DOI: 10.6084/m9.figshare.25988626
title: Supplementary files to generate figures and statistics for "<b>Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode </b><b><i>Caenorhabditis brenneri</i></b>"

description: 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 <i>C. brenneri</i> 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.<br><b>7sp_all_intron_info_ALL.FIN.tab</b> - data (absence/presence, sizes, phase, splicing sites) on 7238 single-copy orthologues of <i>C. elegans</i>, <i>C. briggsae</i>, <i>C. tropicalis,</i> <i>C. brenneri</i>, <i>C. remanei</i>, <i>C. nigoni</i>, and <i>C. inopinata </i>based on exon/intron alignment from GenePainter<br><b>C.brenneri_trees.txt </b>- trees built by IQ-TREE from ProgressiveCactus alignments of <i>C. brenneri</i>, <i>C. elegans</i>, <i>C. remanei</i>, <i>C. tropicalis</i>, <i>C. wallacei</i>, <i>C. doughertyi</i>, <i>C. sp44</i>, <i>C. sp48</i>, <i>C. sp51</i>, and <i>C. sp54</i> within 50kb non-overlapping windows of the <i>C. brenneri</i> genome.<b>C.brenneri_topol.txt </b>- the topologies of those trees<b>C.brenneri_branches.txt</b> - terminal branch lengths of <i>C. brenneri</i> and <i>C. sp48</i> (or just C. brenneri when they are not sister species) from the trees.<b>Cbren_combo_phastcons_50kb.wig</b> - phastCons conservation scores within 50kb non-overlapping windows of the <i>C. brenneri</i> genome<br><b>Cbren_Exons_100Kb.bed</b> - fraction of exons within 100-kb non-overlapping windows of the C. brenneri genome.<b>Cbren_Introns_100Kb.bed</b> - fraction of introns within 100-kb non-overlapping windows of the C. brenneri genome.<b>Cbren_Repeats_100Kb.bed</b> - fraction of repeats within 100-kb non-overlapping windows of the C. brenneri genome.<br><b>Cbren_gt_stats.zip</b> - 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 <i>C. elegans</i>, <i>C. briggsae</i>, <i>C. tropicalis,</i> <i>C. brenneri</i>, <i>C. remanei</i>, <i>C. nigoni</i>, and <i>C. inopinata</i><br><b>Cbren_phasedBlks.csv</b> - inferred syntenic blocks among <i>C. elegans</i>, <i>C. briggsae</i>, <i>C. tropicalis,</i> <i>C. brenneri</i>, <i>C. remanei</i>, <i>C. nigoni</i>, and <i>C. inopinata </i>from<i> </i>the GENESPACE analysis, with <i>C. brenneri</i> as the reference<b>GENESPACE_exon_intron_frac_count_Cbren_vs_othersFIX.txt</b> - fractions of exons, introns, intergenic DNA, number of genes, and number of exons within the syntenic blocks<br><b>Orthogroups.GeneCount.tsv</b> - gene counts within orthogroups from OrthoFinder for <i>C. elegans</i>, <i>C. briggsae</i>, <i>C. tropicalis,</i> <i>C. brenneri</i>, <i>C. remanei</i>, <i>C. nigoni</i>, and <i>C. inopinata</i><b>Orthogroups.tsv </b>- gene lists within orthogroups from OrthoFinder for <i>C. elegans</i>, <i>C. briggsae</i>, <i>C. tropicalis,</i> <i>C. brenneri</i>, <i>C. remanei</i>, <i>C. nigoni</i>, and <i>C. inopinata</i> (C. brenneri genes have index "CAEBREG000000X" instead of "CAEBRE_")<br><br><br>