Transposable element landscape in plant protein-coding genes: mapping insertion patterns and links with gene functions

This upload contains the supplementary tables for the manuscript 'Transposable element landscape in plant protein-coding genes: mapping insertion patterns and links with gene functions.' Figure S1. (A) Shortest scaffold from the L50 set (N50) (Mbp) and (B) Percentage of BUSCO Genes (%) for the genome assemblies of the 12 analyzed species, both obtained from the Phytozome repository. (C) Schematic phylogenetic tree illustrating the evolutionary relationships among the 12 species analyzed in this study. The estimated divergence times were obtained from the TimeTree database (https://timetree.org/). Figure S2. Heatmap of the length of TEs per superfamily in 5’usptream (A), gene body (B), 5′ UTR (C), CDS (D), Intron (E), 3′ UTR (F), and 3’downstream (G). Dendrograms above the heatmaps show the clustering patterns of species. Table S1. TE length (Mbp) for each TE superfamily across the 12 species analyzed in this study. Figure S3. Alignments of the O. sativa CCD4 (A) and LOX1/5 (B) CDS regions with the TE consensus sequences. Black lines indicate the regions that align with TE-derived sequences. Table S2. Mercator4 functional annotation of protein-coding genes. Table S3. TE length per locus. Table S4. Z-scores from the enrichment analysis of TE coverage across gene functional categories. Positive Z-scores indicate overrepresented categories, whereas negative Z-scores indicate underrepresented categories. Categories were considered significantly enriched or depleted when Z-scores were ≥ 1.96 or ≤ −1.96, respectively. Table S5. Mercator4 functional annotation and TE coverage of loci associated with the tricarboxylic acid (TCA) cycle and glutathione metabolism pathways in Zea mays and Oryza sativa. Table S6. List of the 80 mRNA-seq libraries, tissue sources, stress conditions and transcript abundance (Transcripts Per Million, TPM) used for gene expression analysis of the Oryza sativa loci LOC_Os03g49380 and LOC_Os02g47510. Gene expression data were obtained from the Rice Genome Annotation Project website (https://rice.uga.edu/expression.shtml). Table S7. Comparison of Helitron coverage in the genomes analyzed in this study with values reported by Huang et al. (2025).