Supplementary Data for: MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

Orthogroups, species tree and the MicroFinder protein set Files listed below are found in the "./OrthoFinder_results_and_MicroFinder_protein_set/" subdirectory. Sample IDs used throughout correspond to those given in Supplementarty Table 1 of the main manuscript. SubdIrectory containing proteomes for each species included in the OrthoFinder analysis: ./input_proteomes/ SubdIrectory containing annotation GFF files for each species included in the OrthoFinder analysis: ./annotations/ OrthoFinder orthogroups: Orthogroups.txt Per species gene counts per orthogroup annotated with whether each family was identified by KinFin as a broadly conserved "fuzzy" orothogroup and whether the orthogroup was included in the MicroFinder protein set: Orthogroups.GeneCount.KinFin_MicroFinder_annotated.tsv Subdirectory containing multiple sequence alignments for all orthogroups: ./MultipleSequenceAlignments_all_orthogroups/ SubdIrectory containing multiple sequence alignments for conserved single copy orthogroups used for IQTree species tree inference (FASTA headers have been simplified to just contain the species ID): ./species_tree_alignments/ IQtree species tree inference run details: species_tree.concat.iqtree IQtree species tree: species_tree.concat.nwk IQTree best fitting models and partitioning scheme: IQTree.concat.best_model.nex The MicroFinder protein set used in the MicroFinder pipeline: MicroFinder_prot_set.fa Re-curated bird genomes The "./Recuration/" subdirectory contains files used for the MicroFinder-enabled genome assembly curation of 12 previously released bird genomes listed in Supplementary Table 4 of the main manuscript. Subfolders in this directory are named by the TOL ID of each species and contain: PretextView HI-C contact map of the original genome assembly. PretextView savestate showing changes made during re-curation. AGP file summarising changes made to the original assembly. Updated genome assembly FASTA file. PretextView HI-C contact map of the updated genome assembly. Minimap2 alignment file of the original assembly vs the GGswu chicken genome in paf format. Minimap2 alignment file of the updated assembly vs the GGswu chicken genome in paf format. Data for figures and supplementary figures Figure 1 Panel A uses data from Supplementary Table 1 in the main manuscript. Panels B to D are made from pre and post curation pretext maps provided in "./Recuration/bAnsBra1/" of this repository. Figure 2 Phylogenetic tree used in panel A is here: "./OrthoFinder_results_and_MicroFinder_protein_set/species_tree.concat.nwk". Metadata for the phylogenetic tree is in Supplementary Table 2 in the main manuscript. Alignment files for panels B to E are in "./Figures_additional_processed_data/Figure_2/" in this repository. Figure 3 Processed data is in "./Figures_additional_processed_data/Figure_3/" in this repository. Figure 4 The pretext map and relevant savestates used to generate the figure are in "./Figures_additional_processed_data/Figure_3/" in this repository. Figure 5 Data for panels A and B are in Supplementary Table 4 in the main manuscript. The pretext map used for panel C is in "./Recuration/bAnaAcu1/" in this repository. Supplementary Figure 1 Processed data is in "./Figures_additional_processed_data/Supp_figure_1/" in this repository. Supplementary Figures 2 – 12 Pretext maps used to generate the figures are in sub directories of "./Recuration/" named by the corresponding TOL ID. Supplementary Figure 13 Processed fata is in Supplementary Table 5 in the main manuscript.