Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus)

Abstract

BackgroundThe wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense.ResultsThe blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (d N/d S) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition.ConclusionsThis study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3983-0) contains supplementary material, which is available to authorized users.

Pathogen-associated selection on innate immunity genes (TLR4, TLR7) in a neotropical rodent in landscapes differing in anthropogenic disturbance

“…A higher genetic diversity for TLR4 than for TLR7 has also been detected in a recent study across 23 rodent species (Fornůsková et al 2013 ), and similar results have been shown by Liu et al ( 2017 ) in wolves. Variation in TLR diversity is most likely a result of variable pathogen pressures.…”

Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae)

“…The domestic dog has one classical MHCI gene with 73 alleles (Wagner et al 2002;Ross et al 2012;Venkataraman et al 2017); domestic cat has three classical MHCI genes (Yuhki et al 2008) with a number of alleles; and giant panda has four classical MHCI genes, of which Aime-I has 16 alleles (Pan et al 2008;Zhu et al 2013). Liu et al (2017) reported 17 functional alleles from four MHCI genes in four wolf (Canis lupus) individuals. Therefore, it is not surprising that we detected 7−19 PFAs in the four Meles species (Supplementary Tables S2-S5).…”

Origin and evolution of the major histocompatibility complex class I region in eutherian mammals

“…The number of MHCI genes identified to date in eutherian mammals varies from species to species, ranging from 51 genes in the rhesus macaque (Shiina et al, ) to seven in the domestic dog (Yuhki et al, ). The number of functional MHCI genes ranges from about four in the domestic dog to 30 in the rhesus macaque (Liu et al, ; Shiina et al, ; Yuhki et al, ). The numbers of both MHCI genes and PFGs identified in most species in our study (Table ) were well within these ranges, although the killer whale and pangolin were exceptions.…”