Ontology highlight
ABSTRACT:
PROVIDER: PRJNA665779 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12717462_1.fastq.gz | Fastqsanger.gz | |||
| SRR12717462_2.fastq.gz | Fastqsanger.gz | |||
| SRR12717463_1.fastq.gz | Fastqsanger.gz | |||
| SRR12717463_2.fastq.gz | Fastqsanger.gz | |||
| SRR12717464_1.fastq.gz | Fastqsanger.gz |
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Project description:Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. Gall wasps undergo two generations each year, and the galls formed by these two generations exhibit markedly different appearances. We sequenced the transcriptomes of both the sexual and asexual generations of Neuropterus quercusbaccarum and Neuroterus numismalis. The transcriptomes of the generations that occur at the same time of year are more similar to each other than they are to the opposite generation of their respective species.
2024-06-18 | GSE244168 | GEO
Project description:Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary parasites that affect a high variety of plants with a negative impact in the production of crops such as tomato. The infective RKN induces in the roots 4-7 highly specialized feeding cells (giant cells, GCs) developed into a hypertrophy cellular tissue or visible root swelling called M-bM-^@M-^\gallM-bM-^@M-^]. During GCs differentiation drastic alterations in genes expression occurs. However, information on genome-wide transcriptional profiles specifically in GCs is still lacking. With the aim to identify potential targets specifically regulated in GCs, we performed a temporal and spatial differential transcription profiling of tomato (Solanum lycopersicum), during the course of Meloidogyne javanica infection hybridizing TOM1 microarrays with hand-dissected galls at 1, 3, 7 and 14 days post-infection (dpi) and GCs exclusively isolated by LASER CAPTURE MICRODISSECTION (LCM) at 3 and 7 dpi. A GCs and galls comparison, at the same stage of development, reveals clear differences between their transcriptional patterns. For this purpose, a fast and efficient method to isolate LCM GCs from cryopreserved galls in the earliest differentiation state described to date: 48-72-hour post-infection (3 dpi), allowing good RNA preservation, was developed. In galls transcriptomic anaylsis, about 3000 galls and 4400 control uninfected root fragments were carefully hand-dissected at 1, 3, 7 and 14 dpi. Thus, more than 12 plates with 8 individual infected plants each, and 18 plates with the same number of plants as controls were used for only one independent experiment in each time point. Total RNA from two independent experiments was equimolarly pooled at each time of infection, in order to achieve a biological replicate for galls or control regardless. Therefore, a total of 6 independent experiments were performed to obtain 3 independent biological replicates for each infection point of galls and control analyzed. Following isolation, total RNA pooled from galls and control were subjected to a single round of linear amplification. In GCs transcriptomic analysis, independent biological replicates of aRNA from 300 GCs versus 600 control cells (CCs) from control root LCM at 3 and 7 dpi were obtained. Fifty GCs and 100 CCs were independently captured from sections onto separate CapSure HS LCM caps, and total RNA isolation was performed from each cap. RNA from six separate caps was pooled for a single biological replicate of GCs or CCs, respectively. In total, three independent biological replicates were processed. Thus, near to 7000 individual cells were harvested by LCM. The material was obtained from more that 18 independent infection experiments.
2012-06-14 | E-GEOD-30048 | biostudies-arrayexpress
Project description:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age.
2009-11-19 | GSE13927 | GEO
Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.
2014-08-13 | GSE54542 | GEO
Project description:Priming of plant defenses provides increased plant protection against herbivores and reduces the allocation costs of defense. Defense priming in woody plants remains obscure, in particular due to plant development traits such as the endogenous rhythmic growth displayed by oaks (Quercus robur). By using bioassays with oak microcuttings, and by combining transcriptomic and metabolomic analyses, we investigated how leaf herbivory by Lymantria dispar and root inoculation with the ectomycorrhizal fungus Piloderma croceum prime oak defenses. We further investigated how defense priming is modulated by rhythmic growth of the oaks. A first herbivory challenge in oak leaves primed newly grown leaves for an enhanced induction of jamonic acid (JA)-related direct defenses, or enhanced emission of volatiles, depending on the specific growth stage at which the plants where challenged. Root inoculation with Piloderma abolished the enhanced induction of JA-related defenses and volatile emission. Our results indicate that a first herbivore attack primes direct and indirect defenses of newly formed oak leaves, and that the specific display of defense priming is modulated by rhythmic growth. Our results further show that the priming memory in oaks can be transmitted to the next growth cycle even to the leaves of the new shoot unit.
2022-08-27 | GSE212157 | GEO
Project description:Some insects can redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We addressed this possibility using RNA sequencing (RNAseq) to quantify the transcriptional responses of wild grapevine (Vitis riparia Michx.) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae (Fitch 1855)). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology classes were significantly enriched in developing galls, and that expression of many putative genes involved in flower formation was significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall, and perhaps other similar galls, appears to be phenotypically and transcriptionally convergent on the plant carpel.
2018-08-16 | GSE118569 | GEO
Project description:This work aimed to characterize the molecular adaptations occurring in cork oak (Quercus suber) stems in adaptation to drought, and identify key genetic pathways regulating phellem development. One-year-old cork oak plants were grown for additional 6 months under well-watered (WW) or water-deficit (WD) conditions and main stems were targeted for transcriptomic analysis. WD had a negative impact on secondary growth, decreasing the activity of the vascular cambium and phellogen. Following a tissue-specific approach, we analyzed the transcriptional changes imposed by WD in phellem (outer bark), inner bark, and xylem, and found a global downregulation of genes related to cell division, cell wall biogenesis, lignin and/or suberin biosynthesis. Phellem and phloem showed a concerted upregulation of photosynthesis-related genes, suggesting a determinant role of stem photosynthesis in the adaptation of young plants to long-term drought. The data gathered will be important to further harness the diverse genetic background of this species for the development of optimized management practices.
2024-04-29 | E-MTAB-13376 | biostudies-arrayexpress
Project description:The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes. This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using AgilentM-bM-^@M-^Ys web-based eArray software. Labeled target cRNA (complementary RNA) was generated using AgilentM-bM-^@M-^Ys Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of FloridaM-bM-^@M-^Ys Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.
2013-10-25 | E-GEOD-51655 | biostudies-arrayexpress
Project description:Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.
2020-01-07 | GSE143201 | GEO