Table 2.

Homologous segments in the wheat ct and mtDNAs arranged according to the ct-coordinates of the ctDNA segments

CtDNA segment				MtDNA segment				Sequence homology (%)c)
Segm’t no.	Ct-coordinates	Size (bp)	Ct gene	Segm’t no.	Mt-coordinatesb)	Size (bp)	Mt genea)
1	6,696–6,749	54	trnQ*	1a	R 266,815–266,868	54	trnQ-1*	83.3
″	″	″	″	1b	R 174,918–174,971	54	trnQ-2*	83.3
″	″	″	″	1c	R 193,291–193,344	54	trnQ-3*	81.5
2	11,579–11,655	77	trnS-2*	2	R 408,510–408,585	77	trnS-2	81.6
3	18,282–18,754	473	trnC	3	R 97,417–97,861	445	trnC	78.2
4	21,268–21,343	76	rpoB*	4	316,034–316,102	69	-	95.7
5	28,338–28,371	34	rpoC2*	5	68,014–68,047	34	-	91.2
6	33,284–33,319	36	atpF 5′-ex*	6	349,029–349,064	36	-	91.7
7	34,262–34,319	58	atpF 3′-ex*	7	104,644–104,702	59	-	86.2
8	34,309–34,366	58	atpF 3′-ex*	8	162,458–162,515	58	-	96.6
9	34,485–34,513	29	atpF 3′-ex*	9	388,154–388,182	29	-	100.0
10	34,918–35,245	328	atpA*	10	304,646–304,973	328	-	95.7
11	34,918–36,037	1,120	atpA*	11a	R 53,841–54,950	1,110	-	98.1
″	″	″	″	11b	R 390,809–391,918	1,110	-	98.1
12	35,099–35,864	766	atpA*	12	7,265–8,057	793	atp1*	67.7
13	35,542–36,108	567	atpA*	13	119,524–120,049	526	-	87.5
14	40,653–41,098	446	psaA*	14	R 358,076–358,521	446	-	99.8
15	43,932–44,149	218	-	15	R 378,941–379,150	210	-	89.5
16	44,967–45,160	194	trnS-3	16	R 383,409–383,603	195	trnS-3	90.8
17	47,621–47,851	231	trnL 3′-ex	17	R 383,203–383,422	220	-	80.5
18	48,013–48,128	116	trnF	18	R 382,956–383,071	116	trnF	95.7
19	48,072–48,098	27	trnF*	19a	R 55,179–55,205	27	-	100.0
″	″	″	″	19b	304,391–304,417	27	-	100.0
″	″	″	″	19c	R 392,147–392,173	27	-	100.0
20	48,073–48,119	47	trnF*	20	97,436–97,481	46	trnC*	84.8
21	49,041–49,072	32	ndhJ*	21	400,525–400,556	32	-	96.9
22	50,062–50,123	62	ndhC*	22	R 212,481–212,538	58	nad9*	91.4
23	51,175–51,225	51	trnV 3′-ex*	23	249,838–249,890	53	-	88.7
24	52,035–52,107	73	trnM	24	R 436,153–436,225	73	trnM	94.5
25	61,844–62,032	189	psbF*, psbE*	25	452,168–452,356	189	-	88.4
26	62,048–62,218	171	psbE*	26	986–1,157	172	-	90.7
27	63,336–63,441	106	petL	27	R 79,301–79,405	105	-	96.2
28	63,846–63,927	82	trnW	28	R 445,609–445,690	82	trnW	96.3
29	64,017–64,084	68	trnP*	29	R 445,455–445,515	61	-	95.1
30	64,069–64,131	63	trnP*	30a	R 305,100–305,163	64	trnP-1*	82.8
″	″	″	″	30b	R 117,697–117,760	64	trnP-2*	82.8
31	64,246–64,290	45	-	31	R 445,372–445,416	45	-	88.9
32	68,081–68,256	176	clpP*	32	380,710–380,885	176	-	95.5
33	75,509–75,643	135	rps11*	33	R 324,416–324,550	135	-	94.1
34	76,715–76,833	119	rps8*	34	R 99,254–99,373	120	-	86.7
35	77,024–77,395	372	rpl14*	35	R 98,764–99,133	370	-	84.1
36	82,945–82,976	32	trnI*	36	R 157,714–157,745	32	trnI-p	96.9
37	82,945–82,974	30	trnI*	37	184,631–184,660	30	-	83.3
38	83,963–84,016	54	-	38	R 154,459–154,512	54	-	98.1
39	84,711–89,049	4,339	Footnoted)	39	R 417,240–421,558	4,319	-	97.7
40	88,845–89,021	177	-	40	340,755–340,931	177	rps12*	72.3
41	91,016–92,532	1,472	rrn16	41a	300,896–302,827	1,932	rrn18-1	75.6e)
″	″	″	″	41b	R 393,737–395.668	1,932	rrn18-2	75.6e)
″	″	″	″	41c	R 56,769–58,700	1,932	rrn18-3	75.6e)
42	93,226–95,059	1,834	Footnotef)	42	74,171–76,003	1,833	trnA	99.8
43	94,995–97,615	2,621	rrn23	43a	R 371,386–374,530	3,145	rrn26-1	73.7g)
”	″	″	″	43b	R 259,648–262,792	3,145	rrn26-2	73.7g)
44	94,995–95,063h)	69	rrn23*	44	R 170,827–170,895	69	rrn26-p*	79.7
45	94,995–95,059	65	rrn23*	45	75,939–76,003	65	rrn26-p*	98.5
46	98,811–98,896	86	trnN	46	R 428,633–428,718	86	trnN	98.8
47	98,831–98,888	58	trnN*	47a	R 270,543–270,601	59	trnK-1*	79.7
″	″	″	″	47b	R 442,708–442,766	59	trnK-2*	79.7
″	″	″	″	47c	R 178,647–178,705	59	trnK-3*	79.7
48	102,531–102,595	65	ndhF*	48	294,426–294,490	65	nad5b*	81.5
49	109,526–109,596	71	ndhG*	49	R 146,989–147,055	67	-	89.6
50	110,973–111,387	415	ndhA 3′-ex*	50	242,709–243,106	398	-	91.7
51	111,103–111,141	39	ndhA 3′-ex*	51	16,001–16,039	39	nad1c*	82.1
52	111,319–111,361	43	-	52	43,065–43,107	43	-	81.4
53	111,324–111,355	32	-	53a	R 136,911–136,942	32	-	81.3
″	″	″	-	53b	43,726–43,757	32	-	81.3
54	111,389–111,572	184	-	54	R 343,407–343,586	180	-	90.6
Total	-	18,385	-	Total	-	27,733	-	-

a) Suffix “p” to the mt gene indicates a pseudogene. *: Part of the gene located.

b) “R” indicates the mtDNA segment reversed with respect to the corresponding ctDNA segment.

c) Sequence homology (%) = [No. matched nucleotides]/[No. nucleotides in mtDNA segment] × 100.

d) This ctDNA segment contains three ct genes, ndhB, rps7, and 3′-rps12 ex-2.

e) Homology of the 1,246 bp sequences conserved between the ct-rrn16 and mt-rrn18 genes.

f) This ctDNA segment contains three ct genes, trnI 3′-ex, trnA and rrn23*.

g) Homology of the 1,571 bp sequences conserved between the ct-rrn23 and mt-rrn26 genes.

h) The 69 bp 5′-end of no. 43 ctDNA segment.