Bamboo phyllosphere
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ABSTRACT:
PROVIDER: PRJNA1149295 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
2013-06-21 | E-GEOD-48198 | biostudies-arrayexpress
Project description:Plants are colonized by a variety of microorganisms, the plant microbiota. In the phyllosphere, the above-ground parts of plants, bacteria are the most abundant inhabitants. Most of these microorganisms are not pathogenic and the plant responses to commensals or to pathogen infection in the presence of commensals are not well understood. We report the Arabidopsis leaf transcriptome after 3 to 4 weeks of colonization by Methylobacterium extorquens PA1 and Sphingomonas melonis Fr1, representatives of two abundant genera in the phyllosphere, compared to axenic plants. In addition, we also sequenced the transcriptome of Arabidopsis 2 and 7 days after spray-infection with a low dose of P. syringae DC3000 and in combination with the commensals.
2016-06-05 | E-MTAB-4683 | biostudies-arrayexpress
Project description:The small RNA libraries from Moso bamboo (Phyllostachy heterocycla) roots and leaves were constructed by using high definition adapters . The small RNA profiles were analyzed. A collection of micro RNAs with similarity to the micro RNA entries in mirbase were discovered. The putative genomic loci of the micro RNAs were identified. Analysis of small RNA profiles from the root and leaf tissues of young Moso Bamboo seedlings
2014-08-01 | E-GEOD-55305 | biostudies-arrayexpress
Project description:Bamboo is a large Poaceae perennial with 1,642 species worldwide. We reported single-cell transcriptomes of 14,279 filtered single cells derived from the basal root tips of Moso bamboo.
2023-08-21 | GSE229126 | GEO
Project description:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE121216 | GEO
Project description:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE122135 | GEO
Project description:Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles various of growth and developmental processes. Biological function and signal transduction pathway of BR has been well characterized in model plants like Arabidopsis and rice. However, their biological roles are still unclear in tree species, especially in an important non-timber plant moso bamboo, which has great ecological and economic value and distinguish fast-growth feature. Here we reported that reduce endogenous brassinosteroid by biosynthesis inhibitor propiconazole reduced both root and shoot growth in seedling stage. Exogenous BR application promoted shoot bract elongation and inclination of lamina joint and bract. Genome-wide transcriptome analysis were performed to identify hundreds of differential expressed genes by BR and propiconazole treatment in shoot and root parts of bamboo seedling, respectively. GO analysis revealed that BR regulates cell wall related genes, hydrogen peroxide catabolic genes and auxin related genes to promote bamboo root development and elongation. Our study identified BR response genes and provides a comprehensive resource for molecular mechanism research of bamboo growth.
2018-12-11 | GSE123529 | GEO
Project description:Dendrocalamus latiflorus Munro (D. latiflorus) is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and CRISPR-Cas9 gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2,737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135,231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
2021-11-20 | GSE155494 | GEO
Project description:The small RNA libraries from Moso bamboo (Phyllostachy heterocycla) roots and leaves were constructed by using high definition adapters . The small RNA profiles were analyzed. A collection of micro RNAs with similarity to the micro RNA entries in mirbase were discovered. The putative genomic loci of the micro RNAs were identified.
2014-08-01 | GSE55305 | GEO