DOI: 10.5281/zenodo.18336793
title: Supporting Material to Cross-subgenus hybridization between Leishmania and Sauroleishmania informs on parasite genomic compatibility and transcriptomic adaptation

description: Supporting Material to Cross-subgenus hybridization between Leishmania and Sauroleishmania informs on parasite genomic compatibility and transcriptomic adaptation (https://www.biorxiv.org/content/10.1101/2025.03.25.645178v1)

 

The file counts_on_hybrid.tsv contains the raw counts on the genes of the hybrid reference (concatenation of L.Tarentolae and L.infantum).

The file normed_counts_on_hybrid.tsv contains the normalised counts on the genes of the hybrid reference (concatenation of L.Tarentolae and L.infantum).

The files tarinf.fa and tarinf.gff are the reference and annotation of the hybrid (concatenation of GCA_900500625.2 and GCA_009731335.1) used in the DNA and RNA-seq analysis.

The files tarentolae_cleaned.fa is a curated version of GCA_900500625.2 where we kept the first 57 contigs that have a clear chromosome assignation. This version is still 32.2Mb long and contains 97.3% of the original genes. This was used to simplified final visualisation but not required strictly speaking.

The file counts_on_hybrid_dna.tsv contains the raw counts on the genes of the hybrid reference (concatenation of L.Tarentolae and L.infantum) on the genomic data set.

The file Orthogroups_cleaned_and_gp63.tsv contains the list of orthogroups with L.infantum and L.tarentolae gene lists for each orthogroups that was kept (coherence in chromosome inheritance. e.g. a group with genes on different chromosome in L.Tarentolae and L.infantum was removed). GP63 genes were therefore removed because most L.tar are on small contigs .We put back an artifical orthogroup (OG099999) with all L.infatum and L.tarentolae found in chromosome 10. 

There are also 3 PDF documents:



genes_coordinates_individual_chromosomes.pdf  contains the concatenation of 36 plots showing the distribution of the genes along the chromosome. There contain 5 rows. From top to bottom:  (1) localisation of all genes, (2) localisation of genes with zscore>2, (3) localisation of up genes (large RNA) with zscore>2  (4) localisation of down genes (low RNA)  with zscore >2 , and (5) directons (stretch of genes in + or - directions).

go_individual_chromosomes.pdf contains the concatenation of 36 GO enrichments made for each chromosome using genes that have a different ratio of RNA and DNA levels. 

go_individual_chromosomes_z2.pdf contains the concatenation of 36 GO enrichments made for each chromosome using genes that have a different ratio of RNA and DNA levels with z>2. 


The file genes_coordinates_one_panel.png contains is a summary of the PDF file genes_coordinates_individual_chromosomes where we put all plots in one panel (removing x and y labels for space). 

The inter_gene_distance.png file was used to assess whether the genes of interest (zscore>2 and up/down in RNA counts wrt DNA), were spatially clustered along the genome. to do so, we compute the median inter-gene distance for the subset and compared it to a null distribution generated randonly sampling gnes from the full gene set (1000 permutations). as shown in the plotm genome-wide we found no significant clustering. At chromosome level, chr23 and 35 show significant clustering