Ta7DS_sequence_assembly
Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS
This study used DNA isolated from cytogenetic stock with a deletion of the long arm of chromosome 7D by flow sorting of chromosomes.  Short-read data was generated on the Illumina Genome Analyzer II to a coverage depth of 34x, then assembled using Velvet and scaffolded based on synteny with Brachypodium distachyon using a genome-zipper approach.  Syntenic build is publicly available at www.wheatgenome.info.
The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS, and applied second generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole genome sequencing and variation discovery in this important crop.