Table 1. Ploidy estimation for an artificially combined wheat dataset.

Number of subgenomes in which a contig was found a	Estimated ploidy
	One	Two	Three	Four
One	40,642	244	230	2,345
Two	26	193	44	20
Three	1	18	44	12

Reads from the large arms of chromosomes 5A, 5B and 5D were pooled, assembled and used for ploidy estimation. Only contigs with average coverage of 10X or above, and for which the individual ploidy in a given subgenome was estimated to be one were considered.

^aBased on BLAST alignments to the individual assemblies.