A Reference Assembly for Brachypodium Hybridum As a Tool to Study Polyploidy

In order to develop a model for polyploid genome evolution and regulation, we sequenced the genome of the allotetraploid grass Brachypodium hybridum whose subgenomes are derived from ancestors similar or identical to the diploid species B. distachyon and B. stacei. Initial assemblies of the B. hybridum genome from Illumina sequence were highly fragmented and suffered from mis-assembly of the two sub-genomes. To increase contiguity and accuracy, we constructed and sequenced Chicago^TM libraries and used the HiRise^TM assembler to improve the initial assembly. The Dovetail assembly contained 90% of the sequence in just 33 scaffolds with an average size of 5.8Mb. Since B. hybridum contains 15 chromosomes, the assembly essentially produced chromosome arms. We then used a high density genetic map to align and orient the scaffolds into chromosome-scale assemblies. Only two Dovetail scaffolds needed to be broken to fit the genetic positions. Our results suggest that Dovetail genome assembly is highly accurate even for complex polyploidy genomes and is a valuable new tool to dramatically improve chromosome scale assemblies. Improved assemblies are critical for detailed analysis of subgenome structure and evolution, like the analysis that is currently underway for B. hybridum.