Solanum tuberosum

Engineering next level photosynthesis-PhotoBoost is a 4-year research and innovation action that aims to significantly improve the efficiency of photosynthesis in plants. The optimisation of photosynthesis will be achieved by capitalising on multidisciplinary approaches including computational biology, metabolic modelling, systems biology, enzyme and pathway engineering, synthetic biology, and the multigene transformation of two major C3 crops: potato and rice. The PhotoBoost project will deliver ...

Programme: Independent Projects

Public web page: http://www.photoboost.org

Organisms: Solanum tuberosum, Oryza sativa

_p_stRT

project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...

Programme: NIBSys

Public web page: http://www.nib.si/eng/index.php/systems-biology

Start date: 1st Dec 2017

End date: 1st Jan 2020

Organisms: Potato virus Y, Solanum tuberosum

ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato

In this project, the involved partners are trying to develop the knowledge base that will enable the breeding of new potato varieties, tolerant to multiple environmental stressors.

Programme: NIBSys

Public web page: https://adapt.univie.ac.at/

Start date: 1st Jul 2020

End date: 30th Jun 2024

Organisms: Solanum tuberosum

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.

This investigation is published under the CC BY 4.0 license.

Programme: NIBSys

Public web page: Not specified

Organisms: Potato virus Y, Solanum tuberosum

Showing 20 out of a possible 23 Assays Advanced Assays list for this Organism with search and filtering

Disease symptoms

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

Description of observed phenotypic variables in the MOA investigation.

Submitter: Ziva Ramsak

Assay type: Phenotype observation

Technology type: Imaging

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_1A_disease-symptoms, MOA2010-05_1A_disease-symptoms-images, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: Snapshot 1

Created: 18th Feb 2019 at 18:43, Last updated: 4th Mar 2019 at 16:49

Photosynthetic activity

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Phenotype observation

Technology type: Leaf Chamber Fluorometer

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_1B_photosynthetic-activity, MOA2010-05_1B_photosynthetic-activity_LM, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:47, Last updated: 4th Mar 2019 at 16:50

Pathogen abundance

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_1C_pathogen-abundance_qPCR, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:49, Last updated: 4th Mar 2019 at 16:50

Transcriptomics (microarrays)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Gene Expression Profiling

Technology type: Custom Array

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_2_transcriptomics_microarrays_GEO, MOA2010-05_2_transcriptomics_microarrays_R-code, MOA2010-05_2_transcriptomics_microarrays_R-code..., MOA2010-05_2_transcriptomics_microarrays_logFC, MOA2010-05_2_transcriptomics_microarrays_normal..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:51, Last updated: 4th Mar 2019 at 16:50

Transcriptomics (qPCR)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_2_transcriptomics_qPCR, MOA2010-05_2_transcriptomics_qPCR_MIQE, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:52, Last updated: 4th Mar 2019 at 16:50

sRNAomics (sRNA-Seq)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: MicroRNA Profiling

Technology type: Next generation sequencing

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:54, Last updated: 4th Mar 2019 at 16:51

sRNAomics (qPCR)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Q_PCR

Technology type: qPCR

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_3_sRNAomics_qPCR, MOA2010-05_3_sRNAomics_qPCR_MIQE, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:55, Last updated: 4th Mar 2019 at 16:51

sRNAomics (bioinformatics)

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Bioinformatics

Technology type: Interactions

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_3C_sRNAomics_bioinformatics_PHAS-loci, MOA2010-05_3C_sRNAomics_bioinformatics_miRNA-novel, MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA2010-05_3C_sRNAomics_bioinformatics_sRNA-tar..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:56, Last updated: 4th Mar 2019 at 16:51

Degradomics

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Degradome-Seq

Technology type: Next generation sequencing

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_4_degradomics_Degradome-Seq_GEO, MOA2010-05_4_degradomics_Degradome-Seq_targets-..., MOA2010-05_4_degradomics_Degradome-Seq_targets-..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:58, Last updated: 4th Mar 2019 at 16:51

Hormone concentrations

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2013-12

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2013-12_1_hormonomics_GCMS, MOA2013-12_1_hormonomics_GCMS_ANOVA-groups, MOA2013-12_1_hormonomics_R-code, MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 18th Feb 2019 at 18:59, Last updated: 4th Mar 2019 at 16:51

Proteomics

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

No description specified

Submitter: Ziva Ramsak

Assay type: Protein Quantification

Technology type: Orbitrap Velos

Investigation: MOA - Multiomics analysis of potato response to...

Study: MOA2010-05

Organisms: Solanum tuberosum, Potato virus Y

SOPs: No SOPs

Data files: MOA2010-05_5_proteomics_Orbitrap-MaxQuant, MOA2010-05_5_proteomics_Orbitrap-MaxQuant_logFC, MOA2010-05_5_proteomics_Orbitrap-MaxQuant_peptides, MOA2010-05_5_proteomics_Orbitrap-SpectralCounts, MOA2010-05_5_proteomics_Orbitrap-SpectralCounts..., MOA2010-05_5_proteomics_Orbitrap-SpectralCounts..., MOA_Multiomics-Analysis_Phenodata-n-MIAPPE

Snapshots: No snapshots

Created: 4th Mar 2019 at 15:23, Last updated: 4th Mar 2019 at 16:51

_A_01_evigene

_p_stRT

Assay: _A_01_evigene Short Name: 01_evigene Assay Class: DRY Assay Type: evigene Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11 Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Integration

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: Snapshot 1

Created: 7th Nov 2019 at 15:54, Last updated: 16th Nov 2019 at 13:21

_A_02.1_BUSCO

_p_stRT

Assay: _A_02.1_BUSCO Short Name: 02.1_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO on assemblies and tr2aacds output Description: BUSCO on assemblies and tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

Created: 7th Nov 2019 at 15:57, Last updated: 16th Nov 2019 at 12:40

_A_02.2_assembly-contribution-count

_p_stRT

Assay: _A_02.2_assembly-contribution-count Short Name: 02.2_assembly-contribution-count Assay Class: DRY Assay Type: count Title: assembly contribution count Description: assembly contribution count, input/output tr2aacds pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

Created: 7th Nov 2019 at 16:04, Last updated: 26th Feb 2020 at 13:00

_A_02.3_InterProScan

_p_stRT

Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Created: 7th Nov 2019 at 16:46, Last updated: 16th Nov 2019 at 12:35

_A_02.4_STAR

_p_stRT

Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Created: 7th Nov 2019 at 16:48, Last updated: 2nd Jun 2020 at 13:42

_A_02.5_STARlong_matchAnnot

_p_stRT

Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Created: 7th Nov 2019 at 16:50, Last updated: 16th Nov 2019 at 11:55

_A_02.6_TransRate

_p_stRT

Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 11:45

_A_02.7_VecScreen

_p_stRT

Assay: _A_02.7_VecScreen Short Name: 02.7_VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Created: 7th Nov 2019 at 16:58, Last updated: 16th Nov 2019 at 11:37

_A_02.8_DIAMOND

_p_stRT

Assay: _A_02.8_DIAMOND Short Name: 02.8_DIAMOND Assay Class: DRY Assay Type: DIAMOND Title: DIAMOND on raw tr2aacds output Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Created: 7th Nov 2019 at 17:02, Last updated: 16th Nov 2019 at 11:28

View all 23 Assays

Advanced Publications list for this Organism with search and filtering

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

_p_stRT

(Show All)

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden

Date Published: No date defined

Publication Type: Not specified

DOI: 10.1101/845818

Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Created: 19th Nov 2019 at 11:48, Last updated: 8th Dec 2022 at 17:26