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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.