cluster roots and may play key roles in nutrient acquisition, particularly phosphorus (P). To validate this, RT-qPCR analysis of white lupin plants grown under +P (normal P) and -P (P deficiency) conditions elucidated significant differences in the transcript level of GRAS genes. Among them, LaGRAS38 and LaGRAS39 were identified as potential candidates with induced expression in MCR under -P. Additionally, white lupin transgenic hairy root overexpressing OE-LaGRAS38 and OE-LaGRAS39 showed increased root growth, and P concentration in root and leaf compared to those with empty vector control, suggesting their role in P acquisition. We believe this comprehensive analysis of GRAS members in white lupin is a first step in exploring their role in the regulation of root growth, tissue development, and ultimately improving P use efficiency in legume crops under natural environments.

Transcriptomic analysis reveals the molecular mechanisms of Boehmeria nivea L. in response to antimonite and antimonate stresses

Soil antimony (Sb) pollution is a global concern that threatens food security and human health. Boehmeria nivea L. (ramie) is a promising phytoremediation plant exhibiting high tolerance and enrichment capacity for Sb. To reveal the molecular mechanisms and thus enhance the ramie uptake, transport, and detoxification of Sb with practical strategies, a hydroponic experiment was conducted to compare the physiological and transcriptomic responses of ramie towards antimonite (Sb(Ⅲ)) and antimonate (Sb(Ⅴ)). Phenotypic results showed that Sb(Ⅲ) had a stronger inhibitory effect on the growth of ramie. Root Sb content under Sb(Ⅲ) was 2.43 times higher than that in Sb(Ⅴ) treatment. Based on the ribonucleic acid sequencing (RNA-Seq) technique, 3915 and 999 significant differentially expressed genes (DEGs) were identified under Sb(Ⅲ) and Sb(Ⅴ), respectively. Transcriptomic analysis revealed that ramie showed different adaptation strategies to Sb(Ⅲ) and Sb(V). Key DEGs and their involved pathways such as catalytic activity, carbohydrate metabolisms, phenylpropanoid biosynthesis, and cell wall modification were identified to perform crucial roles in Sb tolerance and detoxification. Two heavy metal-associated domain-type genes, six heavy metal-associated isoprenylated plant proteins, and nine ABC transporters showed possible roles in the transport and detoxification of Sb. The significant upregulation of NRAMP5 and three NIPs suggested their roles in the transport of Sb(V). This study is the basis for future research to identify the exact genes and biological processes that can effectively enhance Sb accumulation or improve plant tolerance to Sb, thereby promoting the phytoremediation of Sb-polluted soils.

Transcriptomic analysis reveals key genes and pathways corresponding to Cd and Pb in the hyperaccumulator Arabis paniculata

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata, and aid in future efforts to utilize this plant in phytoremediation.

Transcriptomic Analysis of Cadmium Stressed Tamarix hispida Revealed Novel Transcripts and the Importance of Abscisic Acid Network

Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on the desert and soil with 0.5 to 1% salt content, making it an ideal plant for the research on response to abiotic stresses. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida. In the study, RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 μmol L^-1 CdCl₂ for 24, 48, and 72 h compared with control. In total, 72,764 unigenes exhibited similar sequences in the Non-redundant nucleic acid database (NR database), while 36.3% of all these unigenes may be new transcripts. In addition, 6,778, 8,282, and 8,601 DEGs were detected at 24, 48, and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance Cd resistance ability of T. hispida by regulating the production of ROS under Cd stress and inhibit absorption of Cd. The new transcriptome resources and data that we present in this study for T. hispida may facilitate investigation of molecular mechanisms governing Cd resistance.

