Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies

Chlamydomonas reinhardtii is a widely used reference organism in studies
of photosynthesis, cilia, and biofuels. Most research in this field uses a
few dozen standard laboratory strains that are reported to share a common
ancestry, but exhibit substantial phenotypic differences. In order to
facilitate ongoing Chlamydomonas research and explain the phenotypic
variation, we mapped the genetic diversity within these strains using
whole-genome resequencing. We identified 524,640 single nucleotide
variants and 4812 structural variants among 39 commonly used laboratory
strains. Nearly all (98.2%) of the total observed genetic diversity was
attributable to the presence of two, previously unrecognized, alternate
haplotypes that are distributed in a mosaic pattern among the extant
laboratory strains. We propose that these two haplotypes are the remnants
of an ancestral cross between two strains with ∼2% relative divergence.
These haplotype patterns create a fingerprint for each strain that
facilitates the positive identification of that strain and reveals its
relatedness to other strains. The presence of these alternate haplotype
regions affects phenotype scoring and gene expression measurements. Here,
we present a rich set of genetic differences as a community resource to
allow researchers to more accurately conduct and interpret their
experiments with Chlamydomonas.