Marko Petek

About Marko Petek:

Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology

SEEK ID: https://fairdomhub.org/people/1071

Location: Slovenia

Expertise: Molecular Biology, Transcriptomics, Solanum tuberosum, Plant biology, plant pathways, plant metabolism, Systems Biology

Tools: Molecular biology techniques (RNA/DNA/Protein), Microarray analysis, Bioinformatics, R, RNAseq, RNA interference, metabolic network visualization, metagenomics

ORCID: https://orcid.org/0000-0003-3644-7827

Project positions

Other Projects: pISA-tree (National Institute of Biology) ; SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture (National Institute of Biology) ; _p_stRT (National Institute of Biology) ; ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato (National Institute of Biology)

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

_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: Solanum tuberosum, Potato virus Y

pISA-tree

pISA-tree: Standard project directory tree (ISA compliant)

Development of support for standardization of directory trees to suport ISA framework of research organization. We are developing a set of batch/make files to enable creation of trees for storage of assets (data/presentations/protocols/scripts) and description files that hold associated metadata for Investigation / Study / Assay levels.

Programme: NIBSys

Public web page: http://ablejec.nib.si/doc

Organisms: Not specified

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

Programme: NIBSys

Public web page: http://susphire.info/susphireproject/

Start date: 1st Apr 2018

End date: 31st Mar 2021

Organisms: Planococcus citri, Nicotiana benthamiana, Penicillium chrysogenum

National Institute of Biology

Country: Slovenia

City: Ljubljana

Web page: http://www.nib.si

_I_STRT

_p_stRT

(Show All)

Investigation: _I_STRT
Short Name: STRT
Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Phenodata: ./phenodata_20191022.txt
pISA Investigation creation date: 2019-10-22
pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes

RELATED
...

Created: 24th Oct 2019 at 16:36, Last updated: 26th Nov 2019 at 10:37

_S_03_stCuSTr

_p_stRT

(Show All)

Study: _S_03_stCuSTr
Short Name: 03_stCuSTr
Title: Solanum tuberosum Cultivar-Specific Transcriptomes
Description: Solanum tuberosum Cultivar-Specific Transcriptomes
Raw Data: ../_S_01_sequences/, ../_S_02_denovo/
pISA Study creation date: 2019-10-22
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes

RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/346
/_STUDY_METADATA.TXT
...

Person responsible: Maja Zagorscak

Snapshots: No snapshots

Investigation: _I_STRT

Assays: _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_03.1_filtering, _A_03.2_components, _A_04_TransRate, _A_05_BUSCO

Created: 24th Oct 2019 at 16:40, Last updated: 26th Nov 2019 at 10:36

_S_02_denovo

_p_stRT

Study: _S_02_denovo
Short Name: 02_denovo
Title: De novo assemblies
Description: De novo assemblies for cration of potato reference transcriptomes
Raw Data: ../_S_01_sequences/
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes

RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/343
/_STUDY_METADATA.TXT https://fairdomhub.org/documents/342
...

Person responsible: Marko Petek

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.668.1

Investigation: _I_STRT

Assays: No Assays

Created: 24th Oct 2019 at 16:39, Last updated: 26th Nov 2019 at 10:35

_S_01_sequences

_p_stRT

Study: _S_01_sequences
Short Name: 01_sequences
Title: NGS sequences for de novo assembly
Description: NGS sequences for de novo assembly; input for Study 02_denovo
Raw Data: see: ./reports/SupplementaryTableS1-Input_sequences_information.xlsx
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes

RELATED FILES:
/reports/README.MD
...

Person responsible: Marko Petek

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.667.1

Investigation: _I_STRT

Assays: No Assays

Created: 24th Oct 2019 at 16:38, Last updated: 26th Nov 2019 at 10:35

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

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

Created: 7th Nov 2019 at 17:48, Last updated: 2nd Jun 2020 at 15:42

Supplementary Information

_p_stRT

Supplementary Information linked together

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1261.1

Investigation: _I_STRT

Study: SupplementaryInformation

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryFigure4.pdf, /reports/SupplementaryFile2.html, /reports/SupplementaryFile3.html, /reports/SupplementaryTableS1, /reports/SupplementaryTableS2, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /reports/SupplementaryTableS6, /reports/SupplementaryTableS7, /reports/SupplementaryTableS8, SupplementaryFile1

Created: 13th Mar 2020 at 19:24, Last updated: 8th Apr 2020 at 18:30

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

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

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

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

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

/reports/SupplementaryTableS1

_p_stRT

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies.
Raw and processed reads summary.
Layer _p_stRT/_I_STRT/ _S_01_sequences/reports

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3090.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

Download

Created: 6th Nov 2019 at 15:25, Last updated: 8th Apr 2020 at 18:39

/reports/SupplementaryTableS2

_p_stRT

Supplementary Table S2 - Detailed de novo assemblies information table.
Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation.
Layer _p_stRT/_I_STRT/_S_02_denovo/reports/

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3091.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

Download

Created: 6th Nov 2019 at 15:40, Last updated: 8th Apr 2020 at 18:39

/presentations/Figure2.pdf

_p_stRT

_p_stRT/_I_STRT
pipeline

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3157.1

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 16th Nov 2019 at 11:49, Last updated: 25th Nov 2019 at 00:33

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