Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

Abstract

Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LPsensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) cir-cRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced cir-cRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE cir-cRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.

Genome-Wide Analysis of Long Non-Coding RNAs (lncRNAs) in Two Contrasting Soybean Genotypes Subjected to Phosphate Starvation

“…2b and Fig. S1, the number of DE lncRNAs under LP stress in Bogao is more than that in NN94156, indicating that the Bogao is more sensitive to LP treatment, which is consistent with our previous research in which Bogao was a P-sensitive genotype, while NN94156 was a P-tolerant genotype [30,32]. Furthermore, previous and our results reveals that all the mRNA, circular RNA and lncRNA, Bogao is more sensitive to LP stress than that of NN94156 [30,32].…”

“…5, Fig. 6), which was supported by previous studies focusing LP in soybean [32,42]. Previous research showed that NtMYB12 acts as a phosphorus starvation response enhancement factor and regulates NtCHS and NtPT2 expression, which results in increased avonol and P accumulation and enhances tolerance to LP stress [43].…”

“…Approximately 1,087 million of raw sequencing reads were generated from all 12 libraries, and each sample contained reads ranging from 75.5 to 100.7 million. After discarding adaptor sequences and low-quality reads (Qvalue ≤ 20), more than 90% of total reads were retained [32]. We mapped those clean reads to the soybean reference genome sequence (Wm82.a2.v1).…”

“…The process of RNA extraction and purity, library construction, and Illumina sequencing were according to Lv et al [32]. Brie y, after total RNA was extracted, rRNAs were removed using an Epicentre Ribo-zero rRNA Kit (Epicentre, USA, cat: MRZSR116).…”

Potassium Deficiency Significantly Affected Plant Growth and Development as Well as microRNA-Mediated Mechanism in Wheat (Triticum aestivum L.)

“…K + deficiency affected root development in a wide range of plant species (Jia et al, 2008;Maathuis, 2009;Zhang et al, 2009;Hafsi et al, 2014;Guo et al, 2019). To study the potential miRNA-mediated mechanism in which plant responds to K + deficiency, we have selected and tested a total of 20 miRNAs that are associated with root development (Khan et al, 2011;Couzigou and Combier, 2016;Li and Zhang, 2016) and responses to nutrients (Maathuis, 2009;Kulcheski et al, 2015) including nitrogen and phosphorus deficiency (Bao et al, 2019;Filina et al, 2019;Yang et al, 2019;Asefpour Vakilian, 2020;Hou et al, 2020;Liu et al, 2020;Lv et al, 2020;Tiwari et al, 2020). These 20 miRNAs were miR160, miR164, miR165, miR166, miR167, miR169, miR171, miR172, miR390, miR393, miR396, miR847, miR857, miR156, miR162, miR319, miR395, miR778, miR399, and miR827.…”