- De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-. - Background: Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. - Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. - The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. - Based on similarity searches had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. - functionally annotated under salt, alkali, and drought stress, these include MYB, bZIP, NAC and WRKY family. - DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes. - this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. - We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - According to the Food and Agriculture Organization of the United Nations, more than 400 mil- lion hectares of land on the major continents are af- fected by salt [3]. - Stress- regulatory mechanisms in higher plants have been ana- lyzed by researching many of the genes related to abiotic- stress tolerance at the transcriptional level [11, 12]. - thaliana, about 30% of the transcriptome is considered to be involved in abiotic-stress regulation, and 2409 genes have been iden- tified as being of great importance in drought resistance, salt tolerance, and resistance to cold [27, 28].. - Sophora alopecuroides L. - had significant matches in the Nr database (NCBI re- dundant protein Sequences in the Nt database (NCBI nucleotide Sequences), and in the Swiss-Prot database. - The salt-, alkali-, and drought-treatment samples were examined by GO functional significant enrichment analysis. - In the biological process, the most enriched categories in salt- and drought-treatment were the bio- synthetic, organic substance biosynthetic, and cellular biosynthetic processes. - In contrast, in the alkali- treatment samples, the most enrichment occurred in the metabolic process category. - In the cellular component, the most enrichment occurred in relation to cellular morphology, cell, and intracellular. - In the molecular function, the most enrichment occurred in relation to structural constituents of ribosome, structural molecule activity, and molecular function (Fig. - Of the 1673 DEGs sequenced from the salt-treatment samples, 616 were annotated to 61 metabolic pathways (Table S1). - Of these, 64 up-regulated DEGs were annotated in 25 of the metabolic pathways, and 552 down-regulated genes were annotated in 55 of the metabolic pathways. - In the process of plant secondary metabolite synthesis, the coenzyme A gene, SaCoA, involved in the phenylpro- panoid biosynthesis pathway (ko00940) and phenylalanine metabolism (ko00360), corresponds to the upregulation of differential genes under salt stress. - In the study of Zygophyllum spp., it was found that under salt stress conditions, the CoA contents of the salt-tolerant varieties in the control group and the salt-treated group did not differ significantly, whereas the CoA contents of the salt-sensitive varieties decreased sig- nificantly [33]. - In the ABA signaling pathway, SaPYL4–1, SaPYL4–2, SaPYL4–3, SaPYL4–4, and SaPYL5–1 were found to be related to ABA receptors (Table S2). - This result is consistent with the confirmed relationship between PYL and PP2C in the ABA signaling pathway [34]. - In the signaling pathway of the plant hormone bras- sinolide, a gene SaTCH4 related to xyloglucosyl transfer- ase TCH4 was identified under salt stress. - This gene is involved in the regulation of cell elongation, which may be related to the suppression of plant growth under salt stress conditions [35].. - Of the 8142 DEGs sequenced from the alkali-treatment samples, 2644 DEGs were annotated to 118 metabolic Table 2 BLAST analysis of non-redundant unigenes sequenced for Sophora alopecuroides, against public databases. - pathways in the KEGG database. - Under alkali stress, the positive regulatory gene SaNPR1 was obtained in the signal transduction path- way. - The SaNPR1 gene was annotated as a regulatory protein NPR1-like, which is a positive regulatory gene in the salicylic acid signal pathway. - In the ethylene signaling pathway, 17 genes re- lated to serine/threonine-protein kinase CTR1 were upregulated. - Six negative regulatory genes were ob- tained in the auxin signaling pathway, including the auxin influx carrier (AUX1 LAX family) gene SaAUX1, and. - A_ST&CK ” (panel b) the number of DEGs between the alkali treatment and control, and “ DT&CK ” (panel c) the number of DEGs between the drought treatment and control. - In the gib- berellin signaling pathway, the negatively regulated DELLA protein GAI-like gene SaGAI was obtained, which was mainly involved in plant stem growth and induction of ger- mination. - In the brassinolide signaling pathway, the nega- tively regulated D3-type cyclin isoform 1 gene, SaCYCD3, was obtained, which was mainly involved in the cell division process. - The negative regulatory genes we obtained are mainly involved in the growth and development of plants [43–52]. - Furthermore, we obtained two up-regulated genes in the plant secondary metabolite synthesis pathway, namely SaGCDH and SaOMT6. - These genes are mainly involved in the removal of ROS responding to stress, and thus. - Of the 17,479 DEGs sequenced from the drought- treatment samples, 6546 DEGs were assigned to 121 metabolic pathways. - Of the 121 metabolic pathways, one was an- notated to up-regulated DEGs, and 100 contained both up-regulated and down-regulated genes. - Under drought stress, multiple positively regulated ex- pression genes were obtained in the phytohormone sig- nal transduction pathway and found to participate in the ABA signaling pathway. - 3 Functional classification of the assembled unigenes for Sophora alopecuroides. - These genes are mainly involved in the active oxygen scavenging mechan- ism. - The number of DEGs under saline, alkaline and drought conditions was quite different (Fig. - The number of DEGs in the drought treatment was 17,479, of which 2036 were upregulated and 15,443 were downregulated.. - In the alkaline treatment 8142 DEGs were obtained, of which 