Assembly of Aegilops comosa chromosomes

We sequenced and assembled seven chromosomes of Aegilops comosa. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of Ae. comosa identified candidate sequences. In order to analyze the structure and homeology of Aegilops chromosomes, forty-three mapped wheat cDNAs covering all seven chromosome groups were localized by FISH.

Methods
The flow-sorted chromosomes 1M-7M were used for preparation of libraries for sequencing. Chromosome samples were purified according to (Šimková et al. 2008, BMC Genomics) and 20 ng DNA was fragmented and used to prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Size selection was directed for larger final library size (~1000 bp) and PCR enrichment was done in 9 cycles. Libraries were sequenced on NovaSeq 6000 (Illumina) and 2x150 bp paired-end reads were produced. The raw data were trimmed for low-quality bases using Trimmomatic (Bolger et al. 2014, Bioinformatics) and assembled to scaffolds with Meraculous v2.0.5 (Chapman et al. 2011, PLoS One) using 111 bp k-mers. Scaffolds shorter than 1 kb were eliminated.