Table 1. Quality control and filtering of reads from 454 and Hiseq sequencing.

Sequencing runs	Total Raw Reads	Quality Filter	Contaminants	High-quality reads
454 Reads (root tips)	1,086,240	196,306	81,817	808,117 (74.4%)
Root tip Replicate 1	31,803,479	4,040,700	382,197	27,380,582 (86.09%)
Root tip Replicate 2	34,133,444	3,794,965	419,609	29,918,870 (87.65%)
Root tip Replicate 3	34,873,477	3,632,386	454,067	30,787,024 (88.28%)
Mature root replicate 1	25,348,308	2,801,923	233,118	22,313,267 (88.03%)
Mature root replicate 2	37,575,294	3,886,507	379,931	33,308,856 (88.65%)
Mature root replicate 3	29,033,618	3,166,220	293,685	25,573,713 (88.08%)