Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Sci Rep. 2014 Oct 27:4:6780. doi: 10.1038/srep06780.

Abstract

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Female
  • Gene Library
  • Genome*
  • Genomics / methods*
  • Genotype
  • Haploidy*
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Data
  • Polymorphism, Genetic
  • Reproducibility of Results
  • Takifugu / genetics