A TSS-aware catalogue of microRNA-encoded peptides in tomato (Solanum lycopersicum)

This repository contains the supplementary datasets, computational notebooks and structural prediction files generated for the study "A TSS-aware catalogue of microRNA-encoded peptides in tomato (Solanum lycopersicum)". The dataset supports the identification, annotation, structural characterization and comparative analysis of candidate microRNA-encoded peptides (miPEPs) associated with tomato pri-miRNAs.

The repository is organised into the following files:

• TableS1.xlsx: Metadata and sequence features of the curated tomato miPEP catalog.
• TableS2.xlsx: Physicochemical values and statistical summaries used to support Figures 5 and 6.
• TableS3.xlsx: Predicted ORFs associated with miRNA loci in seven plant species.
• TableS4.xlsx: Exact amino-acid k-mer matches detected between tomato miPEPs and peptide datasets from the surveyed non-tomato species.
• TableS5.xlsx: Association between cross-species detectability of tomato miPEPs and miPEP metadata features.
• TableS6.xlsx: Strand-aware RNA-seq support for MIR loci screened for miPEP prediction in tomato leaves and roots.
• TableS7.xlsx: Exploratory analysis of the association between genomic context and miPEP features in tomato.
• description_tables_full.txt: full description of the tables included.
• eggplant_premiR_candidates_BLAST_EN.ipynb: Homology-based identification of putative eggplant pre-miRNA loci through BLAST alignment of known Solanaceae pre-miRNAs, followed by extraction of candidate genomic regions.
• generic_pri_miRNA_upstream_from_GFF3_chr_to_NC_FIXED.ipynb: Extraction of strand-aware upstream sequences from annotated pri-miRNA loci using genome and GFF3 files, with automated chromosome-to-genome identifier matching.
• miPEPs_ORFs_kmer_overlap_colab.ipynb: Detection of exact amino-acid k-mer matches (6–30 aa) between predicted ORF peptides and the curated tomato miPEP dataset for comparative conservation analyses.
• orfs_from_fasta_ATG_6_200aa_v2_EN.ipynb: Identification and extraction of all ATG-initiated ORFs (6–200 amino acids) from DNA FASTA sequences, including optional reverse-complement strand analysis and peptide FASTA generation.
• upstream_from_miRBase_hairpin_list_noGFF3_EN.ipynb: Extraction of upstream genomic regions from miRBase hairpin sequences when genomic annotations (GFF3 files) are unavailable, using genome mapping to infer precursor coordinates.
• IGV_robust_transcripts_panels.zip: strand-separated IGV/JBrowse-type coverage plots for the 21 robust loci detected overall.
• mipeps_alphafold_prediction.zip: AlphaFold2 structural predictions for all 107 tomato miPEPs, including structure files, confidence metrics and pLDDT-coloured structural visualizations generated from the AlphaFold2 models.
• Alpha_fold_prediction_panels_all.pdf: pdf with all Alpha_fold_prediction images for the 107miPEPs, corresponding to the best prediction for each.
• mipepORFS_mappingdata.zip: BAM alignment files and their associated BAI index files generated and used for visual inspection in IGV (Integrative Genomics Viewer) of genomic regions corresponding to putative miPEPs investigated in this study. The dataset includes files from four leaf samples and four root samples.The BAM files contain sequencing reads aligned to the reference genome used in the analysis. These files preserve the information required to visualize:

• the genomic position of the reads,
• the coverage across each locus,
• the orientation of the alignments

File use

To correctly visualize the alignments from mipepORFS_mappingdata.zip, the files should be opened in IGV together with:

• the corresponding reference genome: Solanum lycopersicum reference genome sequence, assembly SL3.0
• the mipep annotation track used in the study: mipeps_prediction_SL3.0.gtf, included in the file
• For improved visualization and interpretation in IGV, the gene annotation file Solanum_lycopersicum.SL3.0.57.chr.gtf can also be loaded together with the BAM and BAI files.

The tomato reference genome sequence (Solanum lycopersicum assembly SL3.0) and the corresponding gene annotation file can be downloaded from Ensembl Plants.