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.

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants

“…Another example comes from grapevine (Vitis vinifera), where an inbred Pinot Noir derivative was targeted for genome sequencing, but it was not noticed until later that there was either an uncontrolled outcrossing event, or a complete mix-up, so that in the end a Pinot Noir 3 Helfensteiner hybrid, or possibly a selfed Helfensteiner derivative, was sequenced (Jaillon et al, 2007). Similarly, wild-type strains of Chlamydomonas reinhardtii have complex histories, with spontaneous mutations and several examples of misidentification (Gallaher et al, 2015). In at least one case, a mutant line was more closely related to other wild-type lines than its supposed isogenic parent (Blaby et al, 2013).…”

“…There are also several examples of spontaneous mutations in Arabidopsis accessions identified by their phenotypiceffects (Loudet et al, 2008;Laitinen et al, 2010), including one that arose in the Col-0 reference strain (Coustham et al, 2014). Hundreds of mutations have been documented in another Col-0 lab stock by whole-genome sequencing , and thousands of single base pair mutations along with several new transposon insertions have apparently occurred since a standard Chlamydomonas line was established in the laboratory (Gallaher et al, 2015). In Arabidopsis, genome-wide mutation rates are ;1 per generation for single nucleotide polymorphisms and 0.5 per generation for indels Jiang et al, 2014).…”

“…based on whole-genome resequencing, that many common Chlamydomonas laboratory strains are segregants apparently derived from a single cross (Gallaher et al, 2015).…”

Genomic Diversity in Chlamydomonas Laboratory and Field Strains

“…Descendants of these strains show a wide range of phenotypic diversity regarding nitrate and micronutrient utilization, responses to light, and tolerance of iron-limited conditions (see figure, top panel). Gallaher et al (2015) use wholegenome sequencing to resequence a variety of laboratory strains in current use, and they provide valuable insights into the genetic basis for much of the observed phenotypic diversity. In a study of 39 strains, they discovered a total of over 600,000 single nucleotide variants in the 109-Mb Chlamydomonas genome, using CC-503 as the reference genome.…”

“…Geographic clustering of field strains is shown in the bottom panel. (Reprinted from Gallaher et al [2015], Supplemental Figure 1A, and Flowers et al [2015], Figure 2A. ) www.plantcell.org/cgi/doi/10.1105/tpc.15.00778…”