Supplementary Material associated to bioRxiv manuscript: 'Repurposing of Synaptonemal Complex Proteins for Kinetochores in Kinetoplastida'

Supplementary Material for 'Repurposing of Synaptonemal Complex Proteins for Kinetochores in Kinetoplastida'
Figure S1 Expression test of the KKT16 complex subunits. pBA198 (6His-KKT16), pBA200 (KKT18, 6His-KKT16), and pBA202 (KKT18, 6His-KKT16, KKT17) were transformed into E. coli. Protein expression was induced with IPTG at 37°C for 3 hours. Coomassie-stained 12% acrylamide gel of the purification is shown. M: marker.
Table S1 List of primers used in this study.
Table S2Presence/absence profiles of the SYCP2-3 and HOP1 gene family in eukaryotes, including: (1) the sources for 343 genomes and translated transcriptomes, (2) taxonomy for each species, (3) numbers of paralogues per species for SYCP2, SYCP3 and HOP1-like genes, (4) notes and gene names of SYCP2,3 and HOP1 orthologues, (5) information evidence for the kinetochore archetype present in each species (canonical kinetochores: CENP-A and or NDC80 based, kinetoplastid kinetochore: KKT/KKIP proteins present, unknown: no data available, likely canonical: annotated as such, given the presence of canonical kinetochores in related lineages). Of note: orthologues of the meiotic HOP1 HORMA protein were searched in our local database based on previously established HMM models with [8,29]. Divergent candidates were further included based on the presence of extra non-HORMA domains/motifs found among other orthologues (i.e. winged-helix, PHD zinc finger, HORMA-binding closure motif and an extended carboxy-terminal disorder tail).
File S1Text files (.hhr) with the outputs of HMM-vs-HMM profile searches (HHsearch) of full-length KKT16 and KKT17,18 and its separate domains (ARM, PH and coiled coil) against the combined PfamA and pdb70 HHsuite3 databases (see Data & Methods).
File S2Text files containing sequences of the eukaryotic SYCP2, SYCP3 and HOP1-like orthologues used in this study (see Table S2 for presence/absence profiles).
File S3Text files and visualisation of profile HMMs: (1) hmm3.1 profiles used for iterative HMM searches, (2) annotated .hhm + alignment files (.a3m), (3) graphical overview of conservation and secondary structure of annotated .hhm file (.pdf), (4) underlying alignments (.fasta files; if available). See for scripts and explanation of output File S6.
File S4Session files pertaining to the phylogenetic analyses for the ARM+PH and coiled coil Figure 4: (1) newick/nexus tree files, (2) alignments used to infer the phylogenetic trees, (3) log files of the IQ-Tree analysis and the untrimmed alignments.
File S5Jalview session files of panels C of Figure 2 and Figure 3. To achieve the same conservation scoring colour coding use the following settings in Jalview (version 2.11.1.3, RRID: SCR_006459 [103]): ‘colour by annotation’ > Conservation > Above Threshold > Threshold is min/max > threshold 3.5.
File S6Relevant settings/description of software packages and example scripts used to annotate and visualise HMMs and the HHsearch output in Figure 1, Figure 2, Figure 3 and File S3. This uncompressed file contains the following: (1) example folder with executables and generated files, (2) a library of python and perl scripts, (3) visual guidance on how to interpret graphical overviews of HMM figures, (4) overview and manual on how to generate annotated HMM (.pdf). The scripts incorporate a modified version of the visualisation script ‘hhsearch-figgen’ (https://github.com/twemyss/hhsearch-figgen) developed by T.A.W.