Sequence Based Analysis of Flow-Sorted Aegilops geniculata Chromosome 5Mg using a Next Generation Sequencing Approach

Aegilops geniculata is an important member from tertiary gene pool of common wheat and holds tremendous potential for wheat improvement against biotic and abiotic stresses. Chromosome 5M^g from Ae. geniculata TA10437 has been identified as source of important genes for biotic stresses (LR57, Yr40 and Sr53). We flow-sorted full chromosome 5M^g from a disomic substitution line (TA6675) with ~95% of purity.  The DNA was amplified and sequenced using Illumina Hiseq with ~ 50x coverage of the whole chromosome. Two assemble approaches, de novo assemble and reference-based assemble, were used to get as much as possible the assemblies of chromosome 5M^g. The resulting contigs were then annotated based on the ESTs of wheat and gene content in chromosome 5M^g was estimated. The syntenic relationships between chromosome 5M^g and other grass chromosomes including  barley chromosome 4H, rice chromosome 3, 9, 11, 12, Brachypodium chromosome 1, 4 and sorghum chromosome 1, 2, 5, 8 were explored based on the sequence of annotated genes. A virtual gene order of ~2200 5M^g specific genes was inferred from the syntenic regions. The sequence similarities between chromosome  5M^g genes and flow-sorted wheat chromosome 5A, 5B and 5D sequences were estimated as 0.975, 0.972, 0.981 respectively. Transposable elements were annotated based on the TREP and GIRI database. Further progress in the sequence analysis and its application in wheat genomics will be presented.