Skip to main content
. 2020 Apr 27;9:e55336. doi: 10.7554/eLife.55336

Figure 5. Families of WHO genes and their phylogenetic relationship to HO and VDE.

Magenta branches indicate WHO genes that are located at the FBA1 locus, and blue branches indicate WHO genes that are not beside FBA1. 14 WHO families are marked by brackets. Individual WHO gene names are colored by their source genus (black, Torulaspora; orange, Lachancea; gray, other genera). WHO gene names indicate the source species and strain number (if multiple strains were analyzed), WHO family (in uppercase), the name of a neighboring gene in the genome (in lowercase), and the suffix ‘int’ for intact WHO genes or ‘ps’ for WHO pseudogenes. Protein sequences were aligned using MUSCLE and filtered with Gblocks as implemented in Seaview v4.5.0 (Gouy et al., 2010). Badly degraded pseudogenes (relics) were not included. The tree was constructed by maximum likelihood using IQ-TREE v1.6.12 (Trifinopoulos et al., 2016), utilizing the built-in model finder option. Numbers on branches show support values from SH-aLRT and 1000 ultrafast bootstraps, separated by a slash (Trifinopoulos et al., 2016). The tree was rooted using VDE because WHO and HO share a zinc finger domain.

Figure 5.

Figure 5—figure supplement 1. Some Kazachstania species have an intron in FBA1 at a location corresponding to the WHO cleavage site in Torulaspora.

Figure 5—figure supplement 1.

(A) Genome organization around FBA1 in Kazachstania servazzii and its close relatives. Data from 4 strains of K. servazzii are shown. FBA1 genes, exons and fragments are colored magenta and their amino acid coordinates in the Fba1 protein are indicated. The phylogenetic tree topology is from Shen et al. (2018) and Vaughan-Martini et al. (2011). The genomes of 13 other species of Kazachstania that are outgroups to the ones shown here have no FBA1 intron and no WHO genes (data from Shen et al., 2018). (B) Sequence of the intron in the FBA1 gene of K. servazzii strain UCD13. The intron is located between the first and second bases of codon 223. Intron sequence is shown in lowercase, with exons and their translations in uppercase. Core intron sequence motifs are underlined.