The diversity and evolution of wtf genes in fission yeasts.

(A) The gene structures of the wtf genes in the S. pombe reference genome. Rectangles and lines represent exons and introns, respectively. Rectangles with the same color indicate exons that share >50% sequence identity. (B) The similarity network of exons of the wtf genes in the S. pombe reference genome. Sequences that share an identity of >50% form a cluster. The colors of wtf exons correspond to these in panel (A). The exons for each cluster were listed in the Supplementary file 1c. (C) The heatmap of nucleotide identity among exons of the wtf genes in S. pombe reference genome. (D) The distribution wtf genes in 21 S. pombe strains. wtf genes were present in 25 genetic loci. Filled circles and empty circles represent the presence or absence of wtf genes, respectively. Red pentagons indicate putative wtf pseudogenes. The size of circles in purple indicates the number of wtf genes. The relationship among 21 S. pombe strains was inferred based on phylogenetic analysis of 30 randomly selected genes. (E) Phylogenetic relationship of wtf genes in 21 S. pombe strains. The phylogenetic tree is reconstructed using the maximum likelihood method. Filled circles in blue indicate wtf genes in S. pombe reference genome. The number of exons, the presence of solo-LTRs, the putative pseudogene status, the presence of intron-1-ATG codon, the presence of exon-2-ATG codon is shown near the corresponding wtf gene. wtf genes from other fission yeast species were collapsed into a triangle.

The effect of wtf gene on the growth of S. pombe.

(A) Generation of wtf knockout (Δwtf) strains based on the homologous recombination method. Substitution cassette contains a kanMX resistance marker and two homologous sequences flanking the target wtf genes. (B) Spot assay of Δwtf strains. The strains were continuously diluted by a 10-fold gradient to 10-5, and five stock suspensions were spotted onto the YE (Yeast extract) liquid medium.

Recombination analysis of wtf genes.

(A) Split tree of 25 wtf genes of the S. pombe reference genome. (B) Split tree of wtf genes from 21 S. pombe strains. The wtf genes of the S. pombe reference genome are labelled. (C) Recombination rates of wtf genes that belong to groups 1 to 4. Recombination rates were estimated for the full-length wtf sequences, the first exons, and the wtf sequences without the first exons. (D) Breakpoints detected for wtf genes of group1. The exons of wtf4, as a gene position reference, are shown.

Poison and antidote activity of wtf genes and chimeric wtf genes.

wtf23 and wtf18 are highlighted in green and red, respectively. Rectangles represent exons. The start codon ATG is shown. For wtf18, an in-frame ATG codon was introduced right before the start of exon 2, generating wtf18poison/-0M. Spot assay of yeast transformed with the short isoforms (encoding poison-like proteins) and the long isoforms (encoding antidote-like proteins) of wtf23 (A) and wtf18 (B). (C to F) Four chimeric wtf genes were generated through artificial recombination, namely wtfC1 (with exons 1-2 of wtf23 and exons 3-6 of wtf18), wtfC2 (with exons 1-3 of wtf23 and exons 4-6 of wtf18), wtfC3 (with exons 1-4 of wtf23 and exons 5-6 of wtf18), and wtfC4 (with exons 1-5 of wtf23 and exon 6 of wtf18). Spot assay of yeast transformed with the short isoforms (encoding poison-like proteins) and the long isoforms (encoding antidote-like proteins) of wtfC1 (C), wtfC2 (D), wtfC3 (E), and wtfC4 (F) are shown.

The evolutionary mechanisms of wtf genes.

(A) Mechanism of wtf meiotic driver. wtf genes are transcribed into two transcripts, namely long and short isoforms. The long and short isoforms encode antidote and poison, respectively. All spores are exposed to the poison, whereas only those that inherit wtf genes express the antidote and are rescued. Spores without the wtf allele are destroyed, resulting in the drive of wtf. (B) Duplication is insufficient to drive the diversification of wtf genes. Gene duplication of wtfA gives rise to a new wtf gene, wtfAdup. However, wtfAdupgene can be detoxified by the original wtfA gene and thus cannot drive through its host population. (C) When recombination occurs between two parental wtfB and wtfC genes, generating chimeric wtfD gene. wtfD encodes new poison that cannot be detoxified by their parental antidote and the antidote to new poison. The wtfD gene then can spread in its host population.