Supplementary data for "On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa"

Supplementary data for Benz, Raas, Tripathi, et al. 2024 "On the possibility of yet a third kinetochore system in the flagellate phylum Euglenozoa".This dataset includes:Supplementary File S1: cytoscape network file for HHsearch ("FileS1_HHsearch_network_based_on_TableS3.cys"). Supplementary File S2: cytoscape network file for Foldseek ("FileS2_Foldseek_nework_based_on_TableS5.cys")Supplementary File S3: Zip file for CENP-A-V5 confocal images. ("FileS3.zip")The original files of the main figures ("Main Figures.zip")The original files of the supplementary figures & tables ("Supplementary Figures.zip" & "Supplementary Tables.zip"). Detailed legends of the supplementary tables can be found below.Complete set of predicted structures for all P. papillatum folds as predicted with AlphaFold2 ("P_papillatum_AF2_foldome_rank1_pdbs.tar.gz")HH-suite databases used in the homology search bioinformatics pipelines of KKT alignments, cKT alignments and diplonemid orthologous groups ("kkt_kkip_hhsearch_db.tar.gz", "ckt_hhsearch_db.tar.gz", "Diplonemea_hhsearch_db.tar.gz", respectively)Foldseek database of the full P. papillatum foldome ("P_papillatum_af2_foldseek_db.tar.gz") & of the full foldomes of the representative species + the P. papillatum foldome + the curated kinetochore folds ("repspecies_ppal_kkt-kt_foldseek_db.tar.gz")Curated set of AlphaFold2-predicted structures of kinetochore proteins ("kkt-kt_foldseek_db.tar.gz")Output files from hhsearch and foldseek as performed during hte homology searches ("hhsearch_output.tar.gz" & "foldseek_output.tar.gz", respectively)Transcriptomes of Diplonemea spp. used in the bioinformatics pipeline ("Diplonemea_sequence_database.tar.gz")OrthoFinder output run on the Diplonemea dataset ("orthofinder_diplonemea.tar.gz")Legends for supplementary tables:Table S1: source of predicted proteins of eukaryotic transcriptomes and genomes of various eukaryotes used in this studyTable S2: Paradiplonema ID infosheetTable S3: HHsearch searches.a: initial search (KT/KKT vs. Diplonemea OGs) reciprocal search (top 10 Diplonemea OGs ← → Diplonemea OGs + KOG/COG + PFAM + KT/KKT). c: bidirectional hits from reciprocal searchTable S4: HMMsearch –maxTable S5: Foldseek searchesa: initial search (KT/KKT from representative species vs. P. papillatum AF2 structures). b: reciprocal search (top 10 P. papillatum, AF2 structures ← → KT/KKT from representative species + full proteomes of A. thaliana, H. sapiens, S. cerevisiae and T. brucei). c: bidirectional hits from reciprocal searchTable S6: Discoba kinetochore evolution - presence/absence tableTable S7: Pulldown of CENP-A-V5Table S8: Primer sequences used for endogenous tagging