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Table 2 Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii.

From: Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture

   

# of sites

S

# of Indelsg (length nt)

π × 10-3 (SD × 10-3)

θW × 10-3 (SD × 10-3

πsyn × 10-3

πns × 10-3

Tajima's D test (P value)

mtDNA

Complete genomea

15280

134

15 (36)

3.35 (0.68)

3.66 (0.31)

---

---

-0.49 (> 0.10)

 

Protein-codingb

8154

44

1 (6)

2.06 (0.43)

2.20 (0.33)

8.52

0

-0.38 (> 0.10)

 

structural RNA genesc

3502

23

4 (4)

2.42 (0.42)

2.68 (0.56)

---

---

-0.55 (> 0.10)

 

rtl

1118

9

1 (3)

3.07 (0.87)

3.29 (1.10)

7.88

1.89

-0.35 (> 0.10)

 

Intergenicd

2434

58

9 (23)

8.92 (1.88)

9.73 (1.28)

---

---

-0.48 (> 0.10)

 

Silent sitese

5152

99

12 (26)

8.54 (1.03)

9.18 (0.65)

---

---

---

Nuclear DNA

Intronic (overall)

4294

359

47 (216)

33.50 (3.15)

33.81 (1.79)

---

---

-0.16 (> 0.10)

 

Silent sitesf

4824

381

50 (219)

31.96 (3.03)

33.02 (1.88)

---

---

---

 

Exonic (overall)

1614

25

1 (9)

6.02 (0.99)

6.58 (1.29)

19.57

1.42

-0.48 (> 0.10)

 

Exonic (by gene)

CBLP

420

1

0

0.68 (0.47)

0.97 (0.97)

2.77

0

-1.00 (> 0.10)

  

PETC

300

2

0

2.54 (0.78)

2.72 (1.92)

9.69

0

-0.27 (> 0.10)

  

PDK

222

3

0

6.86 (1.88)

5.52 (3.18)

26.35

0

1.10 (> 0.10)

  

MAT3

408

10

1 (9)

10.50 (2.70)

10.00 (3.16)

24.37

4.77

0.27 (> 0.10)

  

SFA

264

9

0

9.74 (2.80)

13.91 (4.64)

41.14

0

-1.59 (> 0.10)

 

Intronic (by gene)

CBLP

578

77

8 (75)

58.30 (7.41)

54.30 (6.20)

---

---

0.26 (> 0.10)

  

PETC

621

43

3 (5)

30.21 (6.07)

28.26 (4.31)

---

---

0.39 (> 0.10)

  

PDK

691

37

8 (42)

23.22 (5.58)

21.86 (3.59)

---

---

0.20 (> 0.10)

  

MAT3

560

30

4 (25)

21.60 (3.03)

21.87 (3.99)

---

---

-0.07 (> 0.10)

  

SFA

847

98

12 (15)

43.57 (4.53)

48.67 (4.77)

---

---

-0.61 (> 0.10)

  

YPT4

790

47

9 (39)

22.66 (4.50)

24.28 (3.54)

---

---

-0.38 (> 0.10)

  

ACTIN

207

27

3 (15)

53.37 (8.18)

53.37 (10.2)

---

---

0.01 (> 0.10)

  1. Note--S, number of segregating sites; Indels, insertion and deletions; π, nucleotide diversity; θW, Theta (per-site) from Watterson estimator; πsyn, nucleotide diversity at synonymous sites; πns, nucleotide diversity at nonsynonymous sites; SD, standard deviation.
  2. a Includes only 1 telomere.
  3. b Includes all protein-coding genes excluding rtl.
  4. c Includes rRNA- and tRNA-coding regions.
  5. d Includes intergenic regions and 1 telomere.
  6. e Includes synonymous sites, intergenic regions, and 1 telomere.
  7. f Includes synonymous sites and intronic regions.
  8. g Nucleotide diversity does not include indels. Consecutive indel sites are counted as single event. Indel length refers to the sum of all indels.