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Table 1 Nucleotide Divergence versus Sequence Class.

From: Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

  # loci Total length (bp) Aligned length (bp) Tree length Branch length Substitution rate* (change/site × 10-9)
      Cattle Dog Human Cattle Dog Human
Overall 84 15507060 5521247 0.5265 0.1681 ± 0.0003 0.1547 ± 0.0003 0.2036 ± 0.0003 2.026 ± 0.003 1.864 ± 0.003 2.016 ± 0.003
Overall-CG 84 15507060 5282306 0.4984 0.1595 ± 0.0003 0.1451 ± 0.0002 0.1938 ± 0.0003 1.921 ± 0.003 1.748 ± 0.003 1.919 ± 0.003
Coding 52 137748 133235 0.1886 0.0644 ± 0.0010 0.0647 ± 0.0010 0.0595 ± 0.0009 0.776 ± 0.012 0.780 ± 0.012 0.589 ± 0.009
UTR 55 152130 115467 0.3855 0.1223 ± 0.0016 0.1472 ± 0.0018 0.1161 ± 0.0015 1.473 ± 0.019 1.773 ± 0.022 1.059 ± 0.010
Unique noncoding 84 9073616 4061797 0.5235 0.1676 ± 0.0003 0.1538 ± 0.0003 0.2021 ± 0.0004 2.019 ± 0.004 1.853 ± 0.003 2.001 ± 0.004
Repetitive 84 6409365 1157484 0.5719 0.1830 ± 0.0006 0.1668 ± 0.0006 0.2221 ± 0.0007 2.205 ± 0.007 2.010 ± 0.007 2.199 ± 0.007
Repetitive-CG 84 6409365 1112423 0.5460 0.1749 ± 0.0006 0.1581 ± 0.0006 0.2129 ± 0.0007 2.108 ± 0.007 1.905 ± 0.007 2.108 ± 0.007
  1. Orthologous sequences were globally aligned with mlagan (Methods). A suboptimal alignment was defined as any alignment which exceeded 3 standard deviations of the mean K2 divergence (window size 2 kb, slide 100 bp). These regions were not included in the analysis. Coding sequence was restricted only to well-annotated human genes (NCBI RefSeq database). UTR regions included 5'- and 3'-UTRs. Repetitive sequences were detected using RepeatMasker (version 3.0.8). Unique noncoding (i.e. not annotated) regions excluded both exonic and repetitive regions. Due to the higher mutation rate of CpG dinucleotides, substitutions without CpG dinucleotides (Overall-CG, Repetitive-CG) were considered in each alignment.
  2. * Substitution rate calculations assume branch times of the cattle, dog and human lineages from the LCA of cattle and dog of 83, 83 and 101 mya, respectively [27,28].
  3. †: If suboptimal alignments were included in the analysis, the overall branch length increases to 0.1707 ± 0.0003, 0.1567 ± 0.0003 and 0.2069 ± 0.0004, respectively (Methods).