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Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

ABSTRACT: Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.

SUBMITTER: Khoei MA

PROVIDER: S-EPMC8705754 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSmall non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. Among these, the most conserved classes are microRNAs (miRNAs) and small interfering RNAs (siRNAs), both of which are produced by RNase III-like enzymes called Dicers. Many plant miRNAs play critical roles in nutrient homeostasis, developmental processes, abiotic stress and pathogen responses. Currently, only 70 miRNA have been identified in soybean.MethodsWe utilized Illumina's SBS sequencing technology to generate high-quality small RNA (sRNA) data from four soybean (Glycine max) tissues, including root, seed, flower, and nodules, to expand the collection of currently known soybean miRNAs. We developed a bioinformatics pipeline using in-house scripts and publicly available structure prediction tools to differentiate the authentic mature miRNA sequences from other sRNAs and short RNA fragments represented in the public sequencing data.ResultsThe combined sequencing and bioinformatics analyses identified 129 miRNAs based on hairpin secondary structure features in the predicted precursors. Out of these, 42 miRNAs matched known miRNAs in soybean or other species, while 87 novel miRNAs were identified. We also predicted the putative target genes of all identified miRNAs with computational methods and verified the predicted cleavage sites in vivo for a subset of these targets using the 5' RACE method. Finally, we also studied the relationship between the abundance of miRNA and that of the respective target genes by comparison to Solexa cDNA sequencing data.ConclusionOur study significantly increased the number of miRNAs known to be expressed in soybean. The bioinformatics analysis provided insight on regulation patterns between the miRNAs and their predicted target genes expression. We also deposited the data in a soybean genome browser based on the UCSC Genome Browser architecture. Using the browser, we annotated the soybean data with miRNA sequences from four tissues and cDNA sequencing data. Overlaying these two datasets in the browser allows researchers to analyze the miRNA expression levels relative to that of the associated target genes. The browser can be accessed at http://digbio.missouri.edu/soybean_mirna/.

Project description:Nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. Although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. In this report, we performed a genome-wide survey of cystatin family genes to explore their relationship to nodulation and nodule development in soybean and identified 20 cystatin genes that encode peptides with 97-245 amino acid residues, different isoelectric points (pI) and structure characteristics, and various putative plant regulatory elements in 3000 bp putative promoter fragments upstream of the 20 soybean cystatins in response to different abiotic/biotic stresses, hormone signals, and symbiosis signals. The expression profiles of these cystatin genes in soybean symbiosis with rhizobium strain Bradyrhizobium japonicum strain 113-2 revealed that 7 cystatin family genes play different roles in nodulation as well as nodule development and senescence. However, these genes were not root nodule symbiosis (RNS)-specific and did not encode special clade cystatin protein with structures related to nodulation and nodule development. Besides, only two of these soybean cystatins were not upregulated in symbiosis after ABA treatment. The functional analysis showed that a candidate gene Glyma.15G227500 (GmCYS16) was likely to play a positive role in soybean nodulation. Besides, evolutionary relationships analysis divided the cystatin genes from Arabidopsis thaliana, Nicotiana tabacum, rice, barley and four legume plants into three groups. Interestingly, Group A cystatins are special in legume plants, but only include one of the above-mentioned 7 cystatin genes related to nodulation and nodule development. Overall, our results provide useful information or clues for our understanding of the functional diversity of legume cystatin family proteins in soybean nodulation and nodule development and for finding nodule-specific cysteine proteases in soybean.

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Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

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