Integrated analysis of small RNAs, transcriptome and degradome sequencing reveal the drought stress network in Agropyron mongolicum Keng

Abstract

Agropyron mongolicum (A. mongolicum) is an excellent gramineous forage with extreme drought tolerance, which lives in arid and semiarid desert areas. However, the mechanism that underlies the response of microRNAs (miRNAs) and their targets in A. mongolicum to drought stress is not well understood. In this study, we analyzed the transcriptome, small RNAome (specifically the miRNAome) and degradome to generate a comprehensive resource that focused on identifying key regulatory miRNA-target circuits under drought stress. The most extended transcript in each collection is known as the UniGene, and a total of 41,792 UniGenes and 1,104 miRNAs were identified, and 99 differentially expressed miRNAs negatively regulated 1,474 differentially expressed target genes. Among them, eight miRNAs were unique to A. mongolicum, and there were 36 target genes. A weighted gene co-expression network analysis identified five hub genes. The miRNAs of five hub genes were screened with an integration analysis of the degradome and sRNAs, such as osa-miR444a-3p.2-MADS47, bdi-miR408-5p_1ss19TA-CCX1, tae-miR9774_L-2R-1_1ss11GT-carC, ata-miR169a-3p-PAO2, and bdi-miR528-p3_2ss15TG20CA-HOX24. The functional annotations revealed that they were involved in mediating the brassinosteroid signal pathway, transporting and exchanging sodium and potassium ions and regulating the oxidation–reduction process, hydrolase activity, plant response to water deprivation, abscisic acid (ABA) and the ABA-activated signaling pathway to regulate drought stress. Five hub genes were discovered, which could play central roles in the regulation of drought-responsive genes. These results show that the combined analysis of miRNA, the transcriptome and degradation group provides a useful platform to investigate the molecular mechanism of drought resistance in A. mongolicum and could provide new insights into the genetic engineering of Poaceae crops in the future.

Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants

“…In Agropyron mongolicum, five miRNAs including osa-miR444a-3p.2, bdi-miR408-5p_1ss19TA, taemiR9774_L-2R-1_1ss11GT, ata-miR169a-3p, and bdi-miR528-np3_2ss15TG20CA were identified that target drought-associated genes such as MADS47T, CCX1, carC, PAO2, and HOX24 that are involved in the regulation of brassinosteroid (BR) mediated signaling pathway, Na + /K + transport, hydrolase activity, and oxidation-reduction process, respectively (Fan et al, 2022). Similarly in Dendrobium huoshanense and grapevine, a miR156 was identified that targets SQUAMOSA-promoter binding protein-like (SPL) and VvSBP8, VvSBP13, respectively that regulate the development of lateral roots under drought stress conditions.…”

Insights into the Early Steps of the Symbiotic Interaction between Soybean (Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing

“…The regulatory functions of miRNAs have been identified in different crops. , Degradome sequencing analysis revealed that ppe-MIR169i-p5_2ss17GT19TG is potentially important for drought stress in Medicago ruthenica . Using transcriptome, miRNAome, and degradation genome analyses, Fan et al identified five hub genes and their regulated/targeted miRNAs in the drought stress network of Agropyron mongolicum . The miR5075-mediated gene interaction network regulating seed vigor in rice was identified using degradome sequencing .…”

“…51 Using transcriptome, miRNAome, and degradation genome analyses, Fan et al identified five hub genes and their regulated/targeted miRNAs in the drought stress network of Agropyron mongolicum. 49 The miR5075mediated gene interaction network regulating seed vigor in rice was identified using degradome sequencing. 52 It is important to note that degradome sequencing does not rely on bioinformatics predictions for miRNA interactions with target genes.…”

“…Essentially, it allows the identification and functional analysis of miRNA-regulated target genes. The regulatory functions of miRNAs have been identified in different crops. , Degradome sequencing analysis revealed that ppe-MIR169i-p5_2ss17GT19TG is potentially important for drought stress in Medicago ruthenica . Using transcriptome, miRNAome, and degradation genome analyses, Fan et al identified five hub genes and their regulated/targeted miRNAs in the drought stress network of Agropyron mongolicum .…”

The Agropyron mongolicum bHLH Gene AmbHLH148 Positively Involved in Transgenic Nicotiana benthamiana Adaptive Response to Drought Stress

“…However, until now, there have been no studies exploring the drought-responsive bHLH family genes in A. mongolicum. In a previous investigation that leveraged transcriptome sequencing data obtained from A. mongolicum during different drought treatment periods (NCBI, PRJNA742257 [50]), 23 bHLH genes were identified through bioinformatics screening. Among them, A. mongolicum's AmbHLH148 exhibited significant upregulation in response to drought stress [51].…”