10.5061/DRYAD.80P28
Ishengoma, Edson
Nelson Mandela African Institution of Science and Technology
Agaba, Morris
Nelson Mandela African Institution of Science and Technology
Data from: Evolution of toll-like receptors in the context of terrestrial
ungulates and cetaceans diversification
Dryad
dataset
2017
Toll-like receptors
functional variation
Okapia johnstoni
Bos taurus
terrestrial ungulates
cetaceans
adaptive evolution
Giraffa camelopardalis
2017-02-06T17:41:30Z
2017-02-06T17:41:30Z
en
https://doi.org/10.1186/s12862-017-0901-7
https://www.treebase.org/treebase-web/search/study/summary.html?id=S20429
710736 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: Toll-like receptors (TLRs) are the frontline actors in the
innate immune response to various pathogens and are expected to be targets
of natural selection in species adapted to habitats with contrasting
pathogen burdens. The recent publication of genome sequences of giraffe
and okapi together afforded the opportunity to examine the evolution of
selected TLRs in broad range of terrestrial ungulates and cetaceans during
their complex habitat diversification. Through direct sequence comparisons
and standard evolutionary approaches, the extent of nucleotide and protein
sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5,
TLR7, TLR9 and TLR10) between giraffe and closely related species was
determined. In addition, comparison of the patterning of key TLR motifs
and domains between giraffe and related species was performed. The
quantification of selection pressure and divergence on TLRs among
terrestrial ungulates and cetaceans was also performed. Results: Sequence
analysis shows that giraffe has 94–99% nucleotide identity with okapi and
cattle for all TLRs analyzed. Variations in the number of Leucine-rich
repeats were observed in some of TLRs between giraffe, okapi and cattle.
Patterning of key TLR domains did not reveal any significant differences
in the domain architecture among giraffe, okapi and cattle. Molecular
evolutionary analysis for selection pressure identifies positive selection
on key sites for all TLRs examined suggesting that pervasive evolutionary
pressure has taken place during the evolution of terrestrial ungulates and
cetaceans. Analysis of positively selected sites showed some site to be
part of Leucine-rich motifs suggesting functional relevance in
species-specific recognition of pathogen associated molecular patterns.
Notably, clade analysis reveals significant selection divergence between
terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of
giraffe TLR3 key substitutions to the structure of the receptor indicates
that at least one of giraffe altered sites coincides with TLR3 residue
known to play a critical role in receptor signaling activity. Conclusion:
There is overall structural conservation in TLRs among giraffe, okapi and
cattle indicating that the mechanism for innate immune response utilizing
TLR pathways may not have changed very much during the evolution of these
species. However, a broader phylogenetic analysis revealed signatures of
adaptive evolution among terrestrial ungulates and cetaceans, including
the observed selection divergence in TLR3. This suggests that long term
ecological dynamics has led to species-specific innovation and functional
variation in the mechanisms mediating innate immunity in terrestrial
ungulates and cetaceans.
Control file for M8 model in PAMLControl file for the positive selection
M8 PAML model used to analyze Toll-like receptors (Table 1)M8.ctlControl
file for M7 model in PAMLControl file for the selection null (M7) PAML
model used to analyze Toll-like receptors (Table 1).M7.ctlSLR raw data for
TLR2TLR2 raw results for site-wise likelihood analysis (Table
1).TLR2_SLR_out.txtSLR raw data for TLR3TLR3 raw results for site-wise
likelihood analysis (Table 1).TLR3_SLR_out.txtSLR raw data for TLR4TLR4
raw results for site-wise likelihood analysis (Table
1).TLR4_SLR_out.txtSLR raw data for TLR5TLR5 raw results for site-wise
likelihood analysis (Table 1).TLR5_SLR_out.txtSLR raw data for TLR7TLR7
raw results for site-wise likelihood analysis (Table
1).TLR7_SLR_out.txtSLR raw data for TLR9TLR9 raw results for site-wise
likelihood analysis (Table 1).TLR9_SLR_out.txtSLR raw data for TLR10TLR10
raw results for site-wise likelihood analysis (Table
1).TLR10_SLR_out.txtTLRs alignments and treesRaw sequence alignments and
trees used to perform selection analyses in TLRs (Table 1, Table 2 and
Figure 3)Giraffe and okapi sequence fileRaw sequences for giraffe and
okapi TLRs used in the analyses.Additional File 1.txt