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Sex Without Crossing Over in the Yeast Saccharomycodes Ludwigii

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Sex Without Crossing Over in the Yeast Saccharomycodes Ludwigii bioRxiv preprint doi: https://doi.org/10.1101/2021.04.22.440946; this version posted April 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 ARTICLE Sex without crossing over in the yeast Saccharomycodes ludwigii Ioannis A. Papaioannou1, Fabien Dutreux2, France A. Peltier1, Hiromi Maekawa1#, Nicolas Delhomme3, Amit Bardhan1, Anne Friedrich2, Joseph Schacherer2,4 and Michael Knop1,5* 1 Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany 2 Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France 3 Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden 4 Institut Universitaire de France (IUF), Paris, France 5 German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany # Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan * To whom correspondence should be addressed: [email protected] Abstract Meiotic recombination is a ubiquitous function of sexual reproduction throughout eukaryotes. Here we report that recombination is extremely suppressed during meiosis in the yeast species Saccharomycodes ludwigii. DNA double-strand break formation, processing and repair are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers. We propose that Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent fertilization within the meiotic tetrad with the absence of meiotic recombination. bioRxiv preprint doi: https://doi.org/10.1101/2021.04.22.440946; this version posted April 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 Main Sex constitutes the prevailing reproductive mode throughout the eukaryotic tree of life1. At its core lies a periodic ploidy cycling, accomplished through meiosis, during which haploid gametes are produced, and mating, which ensures the restoration of the original ploidy level. Meiosis is thought to have arisen early in the eukaryotic evolution and is a ubiquitous attribute of sexual life cycles2. During the first meiotic division (meiosis I), parental chromosomes are recombined and separated, while in the second sister chromatids segregate (meiosis II). Random reassortment and recombination of homologous chromosomes in meiosis I lead to novel genetic constellations in the offspring. These are used as substrates for natural selection, for promotion of advantageous and purging of deleterious genetic combinations3,4. However, the significant complexity and biological costs of sex render its widespread occurrence paradoxical, and the questions of its evolutionary origin, persistence and functions have been outstanding enigmas in biology5–7. Saccharomyces cerevisiae (baker’s yeast) is a premier model organism for the study of cellular, molecular and evolutionary biology, and it has been used to gain major insights into the molecular aspects of meiosis8,9. Following pairing of homologous chromosomes, meiotic recombination is initiated in prophase I with the formation of DNA double-strand breaks (DSBs) by the topoisomerase-like protein Spo1110. Several pathways mediate the subsequent repair of these DSBs and pathway choice is regulated by a multitude of meiosis- specific factors that act in concert with the DNA repair machinery. One possibility involves the use of the homologous chromosome as repair template, which can ultimately lead to the generation of chimeric DNA molecules. This process may involve either reciprocal exchange of the chromosomal regions that flank the DSB site (crossover, CO) or gene conversion without reciprocal exchange (non-crossover, NCO)8,9. Crossing over leads to the establishment of chiasmata (Fig. 1d), which ensure the physical interconnection of bivalents that is important for the faithful segregation of homologous chromosomes in meiosis I11. In many, but not all, organisms this is facilitated by the synaptonemal complex, which mediates stable synapsis9. The extent of genetic exchange in meiosis and thus the generation of genomic diversity are strongly influenced by the frequency and distribution of COs along chromosomes. Homeostatic regulation controls these parameters in many organisms12,13, with different outcomes in different species. These range from one obligatory CO per chromosome in Caenorhabditis elegans14 to 10 or more in Schizosaccharomyces pombe15. Among yeasts, the frequency of meiotic COs per chromosome ranges from an average of 2.5 COs in Lachancea kluyveri to its highest level in Sc. pombe15–19. Furthermore, generation of diversity is influenced by the mating behavior (breeding), which can involve gametes of variable genetic relatedness. Mating occurs between unrelated gametes in outbreeding, which ensures high genetic diversity in the offspring. On the other hand, inbreeding (self- fertilization) refers to mating between genetically related gametes that originate from the bioRxiv preprint doi: https://doi.org/10.1101/2021.04.22.440946; this version posted April 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 3 same individual or clonal line. Inbreeding is generally considered to lead to lower heterozygosity, which can compromise the adaptive potential of populations20. Mating of gametes from the same meiotic event represents a particular type of inbreeding referred to as intratetrad mating or automixis21. This appears to be the most frequent breeding strategy in S. cerevisiae22–24. If automixis brings together chromosomes that had been separated during meiosis I (non-sister components), it is described as “central fusion” or “first division restitution”. This has important genetic consequences, since it maintains parental heterozygosity around the centromeres, reducing the risk of deleterious alleles being exposed due to homozygotization25–27. The degree to which parental heterozygosity is restituted upon intratetrad mating correlates inversely with the frequency of COs during meiosis. In the extreme case of absent crossing over parental genomes would be fully reconstituted and their heterozygosity maintained. Evolutionary models suggested that high frequency of deleterious mutations could promote automixis in the absence of meiotic recombination28. Chromosome segregation in meiosis I without any recombination (achiasmate meiosis) has been observed in one of the two sexes6,29 or in individual chromosomes30,31 of a few organisms. Furthermore, unusually low overall recombination rates have been reported in some species32,33. However, these data should be interpreted with caution since sampling bias, insufficient marker coverage and incomplete genome assemblies may have hindered the identification of COs in many of these cases. In addition, most of these studies could not exclude the possibility of crossing over near chromosome ends, which has been observed in a number of species across kingdoms32. The budding yeast species Saccharomycodes ludwigii (Fig. 1a-b) preferentially undergoes intratetrad mating (Fig. 1c), ensured by strong inter-spore bridges that efficiently keep spores together in pairs of opposite mating types during germination and subsequent mating34,35. This organism was used in the early days of yeast genetics for the pioneering description of heterothallism by Øjvind Winge at the Carlsberg laboratory35,36. During his studies, Winge also observed in this species an unusual segregation pattern of two cell morphology markers35. The subsequent interpretation by Lindegren was that the two genes were not linked and that “each is so close to the spindle attachment that segregation invariably occurs at the Meiosis I without crossing over”37. While it could have been a coincidence that both markers were linked to centromeres, later work by the Oshima lab surprisingly revealed that the same behavior was displayed by any combination of more than 20 genetic markers tested. These findings led to the conclusion that this “may be due to the absence of crossing over in Sd. ludwigii”38,39. Here we continued this work by exploring the extent and types of meiotic interactions between homologous chromosomes in Sd. ludwigii. For this, we performed whole-genome sequencing and high-contiguity de novo assembly of wild-type strains, which enabled a high- resolution DNA variant segregation analysis of meiosis. We combined bioinformatic analyses of the meiotic gene repertoire with a functional study of key meiotic components in order to bioRxiv preprint doi: https://doi.org/10.1101/2021.04.22.440946; this version posted April 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
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