Beckmannia syzigachne
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA290808 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2125726.fastq.gz | Fastqsanger.gz |
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Project description:Beckmannia syzigachne Organism overview
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Project description:Beckmannia syzigachne Raw sequence reads
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Project description:Beckmannia syzigachne Raw sequence reads
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Project description:Beckmannia syzigachne Raw sequence reads
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Project description:Beckmannia syzigachne Transcriptome or Gene expression
| PRJNA491398 | ENA
Project description:The first complete chloroplast genome (cpDNA) sequence of Beckmannia syzigachne was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 136,181 bp in length, contains a large single-copy region (LSC) of 80,345 bp and a small single-copy region (SSC) of 12,810 bp, which were separated by a pair of inverted repeats (IR) regions of 21,513 bp. The genome contains 132 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 39 transfer RNA genes. Further phylogenomic analysis showed that B. syzigachne clustered in a unique clade in the Pooideae subfamily.
| S-EPMC7872532 | biostudies-literature
Project description:Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies.
| S-EPMC4926119 | biostudies-literature
Project description:Weed resistance to herbicide can be conferred by gene mutations, and some mutations can cause pleiotropic effects in some cases. We investigated the pleiotropic effects associated with five specific ACCase mutations (Ile1781Leu, Trp2027Cys, Ile2041Asn, Asp2078Gly, and Gly2096Ala) on the plant growth, seed production, and resource competitiveness in American sloughgrass.Resistant plants (M/M) homozygous for specific ACCase mutation and susceptible wild-type plants (W/W) were derived from single heterozygous mother plant (M/W) by genotyping. Plant growth assay and neighborhood experiments were performed to quantify variation between M/M plants and W/W plants.The Ile1781Leu mutation resulted in slight increases in plant growth in pure stands and improved resource competitiveness under low-competition conditions in pot experiments, but no clear variation was observed under high competitive pressure or field conditions. During competition with wheat plants under field conditions, American sloughgrass plants containing Ile2041Asn ACCase exhibited a significantly lower (12.5%) aboveground biomass but no distinct differences in seed production or resource competitiveness. No significant detrimental pleiotropic effects associated with Gly2096Ala were detected in American sloughgrass.The Trp2027Cys mutation distinctly reduced seed production, especially under high competitive pressure, but did not significantly alter plant growth. The Asp2078Gly mutation consistently reduced not only plant growth and seed production but also resource competitiveness. Synthesis. The Trp2027Cys and Asp2078Gly mutations led to significant fitness costs, which may reduce the frequency of resistance alleles and reduce the propagation speed of resistant weeds in the absence of ACCase inhibitor herbicides. The Ile1781Leu, Ile2041Asn, and Gly2096Ala mutations displayed no obvious fitness costs or displayed very small fitness penalties, which would likely have no effect on the establishment of resistant weeds in the field.
| S-EPMC6392401 | biostudies-literature
Project description:American sloughgrass (Beckmannia syzigachne Steud.) is one of the most troublesome weeds infesting wheat and canola fields in China. Some biotypes cannot be controlled, either by acetolactate synthase (ALS) or acetyl coenzyme A carboxylase (ACCase) inhibitors, which are the main herbicides for controlling this weed. However, very few studies have investigated multiple resistance mechanism in B. syzigachne. In this study, a B. syzigachne biotype with a high resistance to ALS inhibitors we have reported was also showed relatively lower resistance to ACCase inhibitors, with a resistance index around 7. RNA-seq analysis was used to investigate the factors responsible for multiple resistance, and 60,108 unigenes were assembled by de novo transcriptome assembly and then annotated across eight databases. A Pro-197-Ser mutation was identified in the ALS gene by SNPs analysis and validated by PCR, while no mutation was identified in the ACCase gene. Nineteen candidate metabolic genes were screened and their overexpression was confirmed by qPCR. The expression of GST-T3 and GST-U6 in resistant plants ranged from 7.5- to 109.4-folds than that in susceptible ones at different times after two kinds of herbicide treatment. In addition, GST activities in resistant plants were 3.0-5.0 times higher than that in susceptible plants. Other novel resistance factors also showed high correlation with multiple resistance which included four genes encoding disease resistance proteins, a transcription factor (MYC3), and one gene conferring blight resistance. In this research, a B. syzigachne biotype was confirmed to have evolved multiple resistance to ACCase and ALS inhibitors. The Pro-197-Ser mutation in ALS gene and high-level GST activities were confirmed responsible for the multiple resistance. Characterized disease-resistance proteins, transcription factor, and blight-resistance proteins may play an essential role in these multiple herbicide resistance.
| S-EPMC7556300 | biostudies-literature
Project description:Herbicide resistance can be either target-site or non-target-site based. The molecular mechanisms underlying non-target-site resistance (NTSR) are poorly understood, especially at the level of gene expression regulation. MicroRNAs (miRNAs) represent key post-transcriptional regulators of eukaryotic gene expression and play important roles in stress responses. In this study, the miR397 gene from Beckmannia syzigachne (referred to as bsy-miR397) was functionally characterized to determine its role in regulating fenoxaprop-P-ethyl resistance. We showed that (1) bsy-miR397 transcript level is constitutively higher in resistant than in sensitive B. syzigachne plants, whereas bsy-Laccase expression and activity show the opposite trend, and (2) bsy-miR397 suppresses the expression of bsy-Laccase in tobacco, indicating that it negatively regulates bsy-Laccase at the transcriptional level. We found evidences that miR397/laccase regulation might be involved in fenoxaprop-P-ethyl NTSR. First, the rice transgenic line overexpressing OXmiR397 showed improved fenoxaprop-P-ethyl tolerance. Second, following activation of bsy-Laccase gene expression by CuSO4 treatment, fenoxaprop resistance in B. syzigachne tended to decrease. Therefore, we suggest that bsy-miR397 might play a role in fenoxaprop-P-ethyl NTSR in B. syzigachne by down-regulating laccase expression, potentially leading to the enhanced expression of three oxidases/peroxidases genes to introduce an active moiety into herbicide molecules in Phase-2 metabolism. Bsy-miR397, bsy-Laccase, and other regulatory components might form a regulatory network to detoxify fenoxaprop-P-ethyl in B. syzigachne, supported by the differential expression of transcription factors and oxidases/peroxidases in the rice transgenic line overexpressing OXmiR397. This implies how down-regulation of a gene (laccase) can enhance NTSR. Our findings shed light on the daunting task of understanding and managing complex NTSR in weedy plant species.
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