Genetic Variation of Goat Interferon Regulatory Factor 3 Gene and Its Implication in Goat Evolution.
The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats' populations. Fu and Li tests were significantly positive but Tajima's D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.|Department of Animal Science, Niger Delta University, Wilberforce Island, Ammassoma, Bayelsa State, Nigeria.
Moses
M
Okpeku
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.|Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
Ali
A
Esmailizadeh
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
Adeniyi C
AC
Adeola
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
Liping
L
Shu
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
Yesheng
Y
Zhang
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
Yangzi
Y
Wang
Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.
Timothy M
TM
Sanni
Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, USA.
Ikhide G
IG
Imumorin
Department of Animal Science, Berry College, Mount Berry, USA.
Sunday O
SO
Peters
School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China.
Jiajin
J
Zhang
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.|Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650500, China.
Yang
Y
Dong
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
Wen
W
Wang
D000595:Amino Acid Sequence; D000818:Animals; D003062:Codon; D000071278:Domestication; D019143:Evolution, Molecular; D015870:Gene Expression; D049810:Genetic Speciation; D006041:Goats / Q000145:classification / Q000235:genetics* / Q000276:immunology; D006239:Haplotypes; D007113:Immunity, Innate / Q000235:genetics*; D050838:Interferon Regulatory Factor-3 / Q000235:genetics* / Q000276:immunology; D008957:Models, Genetic; D016366:Open Reading Frames; D010802:Phylogeny; D012641:Selection, Genetic; D012756:Sheep / Q000145:classification / Q000235:genetics* / Q000276:immunology
D003062:Codon; D050838:Interferon Regulatory Factor-3