Assembly of Aegilops tauschii, the Ancestor of the Wheat D Genome
Daniela Puiu
,
Johns Hopkins University, School of Medicine, Baltimore, MD
Jan Dvorak
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Karin R. Deal
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Naxin Huo
,
Dept. of Plant Sciences, Davis, CA
Geo Pertea
,
Johns Hopkins University, School of Medicine, Baltimore, MD
Aleksey Zimin
,
Johns Hopkins University, School of Medicine, Baltimore, MD
Steven L. Salzberg
,
Johns Hopkins University, School of Medicine, Baltimore, MD
We have sequenced the 4.3 gigabase Aegilops tauschii genome using pools of 6-10 overlapping BACs. In total, we sequenced 5646 pools at over 100x coverage using Illumina MiSeq paired-end libraries, and we assembled each pool using SOAPdenovo2. The overall contiguity of this assembly is excellent, with a scaffold N50 size of 207 Kb, and the large majority of the BAC pools are anchored to chromosomes.
Although previous efforts to sequence wheat genomes using the whole-genome shotgun method have resulted in fragmented assemblies, very recently NRGene generated a relatively high-quality assembly of Aegilops tauschii using very deep coverage in Illumina HiSeq reads, tightly constrained mate-pair libraries, and their proprietary DeNovoMAGIC2 WGS assembler. This assembly, which had an N50 scaffold size of 1.1 Mb, was provided as part of our project.
We then merged the BAC pool and WGS assemblies. The resulting combined assembly has a scaffold N50 size of 2.8Mb, substantially larger than either of the two component assemblies. The contig N50 size is 93 Kb, compared to 127 Kb (BAC pool assembly) and 16 Kb (WGS assembly).
We will present these results along with general methods for comparing, validating and merging large assemblies.
