Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.

1 2 Despite its fundamental role as a model organism in plant sciences, the green alga 3Chlamydomonas reinhardtii entirely lacks genomic resources for any closely related species, 4 obstructing its development as a study system in several fields. We present highly contiguous 5 and well-annotated genome assemblies for the two closest known relatives of the species, 6Chlamydomonas incerta and Chlamydomonas schloesseri, and a third more distantly related 7 species, Edaphochlamys debaryana. We find the three Chlamydomonas genomes to be highly 8 syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. 9 schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We 10 identify the major centromeric repeat in C. reinhardtii as an L1 LINE transposable element 11 homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that 12 centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We 13 report extensive rearrangements, but limited gene turnover, between the minus mating-type loci 14 of the Chlamydomonas species, potentially representing the early stages of mating-type 15 haplotype reformation. We produce an 8-species whole-genome alignment of unicellular and 16 multicellular volvocine algae and identify evolutionarily conserved elements in the C. reinhardtii 17 genome. We find that short introns (<~100 bp) are extensively overlapped by conserved 18 elements, and likely represent an important functional class of regulatory sequence in C. 19 reinhardtii. In summary, these novel resources enable comparative genomics analyses to be 20 performed for C. reinhardtii, significantly developing the analytical toolkit for this important 21 model system. 22 23 24 25 26 27 28 29 30 31 The unicellular green alga Chlamydomonas reinhardtii is a long-standing model organism across 62 several fields, including cell biology, plant physiology and molecular biology, and algal 63 biotechnology (Salomé and Merchant 2019). Because of its significance, the ~110 Mb haploid 64 genome of C. reinhardtii was among the earliest eukaryotic genomes to be sequenced (Grossman 65 et al. 2003; Merchant et al. 2007), and both the genome assembly and annotation are actively 66 being developed and improved (Blaby et al. 2014). Despite its quality and extensive application, 67 the C. reinhardtii genome currently meets the 'phylogenetically isolated' definition. The closest 68 confirmed relatives of C. reinhardtii that have genome assemblies belong to the clade of 69 multicellular algae that includes Volvox carteri, the Tetrabaenaceae-Goniaceae-Volvocaceae, or 70 TGV clade. Collectively, C. reinhardtii and the TGV clade are part of the highly diverse order 71 Volvocales, and the more taxonomically limited clades Reinhardtinia and core-Reinhardtinia 72 (Nakada et al. 2008; Nakada et al. 2016). Although these species are regularly considered close 73 relatives, multicellularity likely originated in the TGV clade over 200 million years ago (Herron 74 e...

Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

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.

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.