DOI: 10.5061/dryad.1n0g6
title: Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

description: 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.
description: Supplementary Data set
 1Transposable element
 insertion predictions relative to the CC-503 reference assembly based on
 RetroSeq (Kean et al. 2013).tpc00492_SupplementalDS1.xlsxSupplementary Data set 2Structural variant predictions based on the paired-end mapping (PEM) approach of SVDetect (Zeitouni et al. 2010).tpc00492_SupplementalDS2.txtSupplementary Data set 3Summary of protein coding diversity in field isolates of C. reinhardtii. Table includes πN, πS, πN/πS and nonsynonymous and synonymous SNP counts per gene.tpc00492_SupplementalDS3.txtSupplementary Data set 4Summary of πN and πS in field isolates of C. reinhardtii by functional category.tpc00492_SupplementalDS4.txtSupplementary Data set 5Genes with nonsense SNPs and the corresponding genotypes in field isolates and laboratory reference strains of C. reinhardtii.tpc00492_SupplementalDS5.csvSupplementary Data set 6Summary of gene deletion or partial deletion polymorphisms. A gene is listed if at least one of the 20 strains shows a deletion or partial deletion following the coverage breadth criteria described in the Supplemental data. If some strains have partial deletions and others a deletion, the gene is listed as a deletion. The coverage breadth matrix used to infer deletions is available as Supplemental Data Set 7.tpc00492_SupplementalDS6.txtSupplementary Data set 7Coverage breadth matrix used to infer partial and complete gene deletions in field isolates and laboratory reference strains of C. reinhardtii. Coverage breadths are listed for each mRNA in the Creinhardtii_236_gene_exons.gff3 annotation.tpc00492_SupplementalDS7.csvSupplementary Data set 8Candidate major effect mutation counts by functional category. Each row lists numbers of genes affected by each listed class of mutation for each KEGG pathway, PFAM domain family, GO slim, and GO term.tpc00492_SupplementalDS8.txtSupplementary Data set 9De novo assembled contigs from reads failing to map to the CC-503 reference assembly.tpc00492_SupplementalDS9.txtSupplementary Data set 10Predicted proteins from gene predictions on de novo assembled contigs.tpc00492_SupplementalDS10.txtSupplementary Data set 11Normalized coverage depth in 499 bp genomic intervals.tpc00492_SupplementalDS11.csv