Supplementary Information

Supplementary Information linked together

DOI: 10.15490/fairdomhub.1.assay.1261.1

Created at: 14th Apr 2020 at 17:00

Contents

/reports/SupplementaryFigure2.pdf

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.

  • SupplementaryFigure1.pdf

/reports/SupplementaryFigure3.pdf

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.

  • SupplementaryFigure2.pdf

/reports/SupplementaryTableS6

Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count/reports/

  • PacBio_evigeneSummaryStat.xlsx

/reports/SupplementaryTableS1

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

  • SupplementaryTableS1-Input_sequences_information.xlsx

/reports/SupplementaryTableS2

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/

  • SupplementaryTableS2-Primary_potato_transcriptome_assemblies.xlsx

/reports/SupplementaryTableS5

Supplementary Table S5 - Rywal biological evidence filtering results.
Output of 1st filtering step by biological evidence for cv. Rywal.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

  • Rywal_tr.cds.xlsx

/reports/SupplementaryTableS4

Supplementary Table S4 - PW363 biological evidence filtering results.
Output of 1st filtering step by biological evidence for breeding clone PW363.
Layer _p_stRT/ _I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/,

  • SupplementaryTableS4-PW363_biological_evidence_filtering_results.xlsx

/reports/SupplementaryTableS3

Supplementary Table S3 - Désirée biological evidence filtering results.
Output of 1st filtering step by biological evidence for cv. Désirée.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/

  • SupplementaryTableS3-Desiree_biological_evidence_filtering_results.xlsx

SupplementaryFile1

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

  • SupplementaryFile1-Merged_ITAG--PGSC_Phureja_DM_gene_models.zip

/reports/SupplementaryFigure4.pdf

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 _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/

  • SupplementaryFigure4.pdf

/reports/SupplementaryFile3.html

Supplementary File 3 - Taxonomi cclassification of Désirée, PW363 and Rywal representative transcripts.
Sequences were classified using Centrifuge and Sankey plots were generated using Pavian.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_08_cdhit_centrifuge_3cvs-GFFmerged

  • Supplementary File 3.html

/reports/SupplementaryFile2.html

Supplementary File 2 - Multiple sequence alignments using ClustalOmega v1.2.1 or MAFFT v7.271 and MView v1.66. Paralogue clusters on representative and alternative sequences, at least one from each of the four genotypes.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_05_MSA_3cvs-GFFmerged

  • Supplementary File 2.html

/reports/SupplementaryFigure1.pdf

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.

  • Figure3.pdf

/reports/SupplementaryTableS7

Supplementary Table S7 - Paralogue cluster information for cultivar-specific and pantranscriptome sequences extended with annotations and quality classification.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/

  • SupplementaryTableS7-Paralogue_cluster_information.xlsx

/reports/SupplementaryTableS8

Supplementary Table S8 - Read count summary for Désirée drought samples mapped to the representative Phureja DM and Désirée reference transcriptomes.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_07_Desiree-mapping/reports/

  • SupplementaryTableS8-DesireeDrought_mapped_counts.xlsx
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Citation
Zagorscak, M., & Petek, M. (2020). Supplementary Information. FAIRDOMHub. http://doi.org/10.15490/FAIRDOMHUB.1.ASSAY.1261.1
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Created: 14th Apr 2020 at 17:00

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