Bio-remediation approaches for alleviation of cadmium contamination in natural resources

Cadmium (Cd) is a harmful heavy metal that can cause potent environmental and health hazards at different trophic levels through food chain. Cd is relatively non-biodegradable and persists for a long time in the environment. Considering the potential toxicity and non-biodegradability of Cd in the environment as well as its health hazards, this is an urgent issue of international concern that needs to be addressed by implicating suitable remedial approaches. The current article specifically attempts to review the different biological approaches for remediation of Cd contamination in natural resources. Further, bioremediation mechanisms of Cd by microbes such as bacteria, fungi, algae are comprehensively discussed. Studies indicate that heavy metal resistant microbes can be used as suitable biosorbents for the removal of Cd (up to 90%) in the natural resources. Soil-to-plant transfer coefficient (TC) of Cd ranges from 3.9 to 3340 depending on the availability of metal to plants and also on the type of plant species. The potential phytoremediation strategies for Cd removal and the key factors influencing bioremediation process are also emphasized. Studies on molecular mechanisms of transgenic plants for Cd bioremediation show immense potential for enhancing Cd phytoremediation efficiency. Thus, it is suggested that nano-technological based integrated bioremediation approaches could be a potential futuristic path for Cd decontamination in natural resources. This review would be highly useful for the biologists, chemists, biotechnologists and environmentalists to understand the long-term impacts of Cd on ecology and human health so that potential remedial measures could be taken in advance.

Integration of mRNA and miRNA profiling reveals the heterosis of three hybrid combinations of Capsicum annuum varieties

Capsicum annuum is also known as chili which is one of the most important vegetable crops grown in the world. Breeding new varieties with heterosis could improve the quality of pepper, increase yield, growth potential, disease resistance, adaptability, and seed viability. To investigate the heterosis among three cross combinations of different parents, the mRNA-miRNA integrated analysis was performed. A total number of 22,659,009 to 36,423,818 clean data were generated from mRNA-seq with 81 libraries, and the unique mapped reads were from 35,495,567 (86.81%) to 46,466,622 (88.95%). The plant-hormone signal transduction pathway (40 genes) was detected with a higher DEG number. The SAUR32L, GID1, PYR1, EIN2. ERF1, PR1, JAR1-like, IAA from this pathway play a key role in plant development. From the miRNA-seq, the number of clean reads was ranging from 12,132,221 to 25,632,680. A total of 220 miRNAs were predicted in this study, and all of them were identified as novel miRNA. The top three candidate KEGG pathways of miRNA were ribosome signaling pathway (13 miRNAs), spliceosome pathway (13 miRNAs), and plant hormone signal transduction pathways (10 miRNAs). With the mRNA and miRNA integrated analysis, we found some key genes were regulated by some miRNAs. Among them, the scarecrow-like 6 protein can be up or down regulated by mir8, mir120, mir184, mir_214, mir125, and mir130. The function of Della protein was regulated by mir24, mir74, mir94, mir139, and mir190. This study contributes to understanding how heterosis regulates the traits, such as crop production, fruit weight, and fruit length.

Comparative transcriptomic analysis reveals key genes and pathways in two different cadmium tolerance kenaf (Hibiscus cannabinus L.) cultivars

Soil cadmium (Cd) contamination has become a massive environmental problem. Kenaf is an industrial fiber crop with high tolerance to heavy metals and could be potentially used for soil phytoremediation. However, the molecular mechanism of Cd in kenaf tolerance remains largely unknown. In the present study, using two contrasting Cd sensitive kenaf (GH and YJ), the key factors accounting for differential Cd tolerance were investigated. GH has a stronger Cd transport and accumulation ability than YJ. In addition, physiological index investigation on malondialdehyde (MDA) contents and antioxidant enzyme (SOD, POD, and CAT) activities showed GH has a stronger detoxification capacity than YJ. Furthermore, the cell ultrastructure of GH is more stable than that of YJ under Cd stress. Transcriptome analysis revealed 2221 (689 up and 1532 down) and 3321 (2451 up and 870 down) genes were differentially expressed in GH and YJ, respectively. More DEGs (differentially expressed genes) were characterized as up-regulated in GH, indicating GH is inclined to activate gene expression to cope with cadmium stress. GO and KEGG analyses indicate that DEGs were assigned and enriched in different pathways. Plenty of critical Cd-induced DEGs such as SOD2, PODs, MT1, DTXs, NRT1, ABCs, CES, AP2/ERF, MYBs, NACs, and WRKYs were identified. The DEGs involved pathways, including antioxidant, heavy metal transport or detoxification, substance transport, plant hormone and calcium signals, ultrastructural component, and a wide range of transcription factors were suggested to play crucial roles in kenaf Cd tolerance, and accounting for the difference in Cd stress sensitivities.

