UniTato

• Apollo genome browser: UniTato: a web server for evidence and community based Unification of poTato gene models
• Potato DM v4 to v6 gene ID translations ./output/v4-v6.1_translationTable.xlsx (all information); high confidence translation table subset at ./output/Phureja_v4-v6.1_translations.xlsx, unitato.nib.si/downloads, and github.com/NIB-SI/DiNAR/TranslationTables
• Unified GFF/GTF files ./output/Unitato.GFF.zip ./output/Unitato.GTF.zip and corresponding FASTA file are also avalable at unitato.nib.si/downloads

bioRxiv

Input files

GFF3

• ITAG v4: ./input/StPGSC4.04n_ITAG-gene-model_2020-01-17.gff3
• PGSC v4: ./input/StPGSC4.04n_PGSC-gene-model_2022-10-26.gff3
• DMv6.1 http://spuddb.uga.edu http://spuddb.uga.edu/data/DM_1-3_516_R44_potato.v6.1.working_models.gff3.gz

FASTA

• v4 FASTA file: ./input/StPGSC4.04n_2018-01-18_oneliner.fasta
• DMv6.1 http://spuddb.uga.edu http://spuddb.uga.edu/data/DM_1-3_516_R44_potato_genome_assembly.v6.1.fa.gz

Annotations

• PGSC v4 annotations: ./input/Solanum_tuberosum_PGSC_DM_v3.4_converterWithDescriptions.txt
• DMv6.1 http://spuddb.uga.edu http://spuddb.uga.edu/data/DM_1-3_516_R44_potato.v6.1.working_models.func_anno.txt.gz

pan-transcriptome https://doi.org/10.1038/s41597-020-00581-4

• panTranscriptome components: ./input/5cv_weak-components.txt
• ITAG-PGSC-pairs: ./input/ITAG-PGSC-pairs.xlsx
• ITAG v4 CDS len and GC content: ./input/Solanum_tuberosum-ITAG_DM_v1_cds_GC-len https://doi.org/10.1038/s41597-020-00581-4
• PGSC v4 CDS len and GC content: ./input/Solanum_tuberosum_PGSC_merged_GC-len https://doi.org/10.1038/s41597-020-00581-4
• Desiree, Rywal, and PW363 CDS and transcripts:
  • stCuSTr-D_cds_representatives.fasta
  • stCuSTr-D_tr_representatives.fasta
  • stCuSTr-P_cds_representatives.fasta
  • stCuSTr-P_tr_representatives.fasta
  • stCuSTr-R_cds_representatives.fasta
  • stCuSTr-R_tr_representatives.fasta

Liftoff-specific files

• Chromosome: ./input/pairs chroms.txt
• Unplaced: ./input/unplaced_DM404.txt

Proteomes

• Arabidopsis Araport11
• Tomato ITAG4.1
• Benthi Nb HZ version 1
• Tobacco Nt SR1 version 1

Software

• Liftoff fork with adaptation: flanks as integer (instead of percentage): https://github.com/NIB-SI/Liftoff
• Bedtools
• AGAT
• minimap2
• STAR
• Salmon
• miniprot

For more information see README in scripts

R packages

• data.table
• pafr
• stringr
• magrittr
• sqldf
• RColorBrewer
• randomcoloR
• circlize
• VennDiagram
• grDevices
• ggvenn
• ggVennDiagram
• intervals
• igraph
• openxlsx

For more information see sessionInfo() in R Markdown files (.html)

Output

• Translation table: ./output/v4-v6.1_translationTable.xlsx
• GFFs:
  • flank-based: ./output/matched-unmatched-gff/
  • unified v6v4 GFF: UniTato.gff
• miniprot detailed results: ./output/miniprot/

Reports

• many-to-many matches: ./reports/overlaps.xlsx

• Venn: ./reports/01_Venn_wm.tiff

• pan-transcriptome ITAG-PGSC pair matching dependent of the F parameter: ./reports/ITAG-PGSC_F-dependent_pairs-matches.txt

• DMv6.1 wm scaffolds without gene features: ./reports/v6scaffolds-without-v6genes.fasta

• Chord diagram visualisation

• Chr12 inversion visualisation

  Additional information

  DMv6.1

  “High-confidence gene models”, as defined by Pham et al (2020), are based on the following criteria:

• Transcripts per Million value greater than 0 in at least one RNA-Seq library
• Gene models that have a match to a PFAM domain are considered high-confidence
• Gene models that are partial or have matches to transposable element-related PFAM domains are excluded from the high-confidence model set