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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).