Ontology highlight
ABSTRACT:
PROVIDER: PRJNA678588 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13065784_1.fastq.gz | Fastqsanger.gz | |||
| SRR13065784_2.fastq.gz | Fastqsanger.gz | |||
| SRR13065785_1.fastq.gz | Fastqsanger.gz | |||
| SRR13065785_2.fastq.gz | Fastqsanger.gz | |||
| SRR13065786_1.fastq.gz | Fastqsanger.gz |
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Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.
2012-04-16 | GSE35143 | GEO
Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome. Examination of small RNA populations in the sugarcane leaves that show matches against sugarcane LTR-RTs.
2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress
Project description:Rhizosphere is a complex system of interactions between plant roots, bacteria, fungi and animals, where the release of plant root exudates stimulates bacterial density and diversity. However, the majority of the bacteria in soil results to be unculturable but active. The aim of the present work was to characterize the microbial community associated to the root of V. vinifera cv. Pinot Noir not only under a taxonomic perspective, but also under a functional point of view, using a metaproteome approach. Our results underlined the difference between the metagenomic and metaproteomic approach and the large potentiality of proteomics in describing the environmental bacterial community and its activity. In fact, by this approach, that allows to investigate the mechanisms occurring in the rhizosphere, we showed that bacteria belonging to Streptomyces, Bacillus and Pseudomonas genera are the most active in protein expression. In the rhizosphere, the identified genera were involved mainly in phosphorus and nitrogen soil metabolism.
2022-02-28 | PXD007670 | Pride
Project description:The small RNAs and their targets were characterized in sugarcane wild species and cultivars. This was done by deep sequencing the small RNA populations and uncapped mRNAs of young leaves from mature plants.
2023-04-01 | GSE116171 | GEO
Project description:Background and aims The endophytic diazotrophic strain CBAmC of Nitrospirillum amazonense has been reported as a plant growth promoter of sugarcane variety RB867515 when grown under field conditions. The present work aimed to assess the influence of apoplast fluid from RB867515 on the transcriptomic and proteomic profiles of CBAmC cultured in vitro. Methods RNA-Seq in Ion Proton™ and ESI-LC-MS/MS peptide analysis were used to evaluate the transcriptomic and proteomic profiles, respectively, of CBAmC exposed for 2 h to the sugarcane apoplast fluid. Results The bacterial transcriptomic and proteomic profiles were well correlated. The overall response of CBAmC to the apoplast fluid included overexpression of defense systems against reactive oxygen species (ROS) and osmotic stress, RND efflux pumps for toxic compounds, Sec and Tat secretory systems, and assimilative metabolism of iron. In contrast, active transporters of organic compounds, chemotaxis system and flagellum structure were underexpressed. Conclusions The bacterial metabolic pathways / functions activated in response to the sugarcane apoplast fluid are most likely related to its adaptation to the peculiar characteristics of the fluid. The activation of some of those functions could be determinant for its adaptation to the sugarcane apoplastic niche, and perhaps be involved in the previously observed effect of promoting plant growth. SUBMITTER_CITATION: Terra, L.A., de Soares, C.P., Meneses, C.H.S.G. et al. Plant Soil (2019). Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid.
2019-04-26 | GSE130321 | GEO
Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
2016-12-10 | GSE91083 | GEO