Table 1.

Editing extents at plastid RNA editing sites in wild-type and orrm6 mutant plants.

Gene	Genome positiona	Edited nucleotideb	Δ amino acid	WT	orrm6–1	orrm6–2	orrm6 - WTc
accD	57868	C794	S265→L	85.8 ± 3.2	30.7 ± 3.0***	29.0 ± 2.0***	−56.0
accD	58642	C1568	3’-UTR	83.5 ± 1.6	78.8 ± 2.2	78.3 ± 1.3	−4.9
atpF	12707	C92	P31→L	94.9 ± 0.2	95.1 ± 0.3	93.8 ± 0.4	−0.4
atpH	13210	C298	3’-UTR	4.4 ± 0.6	4.5 ± 0.3	4.9 ± 0.3	0.3
clpP	69942	C559	H187→Y	81.3 ± 0.5	82.8 ± 0.7	78.0 ± 0.7**	−1.4
matK	2931	C640	H214→Y	71.9 ± 8.6	74.4 ± 4.8	79.9 ± 0.3	5.2
ndhB	97016	C149	S50→L	56.9 ± 19.9	66.6 ± 11.4	67.3 ± 5.6	10.1
ndhB	96698	C467	P156→L	76.6 ± 4.9	84.0 ± 0.8	86.1 ± 0.5	8.5
ndhB	96579	C586	H196→Y	74.6 ± 3.2	78.8 ± 1.3	81.9 ± 1.0	5.8
ndhB	96457	C708	I236→I	3.6 ± 0.5	3.2 ± 0.2	3.2 ± 0.4	−0.4
ndhB	96439	C726	F242→F	3.5 ± 0.4	3.1 ± 0.3	2.7 ± 0.2	−0.6
ndhB	96419	C746	S249→F	84.8 ± 5.8	72.5 ± 3.3	76.6 ± 2.2	−10.3
ndhB	95650	C830	S277→L	74.7 ± 1.1	75.9 ± 2.0	77.5 ± 1.7	2.0
ndhB	95644	C836	S279→L	66.2 ± 2.5	61.2 ± 2.3	61.0 ± 2.5	−5.0
ndhB	95608	C872	S291→L	61.9 ± 4.5	64.9 ± 1.0	59.3 ± 4.5	0.2
ndhB	95225	C1255	H419→Y	87.8 ± 1.1	87.5 ± 1.4	88.0 ± 1.4	0.0
ndhB	94999	C1481	P494→L	88.2 ± 1.0	84.3 ± 0.7*	85.2 ± 0.7	−3.5
ndhD	117166	C2	T1→M	46.4 ± 4.1	36.8 ± 5.7	51.2 ± 2.0	−2.5
ndhD	116785	C383	S128→L	95.4 ± 1.2	96.9 ± 0.3	96.7 ± 0.8	1.4
ndhD	116494	C674	S225→L	73.8 ± 2.0	74.3 ± 4.9	78.3 ± 2.0	2.5
ndhD	116290	C878	S293→L	79.1 ± 2.0	83.7 ± 1.3	86.2 ± 0.5*	5.8
ndhD	116281	C887	P296→L	76.7 ± 5.7	87.9 ± 0.6	87.9 ± 0.9	11.2
ndhF	112349	C290	S97→L	23.4 ± 4.8	21.4 ± 3.6	26.8 ± 2.7	0.7
ndhG	118858	C50	S17→F	68.4 ± 6.3	81.3 ± 4.0	75.9 ± 1.4	10.2
ndhK-ndhJ	49209	C726d	Intergene	4.2 ± 0.5	0.0 ± 0.0**	0.0 ± 0.0**	−4.2
petL	65716	C5	P2→L	35.1 ± 12.3	50.4 ± 10.4	55.8 ± 11.4	18.0
psbE	64109	C214	P72→S	99.3 ± 0.1	99.1 ± 0.2	99.2 ± 0.0	−0.2
psbF	63985	C77	S26→F	97.1 ± 0.3	6.8 ± 0.2***	6.3 ± 0.3***	−90.5
psbZ	35800	C50	S17→L	61.3 ± 8.6	49.6 ± 8.8	58.9 ± 5.0	−7.1
rpl23	86055	C89	S30→L	82.3 ± 1.9	78.1 ± 0.9	78.5 ± 0.3	−4.0
rpoA	78691	C200	S67→F	58.9 ± 5.4	64.2 ± 4.4	61.7 ± 4.6	4.0
rpoB	25992	C338	S113→L	65.9 ± 16.6	70.4 ± 17.7	65.4 ± 8.3	1.9
rpoB	25779	C551	S184→L	38.1 ± 9.1	30.8 ± 7.7	27.2 ± 2.5	−9.2
rpoB	23898	C2432	S811→L	69.9 ± 7.0	70.0 ± 3.3	60.3 ± 4.9	−4.8
rpoC1	21806	C488	S163→L	20.8 ± 2.9	26.7 ± 1.2	27.4 ± 2.9	6.2
rps4	45095	C734	3’-UTR	3.2 ± 0.2	1.9 ± 0.5	2.5 ± 0.2	−1.0
rps12-intron	69553	C(i1 58)e	intron	19.5 ± 1.1	13.5 ± 3.2	18.6 ± 4.0	−3.5
rps14	37161	C80	S27→L	96.4 ± 0.4	95.1 ± 0.2	94.8 ± 0.3*	−1.4
rps14	37092	C149	P50→L	87.6 ± 2.3	91.0 ± 0.2	90.7 ± 0.4	3.2
ycf3-intron	43350	C(i2 174)f	intron	7.5 ± 0.9	4.5 ± 0.3*	7.8 ± 0.5	−1.4

The editing extents were determined with the whole-transcriptome RNA-seq method. The values (mean ± SE, n = 4) are given as the ratio of the edited transcript to edited plus unedited transcripts. The asterisk indicates significant difference between the mutant and the wild type (WT) (Student's t-test; *, p < 0.05; **, p < 0.01; ***, p < 0.001).

^aThe Arabidopsis plastid genome reference sequence (NCBI accession number NC_000932.1) was used to indicate the genome positions of the editing sites.

^bTheC targets are numbered relative to the nucleotide A of the predicted translation initiation codon ATG, where A = 1.

^cThis column shows the average difference in editing extents between the wild type (WT) and orrm6 mutants.

^dThe C target is numbered relative to the nucleotide A of ATG of the ndhK transcript, where A = 1.

^eThe target C is the 58^th nucleotide of intron 1 (i1 58).

^fThe target C is the 174th nucleotide of intron 2 (i2 174).