Whole-genome resequencing reveals extensive natural variation in the model green alga chlamydomonas reinhardtii

Jonathan M. Flowers, Khaled M. Hazzouri, Gina M. Pham, Ulises Rosas, Tayebeh Bahmani, Basel Khraiwesh, David R. Nelson, Kenan Jijakli, Rasha Abdrabu, Elizabeth H. Harris, Paul A. Lefebvre, Erik F.Y. Hom, Kourosh Salehi-Ashtiani, Michael D. Purugganan

Research output: Contribution to journalArticle

35 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)2353-2369
Number of pages17
JournalPlant Cell
Volume27
Issue number9
DOIs
StatePublished - Jan 1 2015

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    Flowers, J. M., Hazzouri, K. M., Pham, G. M., Rosas, U., Bahmani, T., Khraiwesh, B., Nelson, D. R., Jijakli, K., Abdrabu, R., Harris, E. H., Lefebvre, P. A., Hom, E. F. Y., Salehi-Ashtiani, K., & Purugganan, M. D. (2015). Whole-genome resequencing reveals extensive natural variation in the model green alga chlamydomonas reinhardtii. Plant Cell, 27(9), 2353-2369. https://doi.org/10.1105/tpc.15.00492