The comparison of four mitochondrial genomes reveals cytoplasmic male sterility candidate genes in cotton

Li, Shuangshuang; Chen, Zhiwen; Zhao, Nan; Wang, Yumei; Nie, Hushuai; Hua, Jinping

doi:10.1186/s12864-018-5122-y

BMC Genomics

Table 6 Chimeric ORFs (> 300 bp) presented in 2074A mitogenomes

From: The comparison of four mitochondrial genomes reveals cytoplasmic male sterility candidate genes in cotton

2074 AORF	Start	End	Strand	Length (bp)	2074B	E5903	Tra-dom^c	Uni/R-seq^d	Homologous sequence^e	RNA-Seq Log2
2074 AORF	Start	End	Strand	Length (bp)	2074B	E5903	Tra-dom^c	Uni/R-seq^d	Homologous sequence^e	2074B/2074A	F1-A/2074A
Aorf1	3872	4483	+	612	-^a	*^b	1	U1	No homologous sequence	−11.76	2.73
Aorf2	4461	3700	–	762	–	*	6	U1	583–759, 86%, papaya mtDNA	−12.58	2.62
Aorf3	5180	4878	–	303	–	*	0	U1	154–301, 96%, papaya mtDNA	− 14.54	2.52
Aorf4	27,402	26,845	–	558	Some	some	1	AR4(524)	45 bp, rps3(1–45)^f; 47 bp sdh3	−0.22	2.92
atp8	28,431	27,967	–	463	*	*				−0.35	2.56
Aorf5	86,768	87,067	+	300	–	–	0		98%, other plant mtDNA	−11.92	3.33
Aorf6	143,074	142,757	–	318	Some	–	0		1–301, 95%, Phoenix ductylifera mtDNA	0.00	12.63
Aorf7	144,192	144,596	+	405	–	*	0	U3	No homologous sequence	0.00	9.96
Aorf8	149,251	148,952	–	300	–	*	0	U3	4–242, 94%, Beta vulgaris mtDNA	−13.47	2.25
rrn26	185,940	189,313	+	3374	*	*				1.26	3.17
Aorf9	189,332	189,688	+	357	Some	some	1	AR1(7125)	76 bp, nad7	−0.70	2.41
Aorf10	258,310	257,840	–	471	Some	some	1	up AR2 93 bp	4–424, 92%, Ricinus communis mtDNA	− 0.25	2.66
Aorf11	314,879	315,265	+	387	Some	some	0		43 bp, nad7	−1.00	2.63
Aorf12	323,440	323,838	+	399	Some	some	0		No homologous sequence	−12.06	2.01
rps14	324,431	324,751	+	321	*	*				−1.22	2.09
cob	326,094	327,256	+	1163	*	*				−0.91	3.37
Aorf13	335,286	334,948	–	339	Some	some	0		No homologous sequence	1.26	3.17
Aorf14	343,549	343,223	–	327	–	–	0		36 bp, cox2ex1	−1.25	3.38
rpl2	346,637	347,641	+	1005	*	*				−0.27	2.05
Aorf4–2	348,085	348,642	+	558	Some	some	1	AR4(524)	45 bp, rps3; 47 bp, sdh3	−0.22	2.92
Aorf15^h	388,830	388,447	–	384	Some	some	1		No homologous sequence	−1.08	2.79
Aorf16	397,394	397,735	+	342	–	–	0		No homologous sequence	−1.64	3.41
Aorf17	415,813	415,265	–	549	Some	some	0	up AR2 23 bp	39–527, 94%, Citrullus lanatus mtDNA	−11.92	3.33
Aorf18	449,399	449,001	–	399	–	some	0	U5	123–393, 82%, tobacco mtDNA	−11.06	4.57
Aorf19	452,355	453,074	+	720	–	*	2	U5	No homologous sequence	0.00	15.49
Aorf20	452,473	452,781	+	309	–	*	1	U5	No homologous sequence	0.00	13.35
Aorf21	454,116	453,781	–	336	–	*	0	U5	93%, Mimulus guttatus mtDNA	0.00	14.48
Aorf22	454,900	454,451	–	450	–	*	0	U5	96%, Mimulus guttatus mtDNA	−10.88	3.10
Aorf23	465,398	465,751	+	354	Some	some	0		167–331, other plant mtDNA	0.09	2.15
Aorf24	490,816	491,292	+	477	–	–	2		64 bp, rps4	−2.19	3.93
Aorf25^g	491,321	491,689	+	369	Some	*	0		20 bp, ccmFC	−3.15	4.83
Aorf26	508,562	507,753	–	810	Some	some	0		306–479, other plant mtDNA	1.45	5.21
cox1	631,928	633,518	+	1591	*	*				−0.32	1.86
Aorf28	633,740	634,606	+	867	Some	–	0	up AR1 1760 bp	56 bp, atp4(1–56)^f	−1.47	3.02
cox3	634,937	635,734	+	798	*	*				−0.03	2.69
Aorf27	665,520	666,155	+	636	–	*	0	AR1, U6	No homologous sequence	−4.71	0.35

Note. –^ano detected; *^bhave this ORF; ^cTra-dom: transmembrane domain; ^dUni/R-seq: unique sequence or repeat sequence; ^eHomologous sequence contains the sequence of genes in cotton and mitochondrial sequences of other plants; ^f Aorf4 contain a fragment that is 1-45 bp of rps3, Aorf28 contain a fragment that was 1-56 bp of atp4, identity is 100%; ^gAorf25 is in upstream 70 bp of nad5ex4; ^hthe end of Aorf15 is longer 81 bp than Sorf14

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ISSN: 1471-2164

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