A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Table 1 Summary of assembly and anchoring statistics

Assembly	W7984 (WGS, this report)	Chinese Spring (chromosome sorted shotgun, IWGSC 2014)
Scaffolds ≥1kbp	645,811	2,272,234
Scaffolds ≥1kbp	8.00 Gbp	7.05 Gbp
Map-anchored scaffolds ≥1 kbp (percentage of total assembled base pairs)	437,973	1,175,794
	7.13 Gbp (89.3%)	4.46 Gbp (63.2%)
Scaffolds ≥10 kbp	253,986	91,141
Scaffolds ≥10 kbp	6.55 Gbp	1.31 Gbp
Map-anchored scaffolds ≥10 kbp (percentage of total assembled base pairs)	235,647	74,520
	6.21 Gbp (94.9%)	1.08 Gbp (82.3%)
Full-length cDNAs captured on the assembly (at least 50% length; out of 6,000)	4,663 (77.7%)	4,580 (76.3%)
(minimum length 25%)	5,288 (88.1%)	5,428 (90.5%)
Full-length cDNAs placed on map-anchored scaffolds (at least 50% length)	4,353 (72.6%)	3,404 (56.7%)
Full-length cDNAs placed on map-anchored scaffolds (at least 25% length)	4,863 (81.1%)	3,909 (65.2%)
Concordance of POPSEQ positions	99.4%

This table provides a comparison between the POPSEQ anchored assemblies of W7984 and ‘Chinese Spring’ using a chromosome sorting and WGS approach, respectively. Shown are total scaffolds (minimum length 1 kbp), total map-anchored scaffolds, and capture of known full-length wheat cDNAs on the assemblies both before and after chromosome anchoring. The final row shows concordance as measured by the percentage of pairs of anchored chromosome shotgun contigs and WGS scaffolds that were matched by sequence alignment and were genetically positioned within 5 cM of each other. ‘Chinese Spring’ and WGS scaffolds are paired if there is megablast hit with ≥99% identity and ≥2,000 bp alignment length between them. Only the best hit of each ‘Chinese Spring’ scaffold was considered.

ISSN: 1474-760X