Add Chlamydomonas reinhardtii to catalogue

[aays]

• Name: Chlamydomonas reinhardtii
• Common name: n/a

Description: unicellular isogamous alga with a haploid 110 Mb genome - used in studies of cell motility, but also more recently as a model for evolutionary genetics (especially in light of its facultatively sexual life cycle)

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Note: Maybe you don't know a lot of the things below - but, that's OK!
The criteria are that (a) the choice is reasonable, and (b) the rationale is clear.
What we want is a "reasonable estimate" (or, "best guess") - if you were to use a number in a paper,
what would you use and how would you justify it to your collaborators?
For instance, for "generation time", best would be to cite a paper that actually measures
or estimates generation time. But most species don't have this;
next best would be to give a number used in the literature, and provide a citation that used it
(and hopefully the publication gives a justification also).
Lacking this, you might provide a number from a related species (and a citation for this).

Here is the checklist of things that we need to add a species to the catalogue.
Each thing should be provided, with a justification (maybe short) and a citation.

Demographic information:

• generation time in years
  • ~2.4 mitotic doublings per day -> 365 * 2.4 = 876 doublings per year (Vitova et al 2011, link)
  • 1/876 = 0.0011 years/generation
  • I hope I did this right - please correct me if I'm wrong!
• "default" population size
  • 1.4 * 10^7 (Ness et al 2016, link)

Chromosome structure:

Note: The assembly should be chromosome-level, i.e., not composed of thousands of scaffolds.

• ensembl assembly ID or, if the assembly is not in Ensembl, a list of chromosomes with name and length (in bp)
  • GCA_000002595.3 (Ensembl (Plants) link, ENA link)

Recombination rates:

• genetic map of recombination rates (as a hapmap or csv file)
• genome-wide mean recombination rate (which will be used as the default)
  • 0.015 cM/Mb (Hasan and Ness 2020, link)
  • This is = rho / 2Ne, and is two orders of magnitude lower than lab estimates (9.15 cM/Mb)! But if simulating wild populations of C. reinhardtii, in the absence of a means of modifying the rate of sex in natural populations, this value already takes the infrequency of sex into account
  • If a means of modifying the rate of sex is implemented into stdpopsim, then the 9.15 cM/Mb value is appropriate to use when simulating natural populations, provided the rate of sex is set to 1/840 (see Hasan and Ness 2020)
  • But it is important to note that this is NOT the expected recombination rate in a single cross of C. reinhardtii, and is in fact substantially lower!

Mutation rate:

• genome-wide mean mutation rate
  • μ = 9.63 × 10^−10 (Ness et al 2015, link)

Demographic model:

• as a list of population sizes, growth rates, migration rates, etcetera. (optional)
• citation

Other information:

These are things we don't currently use, but will want to use in the future:

• sex determination system, and which chromosomes are the sex chromosome(s)
  • C. reinhardtii is an isogamous, heterothallic species with mating types determined by a ~500 kb locus on chromosome 6
  • individuals are either MT+ or MT- based on which allele is present at said locus
  • see Umen 2011 for more details
• ploidy
  • haploid