Early responses of maize seedlings to Cu stress include sharp decreases in gibberellins and jasmonates in the root apex

Copper (Cu) interferes with numerous biological functions in plants, including plant growth, which is partly governed by plant hormones. In the present study, Cu stress effect on the roots of pre-emerging maize seedlings in terms of growth, nutrient composition, protein modifications, and root hormone homeostasis was investigated, focusing on possible metabolic differences between the root apex and the rest of the root tissues. Significant decreases in root length and root biomass after 72 h of Cu exposure (50 and 100 μM CuCl₂), accompanied by reductions in Ca, Mg, and P root contents, were found. Cu also generated cell redox imbalance in both root tissues and revealed by altered enzymatic and non-enzymatic antioxidant defenses. Oxidative stress was evidenced by an increased protein carbonylation level in both tissues. Copper also induced protein ubiquitylation and SUMOylation and affected 20S proteasome peptidase activities in both tissues. Drastic reductions in ABA, IAA, JA (both free and conjugated), GA3, and GA4 levels in the root apex were detected under Cu stress. Our results show that Cu exposure generated oxidative damage and altered root hormonal homeostasis, mainly at the root apex, leading to a strong root growth inhibition. Severe protein post-translational modifications upon Cu exposure occurred in both tissues, suggesting that even when hormonal adjustments to cope with Cu stress occurred mainly at the root apex, the entire root is compromised in the protein turnover that seems to be necessary to trigger and/or to sustain defense mechanisms against Cu toxicity.

A MYB transcription factor, BnMYB2, cloned from ramie (Boehmeria nivea) is involved in cadmium tolerance and accumulation

MYB-related transcription factors play important roles in plant development and response to various environmental stresses. In the present study, a novel MYB gene, designated as BnMYB2 (GenBank accession number: MF741319.1), was isolated from Boehmeria nivea using rapid amplification of cDNA ends (RACE) and RT-PCR on a sequence fragment from a ramie transcriptome. BnMYB2 has a 945 bp open reading frame encoding a 314 amino acid protein that contains a DNA-binding domain and shares high sequence identity with MYB proteins from other plant species. The BnMYB2 promoter contains several putative cis-acting elements involved in stress or phytohormone responses. A translational fusion of BnMYB2 with enhanced green fluorescent protein (eGFP) showed nuclear and cytosolic subcellular localization. Real-time PCR results indicated that BnMYB2 expression was induced by Cadmium (Cd) stress. Overexpression of BnMYB2 in Arabidopsis thaliana resulted in a significant increase of Cd tolerance and accumulation. Thus, BnMYB2 positively regulated Cd tolerance and accumulation in Arabidopsis, and could be used to enhance the efficiency of Cd removal with plants.

Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments

Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.

Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis

Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie.

A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie

Background

The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop.

Results

We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome.

Conclusion

This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5878-8) contains supplementary material, which is available to authorized users.

Comparative transcriptomics reveals the selection patterns of domesticated ramie

Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the "all-ramie" transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation-reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering-promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.

