Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii

Abstract

We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ;3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.

Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

“…However, it is interesting to note that the rate of variants within these blocks, 2.0%, was comparable to the 2.4% rate of variation that we observed in CC-2290, as well as the 2.83% average variant rate for wild isolates of Chlamydomonas as reported by Flowers et al (2015). (A) Identification of variants.…”

“…In work cosubmitted with this article, Flowers et al (2015) also observed ways in which mutations present in the sequenced strains of Chlamydomonas were biased toward those that are less deleterious to gene expression. For example, they observed that 28% of genes with premature stop codons encode proteins that are truncated by 5% or less.…”

Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii

“…Therefore, during the RNA-seq mapping, we allowed three mismatches after considering average synonymous polymorphism among the field isolates (nucleotide diversity at synonymous sites, dS = 0.0317, Flowers et al, 2015). As a result, mapping rates range between 82.1% and 98.2% of the total reads (Supplemental Table S2).…”

Genomic Diversity in Chlamydomonas Laboratory and Field Strains

“…In a related study of genomic diversity in Chlamydomonas, Flowers et al (2015) used whole-genome resequencing to analyze genetic diversity in 12 field isolates from Phenotypic variation of Chlamydomonas laboratory strains in response to iron concentration (top panel). Geographic clustering of field strains is shown in the bottom panel.…”

“…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…”