Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis

Smith, David Roy; Lee, Robert W

doi:10.1186/1471-2148-9-120

Table 3 Nucleotide diversity (by region) in the Chlamydomonas reinhardtii plastid genome.

From: Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis

	# of sites^a	S	# of Indels^b (length nt)	π^c × 10^-3 (SD × 10^-3)	π₊^d × 10^-3 (SD × 10^-3)	π_syn × 10^-3	π_nsyn × 10^-3	Tajima's D-Test (P value)
PROTEIN-CODING (by gene)
atpA	501	18	0	17.30 (2.67)	---	71.08	0	0.06 (>0.1)
atpF	213	0	0	0	---	0	0	---
atpI	366	3	0	3.51 (1.43)	---	13.85	0	-1.01 (>0.1)
cemA	462	2	0	2.27 (4.40)	---	5.34	1.34	1.17 (>0.1)
orf1995	1896	8	0	1.41 (0.56)	---	2.57	1.09	-0.96 (>0.1)
petA	954	0	0	0	---	0	0	---
petG	45	0	0	0	---	0	0	---
psaJ	126	0	0	0	---	0	0	---
psbA	435	8	0	9.61 (1.46)	---	36.5	1.7	1.48 (>0.1)
psbK	72	0	0	0	---	0	0	---
rpoC2	252	6	0	13.61 (2.85)	---	10.85	14.33	2.03 (<0.05)
rpl2	321	2	0	3.56 (0.74)	---	7.28	2.36	1.64 (>0.1)
rps2	87	0	0	0	---	0	0	---
rps3	126	0	0	0	---	0	0	---
rps9	462	4	1 (21)	3.50 (1.01)	---	9.78	1.61	-0.04 (>0.1)
rps11	105	0	0	0	---	0	0	---
rps12	321	0	0	0	---	0	0	---
rps19	183	0	0	0	---	0	0	---
tufA	213	0	0	0	---	0	0	---
ycf3	315	2	0	1.81 (1.25)	---	3.84	1.19	-1.28 (>0.1)
ycf4	399	0	0	0	---	0	0	---
INTERGENIC (by region)
atpA/psbI	343	1	0	1.75 (0.51)	1.75 (0.51)	---	---	1.22 (>0.1)
atpF/rps11	1556	86	16 (368)	25.61 (9.77)	30.10 (11.15)	---	---	-1.08 (>0.1)
atpI/psaJ	328	9	0	12.49 (2.42)	12.49 (2.42)	---	---	0.61 (>0.1)
petG/rps3	805	5	3 (3)	2.97 (0.44)	4.50 (0.76)	---	---	0.57 (>0.1)
psaJ/rps12	310	2	0	3.38 (0.65)	3.38 (0.65)	---	---	1.17 (>0.1)
psbK/tufA	828	4	2 (117)	1.18 (0.37)	3.47 (0.53)	---	---	0.06 (>0.1)
psbI/cemA	271	3	2 (2)	5.20 (1.18)	8.86 (2.00)	---	---	0.00 (>0.1)
rpl2/rps19	808	36	9 (164)	27.36 (5.14)	33.69 (5.70)	---	---	0.99 (>0.1)
rps3/rpoC2	1474	88	32 (462)	41.60 (6.65)	53.19 (9.01)	---	---	0.71 (>0.1)
rps9/ycf4	344	1	1 (21)	1.65 (0.53)	3.29 (0.69)	---	---	1.03 (>0.1)
rps18/rps2-1	1115	45	19 (418)	30.47 (9.57)	42.17 (11.33)	---	---	0.90 (>0.1)
ycf3/ycf4	179	0	0	0	0	---	---	---
23S-1/23S-2	909	6	2 (46)	3.97 (0.67)	5.28 (0.89)	---	---	2.10 (<0.05)
23S-2/5S	89	0	0	0	0	---	---	---

Note: S, number of segregating (i.e., polymorphic) sites; Indels, insertion-deletion events; π, nucleotide diversity; π₊, nucleotide diversity including both polymorphic sites and insertion-deletion events; π_syn, nucleotide diversity at synonymous sites; π_nsyn, nucleotide diversity at nonsynonymous sites; SD, standard deviation.
^a Comprises all sites in the nucleotide alignment, including those with indels.
^b Indels involving more than 1 nucleotide are counted as a single event. Indel length includes the sum of all indels and includes consecutive indel events.
^c Only includes sites without indels.
^d Considers all sites, including those with indels. Consecutive indels are counted as a single polymorphic event. Indel states were measured using a multiallelic approach.

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