Transcriptome Analysis Reveals Cotton (Gossypium hirsutum) Genes That Are Differentially Expressed in Cadmium Stress Tolerance

High concentrations of heavy metals in the soil should be removed for environmental safety. Cadmium (Cd) is a heavy metal that pollutes the soil when its concentration exceeds 3.4 mg/kg. Although the potential use of cotton to remediate heavy Cd-polluted soils is known, little is understood about the molecular mechanisms of Cd tolerance. In this study, transcriptome analysis was used to identify Cd tolerance genes and their potential mechanisms in cotton. We exposed cotton plants to excess Cd and identified 4627 differentially expressed genes (DEGs) in the root, 3022 DEGs in the stem and 3854 DEGs in the leaves through RNA-Seq analysis. Among these genes were heavy metal transporter coding genes (ABC, CDF, HMA, etc.), annexin genes and heat shock genes (HSP), amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation–reduction process and metal ion binding. The DEGs were mainly enriched in two pathways, the influenza A and pyruvate pathway. GhHMAD5, a protein containing a heavy-metal binding domain, was identified in the pathway to transport or to detoxify heavy metal ions. We constructed a GhHMAD5 overexpression system in Arabidopsis thaliana that showed longer roots compared to control plants. GhHMAD5-silenced cotton plants showed more sensitivity to Cd stress. The results indicate that GhHMAD5 is involved in Cd tolerance, which gives a preliminary understanding of the Cd tolerance mechanism in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate soils polluted with Cd and potentially other heavy metals.

Activation of a gene network in durum wheat roots exposed to cadmium

BACKGROUND

Among cereals, durum wheat (Triticum turgidum L. subsp. durum) accumulates cadmium (Cd) at higher concentration if grown in Cd-polluted soils. Since cadmium accumulation is a risk for human health, the international trade organizations have limited the acceptable concentration of Cd in edible crops. Therefore, durum wheat cultivars accumulating low cadmium in grains should be preferred by farmers and consumers. To identify the response of durum wheat to the presence of Cd, the transcriptomes of roots and shoots of Creso and Svevo cultivars were sequenced after a 50-day exposure to 0.5 μM Cd in hydroponic solution.

RESULTS

No phytotoxic effects or biomass reduction was observed in Creso and Svevo plants at this Cd concentration. Despite this null effect, cadmium was accumulated in root tissues, in shoots and in grains suggesting a good cadmium translocation rate among tissues. The mRNA sequencing revealed a general transcriptome rearrangement after Cd treatment and more than 7000 genes were found differentially expressed in root and shoot tissues. Among these, the up-regulated genes in roots showed a clear correlation with cadmium uptake and detoxification. In particular, about three hundred genes were commonly up-regulated in Creso and Svevo roots suggesting a well defined molecular strategy characterized by the transcriptomic activation of several transcription factors mainly belonging to bHLH and WRKY families. bHLHs are probably the activators of the strong up-regulation of three NAS genes, responsible for the synthesis of the phytosiderophore nicotianamine (NA). Moreover, we found the overall up-regulation of the methionine salvage pathway that is tightly connected with NA synthesis and supply the S-adenosyl methionine necessary for NA biosynthesis. Finally, several vacuolar NA chelating heavy metal transporters were vigorously activated.

CONCLUSIONS

In conclusion, the exposure of durum wheat to cadmium activates in roots a complex gene network involved in cadmium translocation and detoxification from heavy metals. These findings are confident with a role of nicotianamine and methionine salvage pathway in the accumulation of cadmium in durum wheat.

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich

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.

Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars

Background

Cadmium translocation from roots to shoots is a complex biological process that is controlled by gene regulatory networks. Pak choi exhibits wide cultivar variations in Cd accumulation. However, the molecular mechanism involved in cadmium translocation and accumulation is still unclear. To isolate differentially expressed genes (DEGs) involved in transporter-mediated regulatory mechanisms of Cd translocation in two contrasting pak choi cultivars, Baiyewuyueman (B, high Cd accumulator) and Kuishan’aijiaoheiye (K, low Cd accumulator), eight cDNA libraries from the roots of two cultivars were constructed and sequenced by RNA-sequencing.