6271 were upregulated and 1871 were downregu- lated. - The sum of the numbers in each large circle represents the total number of DEGs between combinations. - The overlapping part of the circles represents DEGs for the treatment combinations. - SaMYB1 belongs to LHY (K12133) of the circadian rhythm – plant pathway (Ko04712) in the KEGG pathway analysis. - We speculate that SaMYB14, SaMYB1, SaMYB5, and SaMYBG might also have similar regulatory functions under salt, alkali, and drought stress.. - and Sab- ZIP5, downregulated under both salt and drought stress (Table S2). - Both SaWRKY27 and SaWRKY33 were upregulated under alkali stress and participated in the plant- pathogen interaction (Ko04626) pathway. - SaWRKY38 was downregulated under both alkali and drought stress conditions. - In peanut, 73 differen- tially expressed AhWRKY genes affected by drought stress were obtained through expression pattern analysis of the WRKY gene family [73]. - The overex- pression of the wheat WRKY transcription factor gene TaWRKY13 can significantly improve salt tolerance in rice, indicating that the WRKY transcription factor was a positive factor responding to salt stress [75].. - We analyzed NAC transcription factors and found that SaNAC2, SaNAC5, and SaNAC25 were upregulated under alkali stress and drought stress (Table S2). - Through transcriptome analysis of 4 cotton varieties, it was determined that 120 NAC transcription factor genes may be involved in response to salt, alkali and drought stress [77]. - Idenfication of the differentially expressed genes (DEGs) To confirm that the DEGs obtained by Illumina Hiseq 2000 and 2500 platform sequencing were credible, 24 DEGs (13 up-regulated and 11 down-regulated) were ran- domly chosen for qRT-PCR analysis (Fig. - Sophora alopecuroides (known as ku dou zi in Chinese medicine) is famous for its tolerance to high salinity, al- kalinity and drought. - alopecuroides under different stress treatments, explored the changes in DEGs and metabolic pathways under salt, alkali, and drought stress, and searched for genes related to abiotic- stress resistance. - This study focuses on the expression of genes in the roots of Sophora alopecuroides, which has some limitations. - In the salt and drought treatments, the most abundant DEG types were those involved in bio- synthesis. - In the alkali treatment, the most abundant DEGs were those involved in metabolic processes. - By cross-analysis of DEGs obtained under the three treatments, we found that only four of the up-regulated DEGs were shared among the three treatments. - Under drought treatment the expression of PYL- related genes in the ABA signaling pathway was differ- ent from that under saline-alkali stress. - In addition, under salt treatment conditions, a down- regulated gene SaTCH4 was identified in the brassinos- teroid biosynthesis pathway, specifically in xyloglucosyl transferase TCH4. - CTR1 encodes a member of the protein kin- ase Raf family, and down-regulates the ethylene response pathway in A. - alopecuroides uses different processes to cope with alkali and drought stress. - Further, this analysis provides a new approach for studying the role of the CTR1 gene in alkali-stress responses in S.. - In the KEGG enrichment path- way sequences, our salt, alkali, and drought treatments all reflected the presence of superoxide dismutase, per- oxidase, and catalase. - We have identi- fied many candidate functional genes that are involved in multiple salt, alkali, and drought stress tolerance mechanisms, and these should be studied further. - For the salt, alkali, and drought treatments, 1.2%. - After 72 h of treatment, the root tissues of the con- trol group and the treatment group were taken, and stored at − 80 °C.. - Then use the 2100 bioanalytical instrument to evaluate the quality of the obtained RNA.. - To verify the reliability of the sequencing results, 24 unigenes were randomly selected for expression analysis. - To perform qRT-PCR, 20 μL of reaction mixture was placed in a 96-well plate in the StepO- nePlus™ Real-Time PCR System using SYBR Premix Ex Taq™ II kit. - The expression level of the actin gene (J01298) was used to normalize target gene expression. - This figure provides the phenotype under salt, alkali and drought treatment (The figures were taken by authors themselves).. - Statistics of the number of DEGs corresponding to KEGG metabolic pathways. - Statistics of the number of transcription factors corresponding to each transcription factor family. - NaCl and Na 2 SiO 3 coexistence strengthens growth of the succulent xerophyte Nitraria tangutorum under drought. - Drought stress responses in crops. - De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. - De novo assembly of the desert tree Haloxylon ammodendron (C. - Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana. - Landscape of the lipidome and transcriptome under heat stress inArabidopsis thaliana. - Transcriptomic and metabolomic analysis reveals the role of CoA in the salt tolerance of Zygophyllum spp.. - Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments. - Reciprocal Regulation of the TOR Kinase and ABA Receptor Balances Plant Growth and Stress Response. - The soybean gene, GmMYBJ2,encodes a R2R3-type transcription factor involved in drought stress tolerance in Arabidopsis thaliana. - Genome-wide analysis of the bZIP transcription factors in cucumber. - Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes. - CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the Raf family of protein kinases. - Cloning and functional analysis of the CTR1 in soybean. - Interactions between biosynthesis, compartmentation and transport in the control of glutathione homeostasis and signaling. - Drought and oxidative load in the leaves of C3 plants: a predominant role for photorespiration? Ann Bot. - Mutation landscape and intra-tumor heterogeneity of two MANECs of the esophagus revealed by multi-region sequencing.
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