_S_P4_cand_all

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Short Name: P4_IDScandidates Title: Generation of the candidate list for cis and trans IDS enzymes from P. citri Description: From the P. citri genome and both de novo transcriptome assembly versions we mined homologues of trans(PF00348, IPR000092) and cis (PF01255, IPR001441) IDS enzymes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/1038

Investigation: _I_T31_mealybug

Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Contr...

Study position: 4

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 712

Created: 16th May 2022 at 10:27

Last updated: 6th Nov 2024 at 15:25

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (7)
Data files (39)
Documents (58)

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Marko Petek

Projects: pISA-tree, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL

Institutions: National Institute of Biology

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

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

PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology

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NIBSys

National Institute of Biology, Department of Biotechnology and Systems Biology projects

Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground

Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology

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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.

Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036

Programme: NIBSys

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

Start date: 1st Apr 2018

End date: 30th Sep 2021

Organisms: Planococcus citri, Nicotiana benthamiana, Penicillium chrysogenum

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_I_T31_mealybug

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

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Marko Petek

Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Submitter: Marko Petek

Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic

Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files

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Created: 16th May 2022 at 10:26, Last updated: 6th Nov 2024 at 15:25

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_S_P4_cand_all-files

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

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Marko Petek

Files connected to study: _S_P4_cand_all

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT, reports/cis_selected_DEanalysis.xlsx, reports/trans_selected_DEanalysis.xlsx

Snapshots: No snapshots

Created: 16th May 2022 at 10:27, Last updated: 6th Nov 2024 at 15:25

_A_candidatemining-bioinfo

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

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Marko Petek

Short Name: candidatemining-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Mining of IDS homologues from genome and de novo transcriptomes of P. citri Description: We selected homologues of cis and trans IDS enzymes in P. citri genome and both versions of the de novo transcriptome. Selection was done based on IPRscan results. pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_IDIsearch-Bioinfo

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

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Marko Petek

Short Name: IDIsearch-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Search of IDI candidates from Pcitri sequences Description: Identifying isopentenyl isomerase candidate genes from genomic and transcriptomic sequences of Pcitri. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/IDIsearch2.xlsx, output/IDIsearch_final.xlsx

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_MSA-bioinfo

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

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Marko Petek

Short Name: MSA-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Multiple sequence alignment of cis and trans candidate IDS Description: MSA and phylogenetic analysis of candidates in MEGA pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/pairwise_distances.xlsx, scripts/MEGAsettings.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_OtherMealybugCandidates-Alignment

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

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Marko Petek

Short Name: OtherMealybugCandidates-Alignment Assay Class: DRY Assay Type: Alignment Title: Alignment of other mealybug candidate enzymes Description: We created alignments and phylogenetic trees of P. citri IDS candidates with IDS homologs mined from the genomes of two other species: Planococcus ficus and Planococcus longispinus, to determine which of the candidates are evolutionarily conserved and their phylogenetic relationships among the three species. pISA Assay creation date: 2021-03-02 ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/Group2_cis.txt, input/Pficus_candidates.txt, input/Planococcus_ficus_Pficus.v0.proteins.fa.i..., input/Plongispinus_candidates.txt, input/Pseudococcus_longispinus_v1.proteins.fa.i..., output/ficus_longispinus_candidates.xlsx

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_smallIDSsubunit-motifs

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

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Marko Petek

Short Name: smallIDSsubunit-motifs Assay Class: DRY Assay Type: motifs Title: Search for P. citri homologs of small IDS subunits Description: Since in plants, some IDS enzymes require a small non-catalytical subunit for their functioning, we decided to determine, whether we could find homologs of such proteins in P. citri sequences and test them in combination with IDS candidates. We performed a motif search in the P.citri proteome. pISA Assay creation date: 2021-04-13 pISA Assay creator: MJU ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/motifsearch.xlsx

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_Strep_CLDS-bioinfo

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

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Marko Petek

Short Name: Strep_CLDS-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Search for Streptomyces CLDS homologue in the generated transcriptomes of P. citri Description: Using BLAST to seqrch for homologues of Streptomyces Cyclolavandulyl diphosphate synthase in P. citri transsctiptome tr1 and tr2 pISA Assay creation date: 2019-12-30 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_cand_all

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/CLDS_candidate_sequences.txt, output/tr1_NODE_8-part-NCBI_nt_tblastn_Alignmen..., output/tr2_NODE_39580-NCBI_nt_tblastn_Alignment...

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

Showing 20 out of a possible 39 Data files Advanced Data files list for this Study with search and filtering