Dataset Information

Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses.

ABSTRACT: DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

SUBMITTER: Xu W

PROVIDER: S-EPMC8493098 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses.

Xu Wenying W Liu Tong T Zhang Huiying H Zhu Hong H

Frontiers in genetics 20210922

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 V ...[more]

PMID: 34630501

Similar Datasets

Project description:By applying Illumina Novaseq 6000, Chlorella sp. TLD6B cells of the control group on day zero and 18, as well as under low salt stress (NaCl1) and under high salt stress (NaCl2) on day 18 were selected for transcriptome sequencing analysis. Meanwhile, 0.05 g/mL ( PEG1) and 0.1 g/mL PEG-6000 (medium for drought stress, PEG2 ) were used to prepare the drought-stressed Chlorella sp. TLD6B cells. Each treatment had two replicates. Clean data were filtered after the removal of adapters, poly-N strands, and low-quality reads. There were no reference genomes for Chlorella sp. TLD6B, and de novo assembly for clean reads was performed by using Trinity. The sequences were compared with databases such as NR, NT, Swiss-Pro, GO, KEGG, PFAM, and KOG using Blast X (e-value ≤ 10-5). The GO annotation of unigenes was obtained using BLAST2GO. FPKM method was used for the analysis of gene expression levels (Trapnell et al., 2010). Out of six samples, a total of 963,078,184 raw reads were generated. A total of 947,225,244 clean reads were obtained based on the base quality score and read length. Meanwhile, the GC percentage in clean reads reached nearly 66.0%, with Q20 being above 96%. A total of 219,577 transcripts with an average length of 1,394 bp were obtained. In total, 155,503 non-redundant unigenes were assembled for the following analyses. The length of the unigenes ranged from 200 bp to 23,825 bp, with an average length of 1,842 bp. Under different salt stress, verification had been conducted with qRT-PCR on nine unigenes of different pathways, which were related to lipid metabolism. The detection results by qRT-PCR were highly correlated with RNA-Seq results (r = 0.890, r2 = 0.791), which indicated that the RNA-Seq data of Chlorella sp. TLD6B under salt stress were accurate and reliable. Our study represents the first detailed analysis of Chlorella sp. TLD6B under salt stress transcriptomes. Hierarchical clustering of differentially expressed genes uncovered several currently uncharacterized genes that may contribute to the function about lipid accumulation of Chlorella sp. TLD6B under salt stress.

Project description:BackgroundDrought and soil salinity are major abiotic stresses. The mechanisms of stress tolerance have been studied extensively in model plants. Caragana korshinskii is characterized by high drought and salt tolerance in northwestern China; unique patterns of gene expression allow it to tolerate the stress imposed by dehydration and semi-desert saline soil. There have, however, been no reports on the differences between C. korshinskii and model plants in the mechanisms underlying their drought and salt tolerance and regulation of gene expression.ResultsThree sequencing libraries from drought and salt-treated whole-seedling- plants and the control were sequenced to investigate changes in the C. korshinskii transcriptome in response to drought and salt stresses. Of the 129,451 contigs, 70,662 (54.12 %) were annotated with gene descriptions, gene ontology (GO) terms, and metabolic pathways, with a cut-off E-value of 10(-5). These annotations included 56 GO terms, 148 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups (COG). On comparison of the transcriptomes of the control, drought- and salt-treated plants, 1630 and 1521 contigs showed significant differences in transcript abundance under drought and salt stresses. Compared to the differentially expressed genes (DEGs) in drought- or salt-treated Arabidopsis in the database, 542 DEGs in drought-treated C. korshinskii and 529 DEGs in salt-treated samples were presumably unique to C. korshinskii. The transcription profiles revealed that genes related to transcription factors, protein kinases, and antioxidant enzymes are relevant to the tolerance of drought and salt stress in this species. The expression patterns of 38 randomly selected DEGs were confirmed by quantitative real-time PCR and were essentially consistent with the changes in transcript abundance identified by RNA-seq.ConclusionsThe present study identified potential genes involved in drought and salt tolerance in C. korshinskii, as well as many DEGs uniquely expressed in drought- or salt-treated C. korshinskii samples compared to Arabidopsis. To our knowledge, this study is the first exploration of the C. korshinskii transcriptome under drought and salt conditions, and these results will facilitate the discovery of specific stress-resistance-related genes in C. korshinskii, possibly leading to the development of novel plant cultivars through genetic engineering.

Project description:Drought and salinity are severe and wide-ranging abiotic stresses that substantially affect crop germination, development and productivity, and seed germination is the first critical step in plant growth and development. To comprehensively investigate small-RNA targets and improve our understanding of miRNA-mediated post-transcriptional regulation networks during Brassica napus seed imbibition under drought and salt stresses, we constructed three small-RNA libraries from B. napus variety ZS11 embryos exposed to salt (200 mM NaCl, denoted "S"), drought (200 g L(-1) PEG-6000, denoted "D"), and distilled water (denoted "CK") during imbibition and sequenced them using an Illumina Genome Analyzer. A total of 11,528,557, 12,080,081, and 12,315,608 raw reads were obtained from the CK, D, and S libraries, respectively. Further analysis identified 85 known miRNAs belonging to 31 miRNA families and 882 novel miRNAs among the three libraries. Comparison of the D and CK libraries revealed significant down-regulation of six miRNA families, miR156, miR169, miR860, miR399, miR171, and miR395, whereas only miR172 was significantly up-regulated. In contrast, comparison of the S library with the CK library showed significant down-regulation of only two miRNA families: miRNA393 and miRNA399. Putative targets for 336, 376, and 340 novel miRNAs were successfully predicted in the CK, D, and S libraries, respectively, and 271 miRNA families and 20 target gene families [including disease resistance protein (DIRP), drought-responsive family protein (DRRP), early responsive to dehydration stress protein (ERD), stress-responsive alpha-beta barrel domain protein (SRAP), and salt tolerance homolog2 (STH2)] were confirmed as being core miRNAs and genes involved in the seed imbibition response to salt and drought stresses. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs as well as the predicted target genes. Our data suggest that diverse and complex miRNAs are involved in seed imbibition, indicating that miRNAs are involved in plant hormone regulation, and may play important roles during seed germination under salt- or drought-stress conditions.

Dataset Information

Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses.

Publications

Mungbean <i>DIRIGENT</i> Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets