Sep 27, 2008

Sequencing of natural strains of Arabidopsis thaliana with short reads

Genome Research
Stephan OssowskiDetlef Weigel

Abstract

Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence. To examine this variation, and as a first step in the 1001 Genomes Project for this species, we produced 15- to 25-fold coverage in Illumina sequencing-by-synthesis (SBS) reads for the reference accession, Col-0, and two divergent strains, Bur-0 and Tsu-1. We aligned reads to the reference genome sequence to assess data quality metrics and to detect polymorphisms. Alignments revealed 823,325 unique single nucleotide polymorphisms (SNPs) and 79,961 unique 1- to 3-bp indels in the divergent accessions at a specificity of >99%, and over 2000 potential errors in the reference genome sequence. We also identified >3.4 Mb of the Bur-0 and Tsu-1 genomes as being either extremely dissimilar, deleted, or duplicated relative to the reference genome. To obtain sequences for these regions, we incorporated the Velvet assembler into a targeted de novo assembly method. This approach yielded 10,921 high-confidence contigs that were anchored to flanking sequences and harbored indels as large as 641 bp. Our methods are broadly applicable for polymorphism discovery in mo...Continue Reading

  • References24
  • Citations250

References

  • References24
  • Citations250

Citations

Mentioned in this Paper

Genome
Nucleic Acid Hybridization Procedure
Genome Mapping
Sequencing
Deletion Mutation
Chromosomes, Plant
Homologous Sequences, Nucleic Acid
Sequence Determinations, DNA
Arabidopsis thaliana extract
Out-of-Frame Deletion

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