Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots
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ABSTRACT:
PROVIDER: PRJNA473360 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7226050_1.fastq.gz | Fastqsanger.gz | |||
| SRR7226050_2.fastq.gz | Fastqsanger.gz | |||
| SRR7226051_1.fastq.gz | Fastqsanger.gz | |||
| SRR7226051_2.fastq.gz | Fastqsanger.gz | |||
| SRR7226042_1.fastq.gz | Fastqsanger.gz |
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Project description:Here, we first systematically identified and characterized responsive mRNAs expressed in roots of sugar beet at a genome-wide scale, focusing on salt-responsive mRNAs.
2020-03-18 | GSE114968 | GEO
Project description:Beet necrotic yellow vein virus (BNYVV) and Beet soil-borne mosaic virus (BSBMV) belong to the genus Benyvirus. Both viruses share a similar genome organization, but disease development induced in their major host plant sugar beet displays striking differences. BNYVV induces excessive lateral root (LR) formation by hijacking auxin-regulated pathways; whereas BSBMV infected roots appear asymptomatic. To elucidate transcriptomic changes associated with the virus-specific disease development of BNYVV and BSBMV, we performed a comparative transcriptome analysis of a virus infected susceptible sugar beet genotype.
2019-11-06 | E-MTAB-8187 | biostudies-arrayexpress
Project description:Spinach and sugar beet plants were grown under either control or salinity stress conditions.
2023-04-27 | PXD010809 | Pride
Project description:BACKGROUND:Beta vulgaris L. is one of the main sugar-producing crop species and is highly adaptable to saline soil. This study explored the alterations to the carbon and nitrogen metabolism mechanisms enabling the roots of sugar beet seedlings to adapt to salinity. RESULTS:The ionome, metabolome, and transcriptome of the roots of sugar beet seedlings were evaluated after 1 day (short term) and 7 days (long term) of 300 mM Na+ treatment. Salt stress caused reactive oxygen species (ROS) damage and ion toxicity in the roots. Interestingly, under salt stress, the increase in the Na+/K+ ratio compared to the control ratio on day 7 was lower than that on day 1 in the roots. The transcriptomic results showed that a large number of differentially expressed genes (DEGs) were enriched in various metabolic pathways. A total of 1279 and 903 DEGs were identified on days 1 and 7, respectively, and were mapped mainly to 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the genes were involved in carbon metabolism and amino acid (AA) biosynthesis. Furthermore, metabolomic analysis revealed that sucrose metabolism and the activity of the tricarboxylic acid (TCA) cycle increased in response to salt stress. After 1 day of stress, the content of sucrose decreased, whereas the content of organic acids (OAs) such as L-malic acid and 2-oxoglutaric acid increased. After 7 days of salt stress, nitrogen-containing metabolites such as AAs, betaine, melatonin, and (S)-2-aminobutyric acid increased significantly. In addition, multiomic analysis revealed that the expression of the gene encoding xanthine dehydrogenase (XDH) was upregulated and that the expression of the gene encoding allantoinase (ALN) was significantly downregulated, resulting in a large accumulation of allantoin. Correlation analysis revealed that most genes were significantly related to only allantoin and xanthosine. CONCLUSIONS:Our study demonstrated that carbon and nitrogen metabolism was altered in the roots of sugar beet plants under salt stress. Nitrogen metabolism plays a major role in the late stages of salt stress. Allantoin, which is involved in the purine metabolic pathway, may be a key regulator of sugar beet salt tolerance.
| S-EPMC7118825 | biostudies-literature
Project description:Background: Sugar beet is an important root crop, accounting for 30 % of the sugar production worldwide. The long growing season make sugar beets exposed to a range of plant pathogens for longer periods than most other crops. Here, contrasting sugar beet genotypes were used for transcriptome analysis to reveal differential responses and new defense genes to Rhizoctonia solani, a soilborn fungal pathogen. Results: After curation of primary RNA-sequencing reads, 16,768 genes deriving from 36 samples composed of two susceptible and two resistant sugar beet genotypes, three time-points (0, two and five days post inoculation), each in three replicates were subjected for analysis. Among the elevated 217 transcripts at 2 dpi, three resistance-like genes (Bv4_088600_cumk, Bv8u_204980_frqg, and Bv_44840_iifo) were activated. By employing edgeR package statistics, 660 genes were significantly different (false discovery rate < 0.05) between resistant and susceptible genotypes in their response to R. solani inoculation. A combination of eukaryotic orthologous group assignments and gene ontology enrichment analyses, revealed three Bet v I/Major latex protein homologous genes (Bv7_162510_pymu, Bv7_162520_etow, Bv_27270_xeas) in the resistant genotypes after five days of fungal challenge. Co-expression network analysis of differentially expressed sugar beet genes further identified a MYB46 transcription factor, a plant disease resistance response protein (DRR206) and a flavonoid o-methyltransferase protein. MYB46 has a key function in secondary cell wall formation and exist as a singleton in the sugar beet genome. The genome of R. solani is enriched in cell wall degrading enzyme encoding genes and it is anticipated that they represent important virulence factors. Compared to Arabidopsis thaliana, sugar beet has 2.4-fold more carbohydrate esterases and particularly large numbers (26-fold) of auxiliary activity encoding genes whose function in cell wall biosynthesis is largely unknown. Conclusions: Based on components identified in this sugar beet transcript data set we conclude that defense responses to R. solani are attributed to a wide range of gene categories but functional information is missing to a large extent. This calls for careful integration to avoid negative side effects to obtain optimal combinations of these traits in order to reach the long-term goal of improved resistance in sugar beet.
2017-12-22 | GSE92859 | GEO
Project description:Sugar beet (Beta vulgaris subsp. vulgaris) is an economically important crop and provides nearly one third of the global sugar production annually. The beet cyst nematode (BCN), Heterodera schachtii, causes major yield losses in sugar beet worldwide. The most effective and economic approach to control this nematode is growing tolerant or resistant cultivars. To identify candidate genes involved in susceptibility and resistance, the transcriptome of sugar beet and BCN in compatible and incompatible interactions at two time points, was studied using mRNA-seq. In total, 16 cDNA libraries were constructed and 442 691 707raw reads were obtained. In the compatible interaction, many alterations in phytohormone-related genes were detected. The effect of exogenous application of methyl jasmonate and ethephon was therefore investigated and the results revealed significant reduction of J2s infection and female development rates in treated susceptible plants. Our results revealed candidate genes putatively involved in the Hs1pro1-induced resistance, such as genes related to phenylpropanoid pathway, putative R genes and genes encoding F-box proteins, zinc finger and NAC transcription factors, ABC transporters, BURP and CYSTM proteins. Also, the transcriptome of BCN in the infected root samples was analyzed and several nematode effector genes were found. Our study is the first investigation of the transcriptome profile in the compatible and incompatible interactions between sugar beet and BCN.
2020-08-08 | GSE135555 | GEO
Project description:By comparing the difference of protein changes between sugar beet with resistance genotype and sensitive genotype after freezing, the mechanism of freezing resistance in sugar beet was revealed.
2023-01-05 | PXD039262 |
Project description:We analyzed lncRNAs and mRNAs from sugar beet leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of lncRNAs and mRNAs and their potential function in the regulation of drought responses.
2023-01-12 | GSE205413 | GEO
Project description:The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.
2014-12-31 | GSE56413 | GEO
Project description:The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.
2014-12-31 | GSE55951 | GEO