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

被引：6
作者：
Fan, Bobo [1 ]
Sun, Fengcheng [2 ]
Yu, Zhuo [1 ]
Zhang, Xuefeng [1 ]
Yu, Xiaoxia [1 ]
Wu, Jing [1 ]
Yan, Xiuxiu [1 ]
Zhao, Yan [3 ]
Nie, Lizhen [2 ]
Fang, Yongyu [2 ]
Ma, Yanhong [1 ]
机构：
[1] Inner Mongolia Agr Univ, Agr Coll, Hohhot, Peoples R China
[2] Inner Mongolia Acad Agr & Anim Husb Sci, Hohhot, Peoples R China
[3] Inner Mongolia Agr Univ, Coll Grassland Resources & Environm, Hohhot, Peoples R China
来源：
FRONTIERS IN PLANT SCIENCE | 2022年 / 13卷
基金：
中国国家自然科学基金;
关键词：
Agropyron mongolicum Keng; drought resistance; microRNAs; transcriptome; degradome; integration analysis; co-expression network; TARGET GENES; EXPRESSION; PLANT; MICRORNAS; CROP; TOLERANCE; MIRNAS; OVEREXPRESSION; IDENTIFICATION; RESISTANCE;
D O I：
10.3389/fpls.2022.976684
中图分类号：
Q94 [植物学];
学科分类号：
071001 ;
摘要：
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.
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页数：21
相关论文
共 95 条
[1]  
Abid U., Heng S., Xiyan Y., Zhang X.L., Drought coping strategies in cotton: increased crop per drop, Plant Biotechnol. J, 15, pp. 271-284, (2017)
[2]  
Addo-Quaye C., Snyder J.A., Park Y.B., Li Y.-F., Sunkar R., Axtell M.J., Sliced microRNA targets and precise loop-first processing of miR319 hairpins revealed by analysis of the physcomitrella patens degradome, RNA, 15, pp. 2112-2121, (2009)
[3]  
Ali N., Shah F., Muhammad A., Usman A., Amanullah, Sumera A., Et al., miRNAs: major modulators for crop growth and development under abiotic stresses, Biotechnol. Lett, 39, pp. 685-700, (2017)
[4]  
Allen E., Xie Z., Gustafson A.M., Carrington J.C., microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants, Cell, 121, pp. 207-221, (2005)
[5]  
Andrew D.B.L., Ainsworth Elizabeth A., Bernacchi Carl J., Rogers A., Ort Donald O.D., Elevated CO<sub>2</sub> effects on plant carbon, nitrogen, and water relations: six important lessons from face, J. Exp. Bot, 60, pp. 2859-2876, (2009)
[6]  
Angelini R., Cona A., Federico R., Fincato P., Tavladoraki P., Tisi A., Plant amine oxidases “on the move”: an update, Plant Physiol. Biochem, 48, pp. 560-564, (2010)
[7]  
Bano N., Fakhrah S., Mohanty C.S., Bag S.K., Transcriptome meta-analysis associated targeting hub genes and pathways of drought and salt stress responses in cotton (gossypium hirsutum): a network biology approach, Front. Plant Sci, 13, (2022)
[8]  
Berninger P., Gaidatzis D., Nimwegen E.V., Zavolan M., Computational analysis of small RNA cloning data, Methods, 44, pp. 13-21, (2008)
[9]  
Bilgin C.C., Ercan A., Baohong Z., Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes, Plant Biotechnol. J, 14, pp. 1727-1746, (2016)
[10]  
Bin T., Yusun S., Aaron N., Xia L., Jie Z., Aiqin W., Et al., Integration of small RNA and degradome sequencing reveals the regulatory network of al-induced programmed cell death in peanut, Int. J. Mol. Sci, 23, pp. 246-264, (2021)
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