Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii  . Issue 9 (21st September 2015)

• Record Type: Journal Article
• Authors: Flowers, Jonathan M.; Hazzouri, Khaled M.; Pham, Gina M.; Rosas, Ulises; Bahmani, Tayebeh; Khraiwesh, Basel; Nelson, David R.; Jijakli, Kenan; Abdrabu, Rasha; Harris, Elizabeth H.; Lefebvre, Paul A.; Hom, Erik F.Y.; Salehi-Ashtiani, Kourosh; Purugganan, Michael D.
• Is Part Of: The Plant Cell. Volume 27:Issue 9(2015)
• Page Start: 2353
• Page End: 2369
• Publication Date: 2015-09-21
• DOI: 10.1105/tpc.15.00492
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : Whole-genome resequencing of Chlamydomonas reveals enormous intraspecific diversity and a reservoir of naturally occurring variation, including candidate loss-of-function alleles. 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.