Abstract
The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.
Highlights
The fission yeast Schizosaccharomyces pombe is a unicellular fungal species belonging to the Taphrinomycotina subphylum of the Ascomycota phylum (Liu et al 2008)
The Illumina genome sequencing data of 161 S. pombe strains with names that begin with the initials JB were downloaded from European Nucleotide Archive (ENA) according to the ENA accession numbers given in Jeffares et al (2015), and are listed in supplementary table S1, Supplementary Material online
Based on single-nucleotide variants (SNVs) in the nuclear genome, Jeffares et al showed that these JB strains have 57 types of nuclear genomes, with 129 strains falling into 25 “clonal clusters” each composed of multiple strains with near-identical nuclear genomes and 32 other strains each possessing a uniquely distinct nuclear genome
Summary
The fission yeast Schizosaccharomyces pombe is a unicellular fungal species belonging to the Taphrinomycotina subphylum of the Ascomycota phylum (Liu et al 2008). In 1947, Urs Leupold, the founder of fission yeast genetics, selected an S. pombe isolate from French grape juice as the subject of his PhD research, and this strain (hereafter referred to as the Leupold strain) has essentially been the only strain used for modern S. pombe molecular biology studies (Osterwalder 1924; Leupold 1950; Hu et al 2015).
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