Table 3. Differentially expressed genes encoding ABC transporters.

Substrate	Gene ID	RPKM_F		RPKM_LB	RPKM_VB
	Up-regulated in bacteroids from both legume hosts
phosphate	NGR_c01440-NGR_c01470	42–323		314–4710	670–5089
phosphonate	NGR_b13310-NGR_b13340	1–4		87–1576	116–1494
sn-glycerol 3-phosphate	NGR_c36780-NGR_c36810	1–4		150–1711	267–1771
aminoethane sulfonate	NGR_b17610-NGR_b17630	1–5		37–80	16–31
aliphatic sulfonate	NGR_c25620-NGR_c25630, NGR_c25650	2–11		170–283	74–153
osmoprotectants	NGR_b12990-NGR_b13020	5–24		31–312	19–185
polar amino acids	NGR_b03480- NGR_b03510	1–26		13–157	14–439
spermidine/putrescine	NGR_b12810-NGR_b12840	1–3		26–149	11–80
iron (III)	NGR_c19530- NGR_c19550	1–6		56–377	56–369
simple sugar	NGR_b03950, NGR_b03970-NGR_b03990	2–4		35–169	17–68
multiple sugar	NGR_b02160-NGR_b02190; NGR_c06670-NGR_c06700;	4–20		18–141	13–191
	NGR_b04010-NGR_b04030, NGR_b04050;	7–69		30–221	26–515
	NGR_b20230-NGR_b20260	4–14		28–71	26–176
	Down-regulated in bacteroids from both legume hosts
alpha-glucoside	NGR_c03100-NGR_c03140	825–2951		35–305	12–256
trehalose/maltose	NGR_b23110-NGR_b23140	62–364		16–37	1–12
D-xylose	NGR_c24220-NGR_c24240	477–2200		20–28	6–15
fructose	NGR_c01100-NGR_c01120	517–3865		42–436	52–949
dipeptide	NGR_c03460-NGR_c03500	518–2642		56–1055	56–768
lipoprotein-releasing	NGR_c10690-NGR_c10700	194–328		90–132	77–128
lipopolysaccharide	NGR_c00180,NGR_c09020-NGR_c09030	165–342		66–87	44–78
glycine betaine/proline	NGR_c27400- NGR_c27420	94–250		28–37	9–42
multiple sugar	NGR_c33060- NGR_c33090; NGR_c30950-NGR_c30980	58–455		12–36	3–41
simple sugar	NGR_c14510-NGR_c14540	97–854		24–356	19–296
branched-chain amino acids	NGR_c25150, NGR_c25170-NGR_c25200	961–4353		105–1230	189–1296
peptides/nickel	NGR_c24410-NGR_c24450	66–370		25–108	21–95
iron complex	NGR_b02510-NGR_b02530; NGR_b11200-NGR_b11230	492–1936		31–38	69–260

Note: RPKM (reads per kilobase per million mapped reads); F, free-living bacteria; LB, L. leucocephala bacteroids; VB, V. unguiculata bacteroids.