Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome sequencing of the Cassava (Manihot esculenta) latex parasite Phytomonas francai

ABSTRACT: Phytomonas are a large and diverse sub-group of plant-infecting trypanosomatids that are relatively poorly understood. Little is known of their biology or how they have adapted to life inside plants. This study sequenced the genome of the Cassava (Manihot esculenta) infecting species Phytomonas francai to provide additional genome resources and new insight into the biology of this poorly understood group of organisms.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Phytomonas francai

SUBMITTER: Steven Kelly

PROVIDER: E-MTAB-5110 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Digital gene expression analysis of ACMV-infected cassava

Project description:Cassava mosaic disease caused by cassava begomoviruses is the most serious disease of cassava in Africa. However, the molecular mechanisms leading to symptom development of infected cassava plants are poorly understood. Here a high throughput digital gene expression profiling (DGE) based on Illumina Solexa sequencing technology was used to investigate the global transcriptional response of cassava to the African cassava mosaic virus infection. Results showed that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis related genes were most affected, which was consistent with the chlorotic symptom on the infected leaves. The upregulation of chlorophyll degradation genes, e.g. the genes encoding chlorophyllase and pheophorbide a oxygenase, as well as the downregulation of the major apoproteins genes in light harvesting complex II (LHCII) identified by the DGE analysis were confirmed by qRT-PCR. Together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, this study reveals that the degradation of chlorophyll plays an important role during ACMV symptom development for the first time. Meanwhile, we believe that the non-lethal effect on photosystem is a trick for virus to avoid fierce host immune response and a result of the long-term co-evolution. This study will provide a road map for future investigations into virus symptom development. ACMV-infected cassava leaves mixture from three independent replicates were collected for RNA extractions at 20 dpi. Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.

2014-04-01 | E-GEOD-47224 | biostudies-arrayexpress

Digital gene expression analysis of ACMV-infected cassava

2014-04-01 | GSE47224 | GEO

Transcriptome sequencing of the Cassava (Manihot esculenta) latex parasite Phytomonas francai

Project description:Transcriptome sequencing of the Cassava (Manihot esculenta) latex parasite Phytomonas francai

| PRJEB15491 | ENA

Induction of leaf curling in cassava plants by the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae)

Project description:Certain phytophagous insects can induce leaf curling in their host plants that may provide protected and nutrient-rich habitats. However, the mechanisms of this induction remain poorly understood. The cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), is a serious pest of the cassava and causes leaf curling. To reveal the mechanisms of leaf-curl induction, we first inoculated varying numbers of mealybugs in different locations, namely, the apical meristem and the stem, on cassava seedlings. Second, we performed transcriptome analysis using the total RNA extracted from leaves. The results showed that a single insect was able to induce leaf curling, but the intensity and frequency of the leaf curling were positively correlated with the number of insects. Furthermore, the leaf curling occurred when the mealybugs fed on or close to the apical meristem but not when they fed on the stem. Transcriptome analysis identified a total of 3,931 differentially expressed genes (DEGs) from intact plants and the plants inoculated with mealybugs at different time points. GO analysis of the biological processes revealed that the DEGs contained a series of factors for leaf development of the adaxial–abaxial axis, and auxin biosynthesis and polarity. This suggests that alterations in these functions may cause leaf curling.

2023-06-15 | GSE234712 | GEO

Genome Sequence of Phytomonas francai, a Cassava (Manihot esculenta) Latex Parasite.

Project description: Not available

| S-EPMC5256229 | biostudies-literature

Large-scale proteome characterization of the cassava root

Project description:Cassava is the most important root crop in the tropics but rapid post-harvest physiological root deterioration (PPD) is a major constraint to commercial cassava production. We used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2400 unique proteins were identified in the cassava root and nearly 300 proteins showed significant abundance regulation during PPD. A candidate gene for reducing PPD was identified from the regulated proteins with enzymatic assays and afterwards verified with a transgene approach. This demonstrates the relevance of proteomics approach for crop improvements.

2014-06-03 | PXD000587 | Pride

Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

Project description:Analysis of transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease transcriptome analysis of two varieties of cassava that differ in their level of resistance to cassava brown streak virus.

2014-04-03 | E-GEOD-56467 | biostudies-arrayexpress

Transcriptome analysis of response to infection of cassava anthracnose disease (CAD) using an oligo-DNA microarray from cassava

Project description:Cassava Anthracnose Disease (CAD) that caused by the fungus Colletotorichum anthracnose is a serious disease of cassava in worldwide. In this study, we aim to establish the cassava oligo-DNA microarray representing approximately 30,000 cassava genes and apply it to investigate the molecular mechanisms against fungal infection using two cassava cultivars; Huay Bong 60 (HB60, resistant line for CAD) and Hanatee (HN, sensitive line for CAD). Based on expression profiling, we showed that the expression of various biotic stress-inducible genes, such as detoxification enzyme related genes is higher in HB60 under the treated conditions and non-treated condition, compared with HN. These results show that stress-inducible signaling pathways including ROS detoxification are constitutively activated in HB60 even under normal growth conditions without stress. These results suggest that our microarray is a useful tool for analyzing the cassava transcriptome and add new insight into the host responses of cassava against fungal infection.

2016-12-31 | GSE63223 | GEO

Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

Project description:Analysis of transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

2014-04-03 | GSE56467 | GEO

Whole genome bisulfite sequencing data of cassava

Project description:Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. It has been reported that landraces lose CMD resistance after regeneration through de novo morphogenesis. We sequenced WGBS data of 14 samples.

2022-05-27 | GSE192748 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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