Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.
Highlights
The feasibility of whole-genome shotgun (WGS) assembly of large and complex eukaryotic genomes was once a much-debated question [1,2]
The advent of nextgeneration sequencing and the comparative ease and speed with which WGS assemblies can be constructed for mammalian and many other genomes allowed sequencing projects to move beyond these concerns, accepting high quality draft genomes with nearly complete gene spaces
Whole-genome shotgun assembly We generated a total of approximately 175-fold coverage Illumina WGS sequence from two bread wheat lines, ‘Synthetic W7984’ (30-fold coverage) and ‘Opata M85’ (15-fold), and a set of 90 doubled haploid (DH) lines derived from W7984/Opata F1 hybrids; the ‘SynOpDH’ population [27] (Tables S1, S2, and S3 in Additional file 1)
Summary
The feasibility of whole-genome shotgun (WGS) assembly of large and complex eukaryotic genomes was once a much-debated question [1,2]. To mitigate some of the computational challenges of genome assembly from short next-generation sequencing reads for these more complex genomes, various ‘divide and conquer’ strategies have been developed. These strategies include chromosome sorting and capture [5], large-insert-clone pooling [6,7], and large-clone tiling paths [5,8].
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