Additional file 1 of Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania

Additional file 1: Tables S1-S9. Table S1. A metadata table including the complete list of 1448 SIDER2 elements in L. infantum with 1262 present in 3'UTRs (predicted by PRED-A-TERM and confirmed for several by Illumina RNA-seq). This table also includes information regarding the genomic location and orientation of SIDER2 elements, their length, their distance from the CDS, CD-Hit-Est clustering, HMMER signature II score and the expression group in L. infantum promastigotes as determined by Illumina RNA-sequencing. Table S2. Metadata table of 1262 SIDER2 sequences located at the 3'UTR subjected to of CD-Hit-Est clustering analysis based on sequence similarity. In a separate sheet (≥ 4 SIDER2/cluster-no paralogs), the list of 74 clusters with ≥ 4 transcripts each harboring a single SIDER2 in their 3'UTR, excluding all paralogous proteins is provided. In another separate sheet (SIDER2 Clusters with paralogs), 19 clusters containing paralogous genes (among the 1127 L. infantum transcripts) harboring a single SIDER2 element in their 3'UTR are listed. In the last sheet (FPKM mean-SD Pro and Ama), expression levels (mean of FPKM values) of 74 clusters harboring up to 4 SIDER2-containing transcripts in L. infantum promastigotes (Pro), axenic amastigotes (Axe Ama) and macrophage-derived amastigotes (Macro Ama) are shown. Table S3. A list of 1127 L. infantum transcripts harboring a SIDER2 element in their 3'UTR as predicted by the PRED-A-TERM software. We also manually examined the Illumina RNA-seq read patterns in IGV to check if they were aligned with the 3' UTRs harboring SIDER2 elements. Table S4. A full list of the L. infantum transcriptome (FPKM values) in promastigotes (Pro), axenic amastigotes (Axe Ama) and macrophage-derived amastigotes (Macro Ama) as resulted from high throughput Illumina-RNA seq analysis. In a separate sheet, only the SIDER2-containing transcripts were analyzed. In another sheet, we summarized the proportion of developmentally regulated SIDER2-containing vs. non-SIDER2 transcripts (see also Fig. 6D). Table S5. Distribution of SIDER2 elements and expression levels of SIDER2-containing transcripts across the 36 L. infantum chromosomes. The comparison of the low-expressed SIDER2-containing transcripts to the low-expressed non-SIDER2 transcripts per chromosome is shown. The chromosome median expression is normalized by the number of chromosomal copies (as determined by Illumina DNA-seq). Table S6. List of developmentally regulated SIDER2-containing transcripts. SIDER2-containing transcripts preferentially expressed in L. infantum promastigotes (Pro) or axenic amastigotes (Axe Ama) and or macrophage-derived amastigotes (Macro Ama) are shown. The cutoff for differentially expressed (DE) SIDER2 transcripts was set at log2: 0.58. In separate sheets, stage-regulated SIDER2 transcripts similarly expressed in axenic and macrophage-derived amastigotes or solely in macrophage amastigotes are shown. Table S7. Table with p-values comparing Gene Ontology (GO) functions (e.g., Biological process/BP, Molecular function/MF and Cellular component/CC) of SIDER2-containing transcripts in L. infantum. Highlighted in red are GOs with a Benjamini corrected p-value < 0.05. Table S8. Table with p-values comparing GO functions (e.g., Biological process/BP, Molecular function/MF and Cellular component/CC) of low-expressed SIDER2-containing transcripts (408) in L. infantum. Highlighted in red are GOs with a Benjamini corrected p-value < 0.05. Table S9. Table with p-values comparing GO function’s enrichment (e.g., Biological process/BP, Molecular function/MF and Cellular component/CC) of developmentally regulated SIDER2-containing transcripts, up- or down-regulated either in L. infantum axenic amastigotes (AxeAma) or macrophage-derived amastigotes (MacroAma). Highlighted in red are GOs with a Benjamini corrected p-value < 0.05.