Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EFY, Salehi-Ashtiani K, Purugganan MD

Date Published: September 25, 2015

DOI: http://dx.doi.org/10.5061/dryad.1n0g6

 

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Title Supplementary Data set 1
Downloaded 10 times
Description Transposable element insertion predictions relative to the CC-503 reference assembly based on RetroSeq (Kean et al. 2013).
Download tpc00492_SupplementalDS1.xlsx (1.503 Mb)
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Title Supplementary Data set 2
Downloaded 13 times
Description Structural variant predictions based on the paired-end mapping (PEM) approach of SVDetect (Zeitouni et al. 2010).
Download tpc00492_SupplementalDS2.txt (5.281 Mb)
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Title Supplementary Data set 3
Downloaded 19 times
Description 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.
Download tpc00492_SupplementalDS3.txt (1.501 Mb)
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Title Supplementary Data set 4
Downloaded 8 times
Description Summary of πN and πS in field isolates of C. reinhardtii by functional category.
Download tpc00492_SupplementalDS4.txt (333.7 Kb)
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Title Supplementary Data set 5
Downloaded 13 times
Description Genes with nonsense SNPs and the corresponding genotypes in field isolates and laboratory reference strains of C. reinhardtii.
Download tpc00492_SupplementalDS5.csv (82.96 Kb)
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Title Supplementary Data set 6
Downloaded 16 times
Description 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.
Download tpc00492_SupplementalDS6.txt (36.95 Kb)
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Title Supplementary Data set 7
Downloaded 17 times
Description 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.
Download tpc00492_SupplementalDS7.csv (2.461 Mb)
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Title Supplementary Data set 8
Downloaded 8 times
Description 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.
Download tpc00492_SupplementalDS8.txt (149.0 Kb)
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Title Supplementary Data set 9
Downloaded 62 times
Description De novo assembled contigs from reads failing to map to the CC-503 reference assembly.
Download tpc00492_SupplementalDS9.txt (253.7 Mb)
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Title Supplementary Data set 10
Downloaded 9 times
Description Predicted proteins from gene predictions on de novo assembled contigs.
Download tpc00492_SupplementalDS10.txt (2.041 Mb)
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Title Supplementary Data set 11
Downloaded 9 times
Description Normalized coverage depth in 499 bp genomic intervals.
Download tpc00492_SupplementalDS11.csv (58.84 Mb)
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When using this data, please cite the original publication:

Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EFY, Salehi-Ashtiani K, Purugganan MD (2015) Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. The Plant Cell 27(9): 2353-2369. http://dx.doi.org/10.1105/tpc.15.00492

Additionally, please cite the Dryad data package:

Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EFY, Salehi-Ashtiani K, Purugganan MD (2015) Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1n0g6
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