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ABSTRACT:
PROVIDER: PRJNA1057803 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phytophthora sansomeana strain:Psa-2310 Genome sequencing and assembly
| PRJNA1057580 | ENA
Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240964 | GEO
Project description:Phytophthora root and stem rot (PRR) caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied, the molecular basis underlying immune responses to the newly recognized pathogen, Phytophthora sansomeana, remains largely unknown. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Through comparative transcriptomic analyses, we identified a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in the resistant lines compared to the susceptible lines, predominantly at 8 and 16 hpi. These DEGs were associated with multiple phytohormones, including ethylene, salicylic acid, and jasmonic acid, along with various transcription factors and signaling cascade proteins. Moreover, DE transposable elements (TEs) were predominantly up-regulated after inoculation, and we found that TEs differentially transcribed in a resistant line were enriched near genes. Notably, we identified a long non-coding RNA (lncRNA) that was significantly differentially transcribed after inoculation exclusively in the resistant lines, potentially regulating two flanking LURP-one-related genes, known as key defense mediators in Arabidopsis against oomycete pathogens. Furthermore, DNA methylation analysis revealed increased CHH (H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in the resistant line compared to the susceptible line. Overall, our results provide insights into the molecular mechanisms underlying resistance to P. sansomeana in soybean and underscore the potential role of lncRNAs and epigenetic regulation in plant defense responses.
2023-11-24 | GSE240965 | GEO
Project description:First draft genome sequence resource of a strain of Fusarium falciforme isolated in Sinaloa, Mexico
| PRJNA843444 | ENA
Project description:We report the H3K27me3 profile on Avr1b locus in two Phytophthora sojae strains P6497 and pssu(z)12 mutant. Nuclei of Phytophthora sojae P6497 and pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) was extracted and digested to 200-400bp using micrococcal nuclease (MNase: NEB M0247S). The antibody Millipore 07-449 was used to immunoprecipitation. We find significant accumulation of H3K27me3 at Avr1b locus in Avr1b silencing strain P6497 and clear H3K27me3 depletion at Avr1b locus in Avr1b unsilenced strain pssu(z)12 mutant T34.
2019-11-25 | GSE127206 | GEO
Project description:L. helveticus is used to modulate cheese flavor and as a starter organism in certain cheese varieties. Our group has compiled a draft (4x) sequence for the 2.4 Mb genome of an industrial strain L. helveticus CNRZ32. The primary aim was to investigate expression of 168 completely sequenced genes during growth in milk and MRS medium using microarrays. Oligonucleotide probes against each of the completely sequenced genes were compiled on maskless photolithography-based DNA microarrays. Additionally, the entire draft genome sequence was used to produce tiled microarrays where the non-interrupted sequence contigs were covered by consecutive 24-mer probes. Keywords: growth conditions response
2007-02-14 | GSE7005 | GEO
Project description:Data from multiple high throughput technologies such as RNA sequencing (RNA-Seq) and protein mass spectrometry (MS/MS) are often used to assist in predicting eukaryote genome features such as genes, splice variants, and single nucleotide variants (SNVs). The genomes of parasitic nematodes causing neglected tropical diseases are often poorly annotated. Angiostrongylus costaricensis, a nematode that causes an intestinal inflammatory disease known as abdominal angiostrongyliasis (AA), is one example. Currently, no drugs or treatments are available for AA, a public health problem in Latin America, especially in Costa Rica and Brazil. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction supplemented the reference annotation with a) novel coding and non-coding genes; b) pieces of evidence of alternative splicing generating new proteoforms; c) a list of SNVs specific to the Brazilian strain (Crissiumal). To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of a parasitic nematode. We hope this supplemented genome annotation can assist the future development of drugs to treat AA caused by either Brazil strain (Crissiumal) or Costa Rica strain.
2023-03-11 | PXD034605 | Pride
Project description:In this study, we used the illumina high throughput sequencing approach (Sequencing-By-Synthesis, or SBS) to develop the sequence resource of black pepper. To identify micro RNAs functioning in stress response of the black pepper plant, small RNA libraries were prepared from the leaf and root of Phytophthora capsici infected plants, leaves from drought stressed and control plants.
2017-08-24 | GSE65782 | GEO