title: Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies.
abstract: 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.
authors: Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 gallaher@chem.ucla.edu.
authors: Sean D
authors: http://orcid.org/0000-0002-9773-6051
authors: SD
authors: Gallaher
authors: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095.
authors: Sorel T
authors: http://orcid.org/0000-0001-7090-5719
authors: ST
authors: Fitz-Gibbon
authors: Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.
authors: Anne G
authors: http://orcid.org/0000-0003-2268-2885
authors: AG
authors: Glaesener
authors: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095.
authors: Matteo
authors: http://orcid.org/0000-0001-9355-9564
authors: M
authors: Pellegrini
authors: Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095.
authors: Sabeeha S
authors: http://orcid.org/0000-0002-2594-509X
authors: SS
authors: Merchant
mesh_terms: D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D004251:DNA Transposable Elements; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D006239:Haplotypes; D007753:Laboratories; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA
chemical_list: D004251:DNA Transposable Elements