Maja Zagorscak

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.

project: pstRT 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, ...

Our world is changing fast! Key global trends are rapid urbanisation, growing and ageing populations, and increased prosperity. This results in depletion of natural and petrochemical resources and climate change, which affects the quality of the environment and people's lives. Therefore, developing a bio-based economy is key to sustain our planet in the long term. Raw materials will have to be recruited from renewable sources.

Industrial biotechnology is potentially a very powerful technology in ...

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.

Despite the intensive use of agrochemicals, plant pathogens are responsible for huge yield losses worldwide. Understanding the interaction between plant and pathogens is crucial to ensure long lasting and environmentally friendly system of plant protection. Therefore research of the most important human food crops in combination with their pathogens is one of the highest priorities for sustainable agriculture.

The aim of the proposed research project is to bring new perspective into understanding ...

Investigation: ISTRT 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 ...

Supplementary Information linked together

Study: S03stCuSTr Short Name: 03stCuSTr Title: Solanum tuberosum Cultivar-Specific Transcriptomes Description: Solanum tuberosum Cultivar-Specific Transcriptomes Raw Data: ../S01sequences/, ../S02denovo/ 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 /STUDYMETADATA.TXT ...

Study: S02denovo Short Name: 02denovo Title: De novo assemblies Description: De novo assemblies for cration of potato reference transcriptomes Raw Data: ../S01_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 /STUDYMETADATA.TXT https://fairdomhub.org/documents/342 ...

Study: S01sequences Short Name: 01sequences Title: NGS sequences for de novo assembly Description: NGS sequences for de novo assembly; input for Study 02denovo Raw Data: see: ./reports/SupplementaryTableS1-Inputsequences_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 ...

Assay: A02.4STAR Short Name: 02.4STAR 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/pathtofiles.txt

Short Name: 07_Desiree-mapping Assay Class: DRY Assay Type: mapping Title: Desiree mapping Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 05MSA3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: MSA 3cv and GFF-merged Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: cdhit_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 09_annotation-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Pan-transcriptome fasta files annotation Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Supplementary Information linked together

Short Name: 08centrifuge3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Centrigufe pan-transcriptome sequence classification Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 06trrep-transrate Assay Class: DRY Assay Type: transrate Title: Cultivar representative transcriptome transrate Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 03components3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 04BUSCO3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 01GCcontent-count Assay Class: DRY Assay Type: count Title: GC content and sequence length Description: A, C, T, G content and sequence length pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data: ../input/pathtofiles.txt

Assay: A03.1filtering Short Name: 03.1filtering Assay Class: DRY Assay Type: filtering Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt

Assay: A02.2assembly-contribution-count Short Name: 02.2assembly-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/pathtofiles.txt

Assay: A01evigene Short Name: 01evigene Assay Class: DRY Assay Type: evigene Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11 Description: See http://eugenes.org/EvidentialGene/about/EvidentialGenetrassemblypipe.html pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/pathtofiles.txt

Assay: A02.1BUSCO Short Name: 02.1BUSCO 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/pathtofiles.txt

Assay: A02.3InterProScan Short Name: 02.3InterProScan 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/pathtofiles.txt

Assay: A02.5STARlongmatchAnnot Short Name: 02.5STARlongmatchAnnot 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 ...

Assay: A02.6TransRate Short Name: 02.6TransRate 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/pathtofiles.txt

Assay: A02.7VecScreen Short Name: 02.7VecScreen 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/pathtofiles.txt

Assay: A02.8DIAMOND Short Name: 02.8DIAMOND 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/pathtofiles.txt

coverage and uniquely mapped spliced reads summary

samtools coverage https://www.htslib.org/doc/samtools-coverage.html

Supplementary Table S8 - Read count summary for Désirée drought samples mapped to the representative Phureja DM and Désirée reference transcriptomes. Layer pstRT/ISTRT/S04stPanTr/A07Desiree-mapping/reports/

Supplementary Figure 3 - Venn diagrams showing the overlap of paralogue clusters in cultivar-specific transcriptomes and merged Phureja DM gene model. Representatives and alternatives of the stPanTr (pan-transcriptome) paralogue cluster are counted as well as alternatives defined at stCuSTr (cultivar-specific transcriptome) step. For Phureja, the merged ITAG and PGSC DM gene models were counted. Layer pstRT/ISTRT/S04stPanTr/A02cdhit_3cvs-GFFmerged/reports/

Supplementary Table S7 - Paralogue cluster information for cultivar-specific and pantranscriptome sequences extended with annotations and quality classification. Layer pstRT/ISTRT/S04stPanTr/A02cdhit_3cvs-GFFmerged/reports/

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer pstRT/ISTRT/ S01_sequences/reports

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 pstRT/ISTRT/S02_denovo/reports/

Number of transcripts from de novo assemblies contributing to cultivar Désirée, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet.

Supplementary File 1 - Merged ITAG/PGSC Phureja DM gene models. Archive containing GTF, CDS and peptide fasta files for merged ITAG and PGSC gene models for S. tuberosum Group Phureja DM genome v4.04

Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences. Layer pstRT/ISTRT/S03stCuSTr/A02.2assembly-contribution-count/reports/

Supplementary Table S5 - Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal. Layer pstRT/ISTRT/S03stCuSTr/A03.1filtering/reports/

Supplementary Table S4 - PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363. Layer pstRT/ ISTRT/S03stCuSTr/A03.1filtering/reports/,

Supplementary Table S3 - Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée. Layer pstRT/ISTRT/S03stCuSTr/A03.1filtering/reports/

Number of transcripts from de novo assemblies contributing to breeding clone PW363, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes.

Number of transcripts from de novo assemblies contributing to cultivar Rywal, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes, PBdn - PacBio.

https://blogs.iu.edu/ncgas/2018/12/17/how-evigene-works/

Description of Tags found on transcript headers https://blogs.iu.edu/ncgas/2018/12/17/how-evigene-works/#step3

pstRT

pstRT

pstRT/ISTRT

pstRT/ISTRT

pstRT

pstRT/ISTRT

pstRT/ISTRT

pstRT/ISTRT/S01_sequences

pstRT/ISTRT/S01_sequences

pstRT/ISTRT/S02_denovo

pstRT/ISTRT/S02_denovo

pstRT/ISTRT/S03_stCuSTr

pstRT/ISTRT/S03_stCuSTr

pstRT/ISTRT/S04_stPanTr

pstRT/ISTRT/S04_stPanTr

pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA https://github.com/NIB-SI/pISA/

pstRT