Endogenous miRNA targets identified by sequencing of the Soybean degradome
ABSTRACT: To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes. Identification of miRNA targerts in soybean roots
Project description:MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. In the study presented here, four root samples from two contrast soybean cultivars, HX3 (Cd-tolerant) and ZH24 (Cd-sensitive), with or without (Cd) cadmium, harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment, was used to acquire expression profiles of a total of 953 unique genes, leading to the successful construction of supervised.
Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).
Project description:MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. Overall design: In the study presented here, four root samples from two contrast soybean cultivars, HX3 (Cd-tolerant) and ZH24 (Cd-sensitive), with or without (Cd) cadmium, harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment, was used to acquire expression profiles of a total of 953 unique genes, leading to the successful construction of supervised.
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie. A total of four samples, two replicates of control plants (CO1 and CO2) and two replicates of cadmium-stressed plants (CdS1 and CdS2) were used for RNA-seq.
Project description:The root proteomics of two cultivars differing in seed Cd accumulation, Fenghua 1 (F, low Cd cultivar) and Silihong (S, high Cd cultivar), were investigated under 0 (CK) and 2 μM Cd (Cd) conditions. The eight root proteins from two biological replicates of both peanut cultivars under Cd-free and Cd treated were obtained from iTRAQ experiments.
Project description:Understanding organisms’ environmental adaptation mechanisms is a fundamental question in ecology and evolution. The oyster Crassostrea gigas is able to accumulate high levels of zinc (Zn) and cadmium (Cd) without self-poisoning, and is thus widely used for pollution detection. However, the molecular mechanisms underlying such stress adaptation are largely unknown. Therefore, this study aimed to provide fundamental insights into the complex Zn/Cd-response regulatory networks.
Project description:Recently, molecular hydrogen (H2) has emerged as a bio-regulator both in animals and plants. Normally, functions of endogenous generated H2 could be mimicked by exogenously applied hydrogen-rich water (HRW) or hydrogen-rich saline (particularly in animals). Although alfalfa seedlings showed more cadmium (Cd) resistance after the administration with HRW, corresponding molecular mechanism is still elusive. To address this gap, iTRAQ-based quantitative proteomics was used. In our experimental conditions, out of 238 significant differential proteins identified in the Cd- and HRW/Cd-treated samples, 60 were unique to Cd-stressed alone samples, 107 were unique to HRW plus Cd treatment samples, and 71 were shared between two groups. Furthermore, 58 proteins from the 238 proteins significantly responded in Cd- and HRW/Cd-treatment samples were selected for further bioinformatics analysis. Interestingly, results indicated that they were classified into six categories: oxidation-reduction process, carbon metabolism, citrate cycle, cysteine and methionine metabolism, metal ion homeostasis, and sulfur compound metabolic process. In addition, the protein expression patterns were consistent with the results of increased non-protein thiols abundant, as well as iron and zinc content, in seedling roots. These suggest that HRW alleviates Cd toxicity mainly by decreasing oxidative damage, enhancing sulfur compound metabolic process, and maintaining nutrient element homeostasis.
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).