Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii

Abstract

Recombination suppression in sex chromosomes and mating type loci can lead to degeneration as a result of reduced selection efficacy and Muller's ratchet effects. However, genetic exchange in the form of noncrossover gene conversions may still take place within crossoversuppressed regions. Recent work has found evidence that gene conversion may explain the low degrees of allelic differentiation in the dimorphic mating-type locus (MT) of the isogamous alga Chlamydomonas reinhardtii. However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence within MT.Here, we calculate degree of linkage disequilibrium (LD) across MT as a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region.We find that degree of LD predicts selection efficacy across MT, and that purifying selection is stronger in shared genes than in MT-limited genes to the point of being equivalent to that of autosomal genes.We argue that while crossover suppression is needed in the mating-type loci of many isogamous systems, these loci are less likely to experience selection to differentiate further. Thus, recombination can act in these regions and prevent degeneration caused by Hill-Robertson effects.

TALE homeobox heterodimer GSM1/GSP1 is a molecular switch that prevents unwarranted genetic recombination in Chlamydomonas

“…In fact, it has long been known that the uniparental inheritance of chloroplast DNA in C. reinhardtii is leaky, with biparental and even paternal progeny emerging from crosses with low frequency (Gilham, ; Sager and Lane, ; Umen and Goodenough, ). More recent genome analysis of natural populations in C. reinhardtii and in another green alga, Ostreococcus tauri , reported that recombination is not rare in the chloroplast genome, suggesting the occurrence of biparental inheritance (Blanc‐Mathieu et al ., ; Hasan et al ., ). These patterns are concordant with the suggestion (Birky, ; Radzvilavicius et al ., ) that biparental inheritance of organelles is ancestral, serving to recombine organelle genomes, and that the selective degradation of minus (chloroplast) or plus (mitochondrial) genomes in C. reinhardtii evolved secondarily to achieve the advantages of uniparental inheritance.…”

Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

“…2015 ; Craig et al. 2019 ; Hasan, Duggal, and Ness 2019 ). After de novo assembly and annotation (see Methods for details), we identified GEVEs in six of the wild strains ( Fig.…”

Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

“…We analyzed publicly available high-throughput genome sequencing data for 33 wild strains of C. reinhardtii . This data was originally generated for population genomic studies of diverse C. reinhardtii strains (Flowers et al ., 2015; Craig et al ., 2019; Hasan et al ., 2019). After de novo assembly and annotation (see Methods for details), we identified GEVEs in six of the wild strains (Figure 1A,B).…”