Meloidogyne incognita - public RNASeq studies
Table of Contents
- Meloidogyne incognita transcriptomes
- RNA-Seq analysis at various developmental stages of the Meloidogyne incognita life cycle
- A transcriptomic comparison of fed and starved Meloidogyne incognita J2 larvae to fresh J2s
- Meloidogyne incognita strain:New Delhi | isolate:IARI Transcriptome or Gene expression
- Transcriptional signatures of invasiveness in Meloidogyne incognita populations from sub-Saharan Africa
- 5 other studies
Analysed
ERP009887: Meloidogyne incognita transcriptomes
Genoscope
As part of the Meloidogyne incognita (root-knot nematode) genome sequencing project we have profiled the transcriptome of this plant parasite across its life cycle using RNA-Seq. The ensemble of transcriptomic data has been used to provide evidence for gene prediction. Genome assembly and accompanying transcriptome data is available at http://meloidogyne.inra.fr
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. (Blanc-Mathieu .. Danchin, 2017)
Design: 7 conditions
| Condition | num. replicates | Developmental stage |
|---|---|---|
| adult female | 1 | adult female |
| adult male | 1 | adult male |
| egg | 1 | egg |
| juvenile | 2 | juvenile |
| juvenile J3-J4 | 1 | juvenile J3-J4 |
| preparasitic J2.1 | 1 | preparasitic J2.1 |
| preparasitic J2.2 | 1 | preparasitic J2.2 |
SRP109232: RNA-Seq analysis at various developmental stages of the Meloidogyne incognita life cycle
Rural Development Administration
Design: 5 conditions
| Condition | num. replicates | Depth | Developmental stage | Geographic location | Host | Isolation source | Temperature |
|---|---|---|---|---|---|---|---|
| Egg | 3 | 15 cm | Egg | South Korea | Solanum lycopersicum | Infected roots | 25 C |
| J2 juveniles | 3 | 15 cm | J2 juveniles | South Korea | Solanum lycopersicum | Infected roots | 25 C |
| J3 | 3 | 15 cm | J3 | South Korea | Solanum lycopersicum | Infected roots | 25 C |
| J4 | 3 | 15 cm | J4 | South Korea | Solanum lycopersicum | Infected roots | 25 C |
| adult female | 3 | 15 cm | adult female | South Korea | Solanum lycopersicum | Infected roots | 25 C |
SRP155330: A transcriptomic comparison of fed and starved Meloidogyne incognita J2 larvae to fresh J2s
ICAR-IARI, New Delhi, INDIA
Design: 3 conditions
| Condition | num. replicates | Developmental stage | Treatment |
|---|---|---|---|
| Fresh juveniles | 2 | second stage juvenile | |
| Mi-sbp-1 ds-RNA | 2 | second stage juvenile | Mi-sbp-1 ds-RNA |
| starvation, 6 days | 2 | second stage juvenile | starvation, 6 days |
SRP155472: Meloidogyne incognita strain:New Delhi | isolate:IARI Transcriptome or Gene expression
ICAR-IARI, New Delhi, INDIA
Design: 4 conditions
| Condition | num. replicates | Developmental stage | Treatment |
|---|---|---|---|
| Control (GFP) | 2 | second stage juvenile | Control (GFP) |
| Control (Untreated) | 2 | second stage juvenile | |
| msp-1 silenced | 2 | second stage juvenile | msp-1 silenced |
| msp-20 silenced | 2 | second stage juvenile | msp-20 silenced |
SRP187776: Transcriptional signatures of invasiveness in Meloidogyne incognita populations from sub-Saharan Africa
Queens University Belfast
Design: 6 conditions
| Condition | num. replicates | Biomaterial provider | Collection date | Description title | Geographic location | Isolate | Isolation source | Sample name | Host | Organism part |
|---|---|---|---|---|---|---|---|---|---|---|
| Kenya | 3 | May-2017 | Kenya | Amaranthus viridae | Tomato | j2 | ||||
| Nig_3_RNASeq_R1_Replicate_1 | 1 | Jun-2017 | Nigeria | Not available | Tomato | j2 | ||||
| Nig_3_RNASeq_R1_Replicate_2 | 1 | Jun-2017 | Nigeria | Not available | Tomato | j2 | ||||
| Nig_3_RNASeq_R1_Replicate_3 | 1 | Jun-2017 | Nigeria | Not available | Tomato | j2 | ||||
| Nigeria 1 | 3 | Jun-2017 | Nigeria | Celosia | Tomato | j2 | ||||
| Nigeria 2 | 3 | Jun-2017 | Nigeria | Not available | Tomato | j2 |
Other
These studies are available in ENA, and the reads successfully align to our genomes.
They have not been included in our analysis for one of the following reasons:
Failed to meet minimal criteria for differential expression analysis, failure to pass data quality filters, or we were unable to interpret accompanying metadata.
ERP010859: Meloidogyne incognita transcriptomes
Genoscope
As part of the Meloidogyne incognita (root-knot nematode) genome sequencing project we have profiled the transcriptome of this plant parasite across its life cycle using RNA-Seq. The ensemble of transcriptomic data has been used to provide evidence for gene prediction. Genome assembly and accompanying transcriptome data is available at http://meloidogyne.inra.fr
SRP003867: Identification of Novel and Conserved MicroRNAs of Root-knot Nematode Using a Deep-sequencing Approach
Bioinformatics, Hunan Agricultural University
Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing. (Wang .. Xie, 2015)
SRP019992: Meloidogyne incognita Variation
Hunan Agricultural University
SRP068483: Transcriptome of early-infected root-knot nematodes by the bacterial pathogen Pasteuria penetrans
Chinese Academy of Tropical Agricultural Sciences
SRP152065: Meloidogyne incognita Transcriptome or Gene expression
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