Results

A total of 244,190 unigenes were obtained. Of them, 6827 DEGs, including BCd₁₀ vs. BCd₀ (690), KCd₁₀ vs. KCd₀ (2733), KCd₀ vs. BCd₀ (2919), and KCd₁₀ vs. BCd₁₀ (3455), were identified. Regulatory roles of these DEGs were annotated and clarified through GO and KEEG enrichment analysis. Interestingly, 135 DEGs encoding ion transport (i.e. ZIPs, P_1B-type ATPase and MTPs) related proteins were identified. The expression patterns of ten critical genes were validated using RT-qPCR analysis. Furthermore, a putative model of cadmium translocation regulatory network in pak choi was proposed.

Conclusions

High Cd cultivar (Baiyewuyueman) showed higher expression levels in plasma membrane-localized transport genes (i.e., ZIP2, ZIP3, IRT1, HMA2 and HMA4) and tonoplast-localized transport genes (i.e., CAX4, HMA3, MRP7, MTP3 and COPT5) than low Cd cultivar (Kuishan’aijiaoheiye). These genes, therefore, might be involved in root-to-shoot Cd translocation in pak choi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3973-2) contains supplementary material, which is available to authorized users.

Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis

G. pentaphyllum (Gynostemma pentaphyllum), a creeping herbaceous perennial with many important medicinal properties, is widely distributed in Asia. Gypenosides (triterpenoid saponins), the main effective components of G. pentaphyllum, are well studied. FPS (farnesyl pyrophosphate synthase), SS (squalene synthase), and SE (squalene epoxidase) are the main enzymes involved in the synthesis of triterpenoid saponins. Considering the important medicinal functions of G. pentaphyllum, it is necessary to investigate the transcriptomic information of G. pentaphyllum to facilitate future studies of transcriptional regulation. After sequencing G. pentaphyllum, we obtained 50,654,708 unigenes. Next, we used RPKM (reads per kilobases per million reads) to calculate expression of the unigenes and we performed comparison of our data to that contained in five common databases to annotate different aspects of the unigenes. Finally, we noticed that FPS, SS, and SE showed differential expression of enzymes in DESeq. Leaves showed the highest expression of FPS, SS, and SE relative to the other two tissues. Our research provides transcriptomic information of G. pentaphyllum in its natural environment and we found consistency in unigene expression, enzymes expression (FPS, SS, and SE), and the distribution of gypenosides content in G. pentaphyllum. Our results will enable future related studies of G. pentaphyllum.

Comparative Transcriptome Analysis between Low- and High-Cadmium-Accumulating Genotypes of Pakchoi (Brassica chinensis L.) in Response to Cadmium Stress

To reduce cadmium (Cd) pollution of food chains, screening and breeding of low-Cd-accumulating cultivars are the focus of much study. Two previously identified genotypes, a low-Cd-accumulating genotype (LAJK) and a high-Cd-accumulating genotype (HAJS) of pakchoi (Brassica chinesis L.), were stressed by Cd (12.5 μM) for 0 h (T0), 3 h (T3) and 24 h (T24). By comparative transcriptome analysis for root tissue, 3005 and 4343 differentially expressed genes (DEGs) were identified in LAJK at T3 (vs T0) and T24 (vs T3), respectively, whereas 8677 and 5081 DEGs were detected in HAJS. Gene expression pattern analysis suggested a delay of Cd responded transcriptional changes in LAJK compared to HAJS. DEG functional enrichments proposed genotype-specific biological processes coped with Cd stress. Cell wall biosynthesis and glutathione (GSH) metabolism were found to involve in Cd resistance in HAJS, whereas DNA repair and abscisic acid (ABA) signal transduction pathways played important roles in LAJK. Furthermore, the genes participating in Cd efflux such as PDR8 were overexpressed in LAJK, whereas those responsible for Cd transport such as YSL1 were more enhanced in HAJS, exhibiting different Cd transport processes between two genotypes. These novel findings should be useful for molecular assisted screening and breeding of low-Cd-accumulating genotypes for pakchoi.

