Supplementary files to generate figures and statistics for "Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri"

In this repository located all supplementary files to generate statistics and figures for the manuscript "This repository contains all supplementary files used to generate statistics and figures for the manuscript "Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri".The genome and annotation files for C. brenneri are located in a different FigShare directory (doi:10.6084/m9.figshare.25988629), and also from the ENA or NCBI databases under the accession number GCA_964036135.1. 7sp_all_intron_info_ALL.FIN.tab - data (absence/presence, sizes, phase, splicing sites) on 7238 single-copy orthologues of C. elegans, C. briggsae, C. tropicalis, C. brenneri, C. remanei, C. nigoni, and C. inopinata based on exon/intron alignment from GenePainter C.brenneri_trees.txt - trees built by IQ-TREE from ProgressiveCactus alignments of C. brenneri, C. elegans, C. remanei, C. tropicalis, C. wallacei, C. doughertyi, C. sp44, C. sp48, C. sp51, and C. sp54 within 50kb non-overlapping windows of the C. brenneri genome.C.brenneri_topol.txt - the topologies of those treesC.brenneri_branches.txt - terminal branch lengths of C. brenneri and C. sp48 (or just C. brenneri when they are not sister species) from the trees.Cbren_combo_phastcons_50kb.wig - phastCons conservation scores within 50kb non-overlapping windows of the C. brenneri genome Cbren_Exons_100Kb.bed - fraction of exons within 100-kb non-overlapping windows of the C. brenneri genome.Cbren_Introns_100Kb.bed - fraction of introns within 100-kb non-overlapping windows of the C. brenneri genome.Cbren_Repeats_100Kb.bed - fraction of repeats within 100-kb non-overlapping windows of the C. brenneri genome. Cbren_gt_stats.zip - a zip archive containing statistics on gene lengths, intron lengths, and the number of exons from GT for 1-to-1 orthologs and for all genes for C. elegans, C. briggsae, C. tropicalis, C. brenneri, C. remanei, C. nigoni, and C. inopinata Cbren_phasedBlks.csv - inferred syntenic blocks among C. elegans, C. briggsae, C. tropicalis, C. brenneri, C. remanei, C. nigoni, and C. inopinata from the GENESPACE analysis, with C. brenneri as the referenceGENESPACE_exon_intron_frac_count_Cbren_vs_othersFIX.txt - fractions of exons, introns, intergenic DNA, number of genes, and number of exons within the syntenic blocks Orthogroups.GeneCount.tsv - gene counts within orthogroups from OrthoFinder for C. elegans, C. briggsae, C. tropicalis, C. brenneri, C. remanei, C. nigoni, and C. inopinataOrthogroups.tsv - gene lists within orthogroups from OrthoFinder for C. elegans, C. briggsae, C. tropicalis, C. brenneri, C. remanei, C. nigoni, and C. inopinata (C. brenneri genes have index "CAEBREG000000X" instead of "CAEBRE_")