title: Improving the ostrich genome assembly using optical mapping data.
abstract: BACKGROUND
  The ostrich (Struthio camelus) is the tallest and heaviest living bird. Ostrich meat is considered a healthy red meat, with an annual worldwide production ranging from 12,000 to 15,000 tons. As part of the avian phylogenomics project, we sequenced the ostrich genome for phylogenetic and comparative genomics analyses. The initial Illumina-based assembly of this genome had a scaffold N50 of 3.59 Mb and a total size of 1.23 Gb. Since longer scaffolds are critical for many genomic analyses, particularly for chromosome-level comparative analysis, we generated optical mapping (OM) data to obtain an improved assembly. The OM technique is a non-PCR-based method to generate genome-wide restriction enzyme maps, which improves the quality of de novo genome assembly.
  
  
  RESULTS
  In order to generate OM data, we digested the ostrich genome with KpnI, which yielded 1.99 million DNA molecules (>250 kb) and covered the genome at least 500×. The pattern of molecules was subsequently assembled to align with the Illumina-based assembly to achieve sequence extension. This resulted in an OM assembly with a scaffold N50 of 17.71 Mb, which is 5 times as large as that of the initial assembly. The number of scaffolds covering 90% of the genome was reduced from 414 to 75, which means an average of ~3 super-scaffolds for each chromosome. Upon integrating the OM data with previously published FISH (fluorescence in situ hybridization) markers, we recovered the full PAR (pseudoatosomal region) on the ostrich Z chromosome with 4 super-scaffolds, as well as most of the degenerated regions.
  
  
  CONCLUSIONS
  The OM data significantly improved the assembled scaffolds of the ostrich genome and facilitated chromosome evolution studies in birds. Similar strategies can be applied to other genome sequencing projects to obtain better assemblies.
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China.
authors.forename: Jilin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Cai
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China ; Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, DK Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000818:Animals; D016678:Genome / Q000235:genetics*; D010802:Phylogeny
keywords: Genome assembly; Optical mapping; Ostrich