title: 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.
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates Center for Genomics and Systems Biology, New York University, New York, New York 10003.
authors.forename: Jonathan M
authors.identifier: http://orcid.org/0000-0002-8752-205X
authors.initials: JM
authors.lastname: Flowers
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Khaled M
authors.initials: KM
authors.lastname: Hazzouri
authors.affiliation: Center for Genomics and Systems Biology, New York University, New York, New York 10003.
authors.forename: Gina M
authors.identifier: http://orcid.org/0000-0002-8058-7862
authors.initials: GM
authors.lastname: Pham
authors.affiliation: Center for Genomics and Systems Biology, New York University, New York, New York 10003.
authors.forename: Ulises
authors.initials: U
authors.lastname: Rosas
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Tayebeh
authors.initials: T
authors.lastname: Bahmani
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates Division of Science and Math, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Basel
authors.identifier: http://orcid.org/0000-0001-7026-1263
authors.initials: B
authors.lastname: Khraiwesh
authors.affiliation: Division of Science and Math, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.affiliation: Division of Science and Math, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Kenan
authors.identifier: http://orcid.org/0000-0003-2680-1239
authors.initials: K
authors.lastname: Jijakli
authors.affiliation: Division of Science and Math, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Rasha
authors.initials: R
authors.lastname: Abdrabu
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708.
authors.forename: Elizabeth H
authors.initials: EH
authors.lastname: Harris
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Paul A
authors.identifier: http://orcid.org/0000-0003-0028-7753
authors.initials: PA
authors.lastname: Lefebvre
authors.affiliation: Department of Biology, University of Mississippi, Oxford, Mississippi 38677.
authors.forename: Erik F Y
authors.identifier: http://orcid.org/0000-0003-0964-0031
authors.initials: EF
authors.lastname: Hom
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates Division of Science and Math, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates ksa3@nyu.edu mp132@nyu.edu.
authors.forename: Kourosh
authors.initials: K
authors.lastname: Salehi-Ashtiani
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates Center for Genomics and Systems Biology, New York University, New York, New York 10003 ksa3@nyu.edu mp132@nyu.edu.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D000483:Alleles; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D007753:Laboratories; D005810:Multigene Family; D009154:Mutation; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins