Dataset Information

Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra.

ABSTRACT: Salix integra is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances in genomics for Salix are promising for future improvement in identification of new candidate genes involved in metal tolerance and accumulation. Thus, high-throughput transcriptome sequencing is essential for generating enormous transcript sequences from S. integra, especially for the purpose of Cd toxicity-responsive genes discovery. Using Illumina paired-end sequencing, approximately 60.05 million high-quality reads were obtained. De novo assembly yielded 80,105 unigenes with an average length of 703 bp, A total of 50,221 (63%) unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases. GO annotation reveals 1849 Cd responsive genes involving in Cd binding, transport, and detoxification and cellular Cd homeostasis, and these genes were highly enriched in plant response to Cd ion and Cd ion transport. By searching against the PlantCyc database, 509 unigenes were assigned to 14 PlantCyc pathways related to Cd transport and cellular detoxification, and many of them are genes encoding heavy metal ATPases (HMAs), nature resistance-associated with microphage proteins (NRAMPs), ATP-binding cassette (ABC) transporters, etc., Comprehensive RT-qPCR analysis of these selected genes in different tissues of S. integra under the control and Cd treatment revealed metallothionein-like protein (MT2A and MT2B), Metal tolerance protein (MTP1), ABCB25, NRAMP5, and ZIP1 may be involved in the Cd transport and detoxification in leaves, while NRAMP2, ZIP8, and NRAMP5 may be related to Cd transport in roots. Our study will enrich the sequence information of S. integra in public database, and would provide some new understanding of the molecular mechanisms of heavy metal tolerance and detoxification in willows.

SUBMITTER: Shi X

PROVIDER: S-EPMC5083712 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating <i>Salix integra</i>.

Shi Xiang X Sun Haijing H Chen Yitai Y Pan Hongwei H Wang Shufeng S

Frontiers in plant science 20161028

<i>Salix integra</i> is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances i ...[more]

PMID: 27840630

Similar Datasets

Project description:The application of plant-microbial remediation of heavy metals is restricted by the difficulty of exogenous microbes to form large populations and maintain their long-term remediation efficiency. We therefore investigated the effects of inoculation with indigenous heavy-metal-tolerant rhizosphere microbes on phytoremediation of lead (Pb) by Salix integra. We measured plant physiological indexes and soil Pb bioavailability and conducted widespread targeted metabolome analysis of strains to better understand the mechanisms of enhance Pb accumulation. Growth of Salix integra was improved by both single and co-inoculation treatments with Bacillus sp. and Aspergillus niger, increasing by 14% in co-inoculated plants. Transfer coefficients for Pb, indicating mobility from soil via roots into branches or leaves, were higher following microbial inoculation, showing a more than 100% increase in the co-inoculation treatment over untreated plants. However, Pb accumulation was only enhanced by single inoculation treatments with either Bacillus sp. or Aspergillus niger, being 10% greater in plants inoculated with Bacillus sp. compared with uninoculated controls. Inoculation mainly promoted accumulation of Pb in aboveground plant parts. Superoxide dismutase and catalase enzyme activities as well as the proline content of inoculated plants were enhanced by most treatments. However, soil urease and catalase activities were lower in inoculated plants than controls. Proportions of acid-soluble Pb were 0.34 and 0.41% higher in rhizosphere and bulk soil, respectively, of plants inoculated with Bacillus sp. than in that of uninoculated plants. We identified 410 metabolites from the microbial inoculations, of which more than 50% contributed to heavy metal bioavailability; organic acids, amino acids, and carbohydrates formed the three major metabolite categories. These results suggest that both indigenous Bacillus sp. and Aspergillus niger could be used to assist phytoremediation by enhancing antioxidant defenses of Salix integra and altering Pb bioavailability. We speculate that microbial strains colonized the soil and plants at the same time, with variations in their metabolite profiles reflecting different living conditions. We also need to consider interactions between inocula and the whole microbial community when applying microbial inoculation to promote phytoremediation.

Project description:Perennial ryegrass (Lolium perenne L.) is an important forage grass and has the potential to be used in phytoremediation, while little information is available regarding the transcriptome profiling of ryegrass leaves in response to high levels of Cd. To investigate and uncover the physiological responses and gene expression characteristics of perennial ryegrass under Cd stress, a pot experiment was performed to study the transcriptomic profiles of ryegrass with Cd-spiked soils. Transcriptome sequencing and comparative analysis were performed on the Illumina RNA-Seq platform at different concentrations of Cd-treated (0, 50 and 500 mg·kg−1 soil) ryegrass leaves and differentially expressed genes (DEGs) were verified by RT-qPCR. The results show that high concentrations of Cd significantly inhibited the growth of ryegrass, while the lower concentrations (5 and 25 mg·kg−1) showed minor effects. The activity levels of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and malondialdehyde (MDA) increased in Cd-treated ryegrass leaves. We identified 1103 differentially expressed genes (DEGs) and profiled the molecular regulatory pathways of ryegrass leaves with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in response to Cd stress. Cd stress significantly increased the membrane part, the metabolic process, the cellular process and catalytic activity. The numbers of unigenes related to signal transduction mechanisms, post-translational modification, replication, recombination and repair significantly increased. KEGG function annotation and enrichment analysis were performed based on DEGs with different treatments, indicating that the MAPK signaling pathway, the mRNA surveillance pathway and RNA transport were regulated significantly. Taken together, this study explores the effect of Cd stress on the growth physiology and gene level of ryegrass, thus highlighting significance of preventing and controlling heavy metal pollution in the future.

Project description:The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were "sulfur metabolism" and "glutathione metabolism", and the target pathways of NAP subfamily SiNACs were "ribosome" and "phenylpropanoid biosynthesis". This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

Dataset Information

Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra.

Publications

Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating <i>Salix integra</i>.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets