The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

Bortiri, Esteban; Coleman-Derr, Devin; Lazo, Gerard R; Anderson, Olin D; Gu, Yong Q

doi:10.1186/1756-0500-1-61

Table 1 Substitution rates in grasses. Chloroplast genes are divided into seven groups according to the function of their product. For groups of more than one gene the top row gives the mean substitution rate, and the second and third rows show the genes, within that group, with the maximum and minimum rates respectively. ENV: Envelope membrane. MAT: maturaseK. NADH: NADH genes. PS: Photosynthetic genes. RP: ribosomal genes. RNPol: RNA polymerase genes. B: Brachypodium. W: wheat. R: rice. M: maize.

From: The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

GENE GROUP	NO. OF GENES	SYNONYMOUS SUBSTITUTIONS¹				NONSYNONYMOUS SUBSTITUTIONS¹				NNONSYNONYMOUS/SYNONYMOUS RATIO
		B	W	R	M	B	W	R	M	B	W	R	M
RNPol	4	0.371	0.359	0.358	0.36	0.131	0.126	0.131	0.128	0.35	0.35	0.37	0.35
Max		rpoC1 0.452	rpoC1 0.423	rpoC1 0.428	rpoC1 0.42	rpoC2 0.172	rpoC2 0.162	rpoC2 0.166	rpoC2 0.159	rpoC2 0.6	rpoC2 0.57	rpoC2 0.61	rpoC2 0.54
Min		rpoC2 0.289	rpoC2 0.286	rpoC2 0.273	rpoC2 0.296	rpoB 0.088	rpoB 0.084	rpoB 0.087	rpoB 0.089	rpoC1 0.24	rpoB 0.24	rpoC1 0.25	rpoC1 0.25
ENV	1	0.46	0.454	0.422	0.44	0.2	0.193	0.2	0.188	0.44	0.43	0.47	0.43
MAT	1	0.448	0.47	0.466	0.45	0.225	0.209	0.212	0.213	0.5	0.44	0.46	0.47
NADH	11	0.362	0.354	0.358	0.36	0.092	0.092	0.091	0.09	0.25	0.26	0.25	0.25
Max		ndhH 0.463	ndhH 0.461	ndhH 0.445	ndHA 0.448	ndhF 0.188	ndhF 0.18	ndhF 0.181	ndhF 0.172	ndhF 0.55	ndhF 0.53	ndhF 0.51	ndhF 0.49
Min		ndhB 0.062	ndhB 0.076	ndhB 0.059	ndhB 0.065	ndhB 0.028	ndhB 0.04	ndhB 0.029	ndhB 0.025	ndhC 0.125	ndhH 0.14	ndhH 0.13	ndhH 0.15
PS	32	0.370	0.362	0.353	0.36	0.039	0.041	0.039	0.039	0.11	0.12	0.11	0.11
Max		psaC 0.554	psaC 0.571	psaC 0.519	psaC 0.485	atpE 0.158	atpE 0.158	atpE 0.15	atpE 0.147	atpE 0.42	atpF 0.42	atpF 0.47	atpF 0.53
Min		psbL 0.2	psbL 0.16	psbL 0.16	psbL 0.16	petG, psbI 0	petG, psbI 0	petG psbM psbT 0	petG, psbF psbI psbT 0	petD 1.24 × 10^-2	petB 9.52 × 10^-3	petD 1.7 × 10^-2	petD 6.83 × 10^-3
PR	1	0.442	0.412	0.426	0.427	0.161	0.161	0.168	0.161	0.36	0.39	0.39	0.38
RP	22	0.312	0.297	0.302	0.287	0.121	0.121	0.127	0.121	0.39	0.41	0.42	0.42
Max		rps8 0.489	rps8 0.469	rps8 0.48	rps8 0.47	rpl22 0.251	rpl22 0.248	rpl22 0.256	rpl22 0.256	rpl2 1.1	rpl2 0.98	rpl2 1.18	rpl2 1.18
Min		rps12 0.05	rps12 0.045	rps12 0.05	rps12 0.056	rps12 0.028	rps12 0.028	rps12 0.035	rps12 0.026	rps14 0.2	rpl16 0.21	rps14 0.2	rps14 0.18

¹ Rates were calculated using the method of Nei and Gojobori [27] using tobacco as an outgroup to Brachypodium, wheat, rice, and maize.

Back to article page

ISSN: 1756-0500

Contact us

Submission enquiries: bmcresearchnotes@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Research Notes

Contact us