Table I. Genomic distribution of the reads and base coverage for the different conditions.

Distribution	No. of Mapped Reads	Reads	bp Covered
All map reads (no known junctions)		%
Noninoculated roots	9,630,799	100	28,124,194
Inoculated roots	24,971,580	100	31,231,171
cPTIO-treated inoculated roots	24,548,808	100	37,288,391
Nodules	15,220,330	100	29,672,799
All	74,371,517	100	48,478,409
Coding sequences
Noninoculated roots	7,448,707	77.34	17,145,704
Inoculated roots	19,982,322	80.02	18,749,601
cPTIO-treated inoculated roots	18,838,610	76.74	19,480,139
Nodules	12,349,557	81.13	17,447,569
All	58,619,196	78.82	22,131,430
UTRs
Noninoculated roots	1,299,977	13.50	3,711,333
Inoculated roots	2,790,178	11.17	3,959,526
cPTIO-treated inoculated roots	3,174,530	12.93	4,671,251
Nodules	1,570,623	10.32	3,741,933
All	8,835,308	11.88	5,502,782
Introns
Noninoculated roots	146,403	1.52	3,205,597
Inoculated roots	234,802	0.94	3,781,346
cPTIO-treated inoculated roots	364,144	1.48	6,427,895
Nodules	188,121	1.23	3,487,953
All	933,471	1.25	10,395,202
New coding sequences on annotated genes
Noninoculated roots	159,973	1.66	1,225,276
Inoculated roots	285,762	1.14	1,338,164
cPTIO-treated inoculated roots	387,905	1.58	1,666,726
Nodules	208,173	1.36	1,272,683
All	1,041,813	1.40	1,989,813
New TUs
Noninoculated roots	33,501	0.35	57,548
Inoculated roots	126,469	0.50	63,179
cPTIO-treated inoculated roots	118,831	0.48	73,094
Nodules	52,004	0.34	75,795
All	330,805	0.44	103,984
Intergenic
Noninoculated roots	542,238	5.63	2,778,736
Inoculated roots	1,552,047	6.21	3,339,355
cPTIO-treated inoculated roots	1,664,788	6.78	4,969,286
Nodules	851,852	5.59	3,646,866
All	4,610,925	6.20	8,355,198
Known junctions
Noninoculated roots	862,939	8.96
Inoculated roots	2,299,765	9.21
cPTIO-treated inoculated roots	1,643,062	6.69
Nodules	1,578,057	10.36
All	6,383,823	8.58