Transcriptome Analysis of Ramie (Boehmeria nivea L. Gaud.) in Response to Ramie Moth (Cocytodes coerulea Guenée) Infestation

The ramie moth Cocytodes coerulea Guenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore, de novo assembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

Transcriptome Analysis of Pepper (Capsicum annuum) Revealed a Role of 24-Epibrassinolide in Response to Chilling

Brassinosteroids (BRs) have positive effects on many processes during plant growth, development, and various abiotic stress responses. However, little information is available regarding the global gene expression of BRs in response to chilling stress in pepper. In this study, we used RNA sequencing to determine the molecular roles of 24-epibrassinolide (EBR) during a chilling stress response. There were 39,829 transcripts, and, among them, 656 were differently-expressed genes (DEGs) following EBR treatment (Chill+EBR) compared with the control (Chill only), including 335 up-regulated and 321 down-regulated DEGs. We selected 20 genes out of the 656 DEGs for RT-qPCR analysis to confirm the RNA-Seq. Based on GO enrich and KEGG pathway analysis, we found that photosynthesis was significantly up-enriched in biological processes, accompanied by significant increases in the net photosynthetic rate (Pn), Fv/Fm, and chlorophyll content. Furthermore, the results indicate that EBR enhanced endogenous levels of salicylic acid (SA) and jasmonic acid (JA) while suppressing the ethylene (ETH) biosynthesis pathway, suggesting that BRs function via a synergistic cross-talk with SA, JA, and ETH signaling pathways in response to chilling stress. In addition, EBR induced cellulose synthase-like protein and UDP-glycosyltransferase, suggesting a contribution to the formation of cell wall and hormone metabolism. EBR also triggered the calcium signaling transduction in cytoplasm, and activated the expression of cellular redox homeostasis related genes, such as GSTX1, PER72, and CAT2. This work, therefor, identified the specific genes showed different expression patterns in EBR-treated pepper and associated with the processes of hormone metabolism, redox, signaling, transcription, and defense. Our study provides the first evidence of the potent roles of BRs, at the transcription level, to induce the tolerance to chilling stress in pepper as a function of the combination of the transcriptional activities, signaling transduction, and metabolic homeostasis.

Breadfruit (Artocarpus altilis) gibberellin 2-oxidase genes in stem elongation and abiotic stress response

Breadfruit (Artocarpus altilis) is a traditional staple tree crop in the Oceania. Susceptibility to windstorm damage is a primary constraint on breadfruit cultivation. Significant tree loss due to intense tropical windstorm in the past decades has driven a widespread interest in developing breadfruit with dwarf stature. Gibberellin (GA) is one of the most important determinants of plant height. GA 2-oxidase is a key enzyme regulating the flux of GA through deactivating biologically active GAs in plants. As a first step toward understanding the molecular mechanism of growth regulation in the species, we isolated a cohort of four full-length GA2-oxidase cDNAs, AaGA2ox1- AaGA2ox4 from breadfruit. Sequence analysis indicated the deduced proteins encoded by these AaGA2oxs clustered together under the C19 GA2ox group. Transcripts of AaGA2ox1, AaGA2ox2 and AaGA2ox3 were detected in all plant organs, but exhibited highest level in source leaves and stems. In contrast, transcript of AaGA2ox4 was predominantly expressed in roots and flowers, and displayed very low expression in leaves and stems. AaGA2ox1, AaGA2ox2 and AaGA2ox3, but not AaGA2ox4 were subjected to GA feedback regulation where application of exogenous GA3 or gibberellin biosynthesis inhibitor, paclobutrazol was shown to manipulate the first internode elongation of breadfruit. Treatments of drought or high salinity increased the expression of AaGA2ox1, AaGA2ox2 and AaGA2ox4. But AaGA2ox3 was down-regulated under salt stress. The function of AaGA2oxs is discussed with particular reference to their role in stem elongation and involvement in abiotic stress response in breadfruit.