Analysis of eRF1, UPF1/2 and tRNAs in ciliate genomes

Analysis of genetic code, eRF1 and presence of UPF proteins in ciliates. Genomes and transcriptomes of ciliates were retrieved from NCBI and EukProt. Schematic phylogenetic tree is based on 18S phylogenetic analyses performed previously (Boscaro et al. 2018, Lian et al. 2020, Tsai et al. 2022). Major ciliate clades are depicted next to species names. Dataset shows the kind of data used for particular species as explained above the figure. Genetic code was retrieved from NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) and/or from a previous study (Swart et al. 2016). In genomic datasets, all tRNAs were predicted by Aragorn (Laslett and Canback 2004) with default settings. Presence of stop-codon recognizing tRNAs is marked by “+”, while their absence by “-“; unknown presence in other datasets is marked by “?”. eRF1 and UPF proteins were identified by BLAST 2.11.0+ (Altschul et al 1990), number indicates the count of homologues.