Solanum tuberosum

Details about this organism

Synonyms (1)

Solanum tuberosum subsp. tuberosum

Definitions (0)

None defined

Strain details

Name	Provider name	Provider's strain ID	Genotypes	Phenotypes	Synonym	Comments	Based on

Related items

_p_stRT

Solanum tuberosum Reference Transcriptomes

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: Solanum tuberosum, Potato virus Y

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

_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

Contributor: Maja Zagorscak

Biological problem addressed: Integration

Snapshots: No snapshots

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, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 14:21

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts

Created: 7th Nov 2019 at 16:57, Last updated: 16th Nov 2019 at 13:40

_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

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate, /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

Created: 7th Nov 2019 at 17:46, Last updated: 16th Nov 2019 at 13:35

_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

Contributor: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output, /reports/Figure3.pdf, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /scripts

Created: 7th Nov 2019 at 17:04, Last updated: 16th Nov 2019 at 13:10

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

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, /scripts/STAR_commands.txt

Created: 7th Nov 2019 at 17:48, Last updated: 16th Nov 2019 at 13:03

_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
...

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: No snapshots

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...

Created: 7th Nov 2019 at 17:50, Last updated: 16th Nov 2019 at 12:55

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts

Created: 7th Nov 2019 at 17:54, Last updated: 16th Nov 2019 at 12:45

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

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

Created: 7th Nov 2019 at 17:58, Last updated: 16th Nov 2019 at 12:37

_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

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts

Created: 7th Nov 2019 at 18:02, Last updated: 16th Nov 2019 at 12:28

_A_04_TransRate

_p_stRT

Assay: _A_04_TransRate
Short Name: 04_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate post filtering and reassignment
Description: TransRate post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output, /scripts/run_TransRate_commands.sh

Created: 7th Nov 2019 at 18:09, Last updated: 16th Nov 2019 at 12:22

_A_05_BUSCO

_p_stRT

Assay: _A_05_BUSCO
Short Name: 05_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO post filtering and reassignment
Description: BUSCO post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts, /transfer

Created: 7th Nov 2019 at 18:11, Last updated: 16th Nov 2019 at 12:08

_A_01_evigene_1_3cvs-gffmerged

_p_stRT

Assay: _A_01_evigene_1_3cvs-gffmerged
Short Name: 01_evigene_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: tr2aacds on cv rep and gffmerged
Description: tr2aacds on cv rep and gffmerged
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Contributor: Maja Zagorscak

Biological problem addressed: Integration

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/StPGSC4.04n_PGSC-ITAG-merged_representat..., /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /input/path_to_files.txt, /other/Figure1.pdf, /output, /scripts

Created: 7th Nov 2019 at 16:33, Last updated: 16th Nov 2019 at 11:44

_A_04-MSA

_p_stRT

Assay: _A_04-MSA
Short Name: 04-MSA
Assay Class: DRY
Assay Type: MSA
Title: Multiple sequence alignment, pantranscriptomes' paralogue clusters
Description: Multiple sequence alignment, pantranscriptomes' paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Contributor: Maja Zagorscak

Biological problem addressed: Multiple sequence alignment

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/D_P_R_g.tar.gz, /input/selected_4_wc.tar.gz, /other/Figure5.pdf, /output, /reports/Figure4.pdf/, /reports/Merged.aa.html, /reports/SupplementaryFigure3.pdf, /reports/stPanTr_geneCount_paralogue-clusters.tiff, /scripts, /testSet

Created: 24th Oct 2019 at 16:46, Last updated: 16th Nov 2019 at 11:39

_A_05_BUSCO-Stat

_p_stRT

Assay: _A_05_BUSCO-Stat
Short Name: 05_BUSCO-Stat
Assay Class: DRY
Assay Type: Stat
Title: BUSCO plots
Description: BUSCO plots
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Analyst: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Contributor: Maja Zagorscak

Biological problem addressed: Visualization

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/BUSCO_stPanTr_embryophyta_odb9.tsv, /intermediate/BUSCOall_embryophyta_odb9.tsv, /intermediate/evg_out.tsv, /reports/BUSCO1.pdf, /reports/BUSCO_plots.html, /scripts/BUSCO_plots.Rmd

Created: 7th Nov 2019 at 16:37, Last updated: 16th Nov 2019 at 11:32

_A_03_BUSCO_1_3cvs-gffmerged

_p_stRT

Assay: _A_03_BUSCO_1_3cvs-gffmerged
Short Name: 03_BUSCO_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: BUSCO on pantranscriptome
Description: BUSCO on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts

Created: 7th Nov 2019 at 16:26, Last updated: 16th Nov 2019 at 11:07

_A_02_components_1_3cvs-gffmerged

_p_stRT

Assay: _A_02_components_1_3cvs-gffmerged
Short Name: 02_components_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: paralogue clusters on pantranscriptome
Description: paralogue clusters on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /output, /scripts

Created: 7th Nov 2019 at 16:29, Last updated: 16th Nov 2019 at 10:56

_A_03.2_components

_p_stRT

Assay: _A_03.2_components
Short Name: 03.2_components
Assay Class: DRY
Assay Type: components
Title: Components: tr2aacds headers, cdhit-2d
Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input, /intermediate_4_cdhit-2d.tar.gz, /output, /scripts

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

Hormone concentrations

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

No description specified

Contributor: Ziva Ramsak

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

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

Created: 18th Feb 2019 at 19:59, Last updated: 4th Mar 2019 at 17:51

Proteomics

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

No description specified

Contributor: Ziva Ramsak

Assay type: Protein Quantification

Technology type: Orbitrap Velos

Snapshots: No snapshots

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

Created: 4th Mar 2019 at 16:23, Last updated: 4th Mar 2019 at 17:51

Degradomics

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

No description specified

Contributor: Ziva Ramsak

Assay type: Degradome-Seq

Technology type: Next generation sequencing

Snapshots: No snapshots

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

Created: 18th Feb 2019 at 19:58, Last updated: 4th Mar 2019 at 17:51

View all 28 items

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 Zagorscak, Ziva Ramsak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/845818

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

Created: 19th Nov 2019 at 12:48, Last updated: 19th Nov 2019 at 12:57