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Published August 18, 2016 | Version v1
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Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

Authors/Creators

  • 1. New York University Abu Dhabi
  • 2. New York University
  • 3. Duke University
  • 4. University of Minnesota
  • 5. University of Mississippi

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.

Notes

Supplementary Data set 1
Transposable element insertion predictions relative to the CC-503 reference assembly based on RetroSeq (Kean et al. 2013).
tpc00492_SupplementalDS1.xlsx
Supplementary Data set 2
Structural variant predictions based on the paired-end mapping (PEM) approach of SVDetect (Zeitouni et al. 2010).
tpc00492_SupplementalDS2.txt
Supplementary Data set 3
Summary 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.txt
Supplementary Data set 4
Summary of πN and πS in field isolates of C. reinhardtii by functional category.
tpc00492_SupplementalDS4.txt
Supplementary Data set 5
Genes with nonsense SNPs and the corresponding genotypes in field isolates and laboratory reference strains of C. reinhardtii.
tpc00492_SupplementalDS5.csv
Supplementary Data set 6
Summary 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.txt
Supplementary Data set 7
Coverage 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.csv
Supplementary Data set 8
Candidate 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.txt
Supplementary Data set 9
De novo assembled contigs from reads failing to map to the CC-503 reference assembly.
tpc00492_SupplementalDS9.txt
Supplementary Data set 10
Predicted proteins from gene predictions on de novo assembled contigs.
tpc00492_SupplementalDS10.txt
Supplementary Data set 11
Normalized coverage depth in 499 bp genomic intervals.
tpc00492_SupplementalDS11.csv

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tpc00492_SupplementalDS10.txt

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Additional details

Related works

Is cited by
10.1105/tpc.15.00492 (DOI)