Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

ABSTRACT: Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation. We used microarrays to characterize gene expression patterns in the root rot pathogen Phytophthora sojae and its host Glycine max. Keywords: infection time course, zoospore germination time course, media formulation response 28 samples from 9 treatments; 2 to 5 biological replicates per treatment.

ORGANISM(S): Phytophthora sojae

SUBMITTER: Mark Gijzen

PROVIDER: E-GEOD-15100 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The Phytophthora sojae avirulence locus Avr3c encodes a multi-copy RXLR effector with sequence polymorphisms among pathogen strains.

Dong Suomeng S Qutob Dinah D Tedman-Jones Jennifer J Kuflu Kuflom K Wang Yuanchao Y Tyler Brett M BM Gijzen Mark M

PloS one 20090515 5

Root and stem rot disease of soybean is caused by the oomycete Phytophthora sojae. The avirulence (Avr) genes of P. sojae control race-cultivar compatibility. In this study, we identify the P. sojae Avr3c gene and show that it encodes a predicted RXLR effector protein of 220 amino acids. Sequence and transcriptional data were compared for predicted RXLR effectors occurring in the vicinity of Avr4/6, as genetic linkage of Avr3c and Avr4/6 was previously suggested. Mapping of DNA markers in a F(2) ...[more]

PMID: 19440541

Similar Datasets

Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

Project description:Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation. We used microarrays to characterize gene expression patterns in the root rot pathogen Phytophthora sojae and its host Glycine max. Keywords: infection time course, zoospore germination time course, media formulation response

2009-06-22 | GSE15100 | GEO

Digital gene expression profiling of the Phytophthora sojae transcriptome

Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.

2011-09-01 | E-MTAB-4039 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora sojae mycelium small RNAs were sequenced and aligned to the P. sojae genome for analysis. *Raw data files (fastq) are unavailable for this study.

2013-10-21 | E-GEOD-50032 | biostudies-arrayexpress

Digital gene expression profiling of the Phytophthora sojae transcriptome

Project description:The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes expression patterns suggested four groups: 1) mycelia and zoosporangia (MY and SP); 2) zoospores and cysts (ZO and CY); 3) germinating cysts (GC); 4) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression pattern clusters were obtained and the top 16 ones, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and non-coding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis related gene families revealed that most were infection induced, but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established. The five axenically grown stages were mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY), and germinating cysts (GC). The five infection stages, 1.5, 3, 6, 12 and 24 h after inoculation onto susceptible soybean leaf tissues (IF1.5h to IF24h).

2011-09-01 | E-GEOD-29651 | biostudies-arrayexpress

Host and pathogen gene expression during early infection of soybean seedlings by Phytophthora sojae, analyzed by ABI Solid RNA sequencing

Project description:Hypocotyls of soybean (Glycine max) seedlings of cultivar Williams were inoculated with mycelia of the oomycete pathogen Phytophthora sojae grown in liquid V8 medium or the hypocotyls were mock inoculated. After 12 hours, the sites of inoculation were excised from the hypocotyls and frozen for RNA extraction. Phytophthora sojae mycelia used for inoculation was saved for RNA extraction also

2021-08-28 | GSE182773 | GEO

Microarray Analysis of Phytophthora sojae Gene Expression During Early Infection

Project description:P.sojae isolate P6954 - that is nearly identical with strain P6947 with the only exception that P6954 expresses Avr1b during infection is used in this study. 2 days post culture, P.sojae mycelia are inoculated onto 9 day old soybean hypocotyls of highly susceptible cultivar Sloan that were grown under natural sunlight inside a green house. Infected samples were harvested after 0, 3, 6 and 12 hours. We analyzed 12 soybean arrays.

2010-07-19 | E-GEOD-22978 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA

Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora infestans mycelium small RNAs were sequenced and aligned to the P. infestans genome for analysis.

2013-10-21 | E-GEOD-50030 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA

Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level. Phytophthora ramorum mycelium small RNAs were sequenced and aligned to the P. ramorum genome for analysis. *Raw data files (fastq) are unavailable for this study.

2013-10-21 | E-GEOD-50031 | biostudies-arrayexpress

Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae

Project description:Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions. 22 samples were sequenced, 11 inoculated with P. sojae, the other 11 were mock-inoculated

2014-04-16 | E-GEOD-48524 | biostudies-arrayexpress

Phytophthora sojae, race 2, infection of soybean hypocotyls

Project description:Examination of soybean hypocotyls, G. max cv. Harosoy (Rps7), at 3, 6, 12, 24 and 48 hours after inoculation with P. sojae, race 2, isolate P6497 Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae. P. Moy, D. Qutob, B. P. Chapman, I. Atkinson, and M. Gijzen. Pages 1051-1062. Publication no. M-2004-0728-01R. Molecular Plant-Microbe Interactions, October 2004, Volume 17, Number 10. Keywords: time-course

2004-09-14 | GSE1352 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data