Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing

Abstract

The major histocompatibility complex (MHC) is a key genomic model region for understanding the evolution of gene families and the co-evolution between host and pathogen. To date, MHC studies have mostly focused on species from major vertebrate lineages. The evolution of MHC classical (Ia) and non-classical (Ib) genes in pigs has attracted interest because of their antigen presentation roles as part of the adaptive immune system. The pig family Suidae comprises over 18 extant species (mostly wild), but only the domestic pig has been extensively sequenced and annotated. To address this, we used a DNA-capture approach, with probes designed from the domestic pig genome, to generate MHC data for 11 wild species of pigs and their closest living family, Tayassuidae. The approach showed good efficiency for wild pigs (~80% reads mapped, ~87× coverage), compared to tayassuids (~12% reads mapped, ~4× coverage). We retrieved 145 MHC loci across both families. Phylogenetic analyses show that the class Ia and Ib genes underwent multiple duplications and diversifications before suids and tayassuids diverged from their common ancestor. The histocompatibility genes mostly form orthologous groups and there is genetic differentiation for most of these genes between Eurasian and sub-Saharan African wild pigs. Tests of selection showed that the peptide-binding region of class Ib genes was under positive selection. These findings contribute to better understanding of the evolutionary history of the MHC, specifically, the class I genes, and provide useful data for investigating the immune response of wild populations against pathogens.

Comparative Analysis of SLA-1, SLA-2, and DQB1 Genetic Diversity in Locally-Adapted Kenyan Pigs and Their Wild Relatives, Warthogs

“…The major histocompatibility complex (MHC) proteins play a vital role in binding and presenting endogenous and exogenous epitopes derived from the host or pathogen to the circulating T-cells, initiating a T-cell-mediated immune response [ 1 , 2 , 3 , 4 , 5 ]. MHC structure and functions have been widely studied in different species, including comparative MHC genetic diversity analyses in humans and the Suidae family that comprises Sus scrofa (wild boars), Sus scrofa domesticus (domestic pig), and warthogs ( Phacochoerus africanus ) [ 2 , 6 , 7 , 8 ]. However, no comparative MHC data are available from locally-adapted Kenyan pigs.…”

Genetic Association between Swine Leukocyte antigen Class II Haplotypes and Reproduction Traits in Microminipigs

“…A total of 151 loci were annotated within the 2.4-Mb sequences, including three classical ( SLA-1 , SLA-2 , and SLA-3 ), and three non-classical class I genes ( SLA-6 , SLA-7 , and SLA-8 ) in the class I region, and four classical ( DRA, DRB1 , DQA , and DQB1 ), and four non-classical class II genes ( DMA , DMB , DOA , and DOB ) in the class II region as expressed SLA genes [5]. Based on the genomic and cDNA sequences in the SLA loci, many kinds of molecular-based SLA typing systems, including polymerase chain reaction (PCR) - sequence-specific primers (SSPs) [6,7], -fluorescently labeled sequence-specific oligonucleotide probes (SSOPs) [8], and -sequence-based typing (SBT) by traditional Sanger methods and/or next generation sequencing (NGS) [4,9,10,11,12] have been reported to assign SLA class I and II alleles. A systematic nomenclature for the SLA genes, alleles, and haplotypes are established by the SLA Nomenclature Committee, formed in 2002.…”

Collared peccary (Pecari tajacu ) are susceptible to porcine reproductive and respiratory syndrome virus (PRRSV)

“…Cross‐reactions among mammalian species will occur if secondary antibody is not preadsorbed to eliminate reactions with nontarget species. The likelihood of cross reactivity is further enhanced in this case because pigs ( Suidae ) and peccaries ( Tayassuidae ) share a common ancestry (Esteves & Binaghi, ; Frantz et al., ; Lee et al., ; Orliac et al., ). Throughout the study, ELISA S/P values were uniformly lower in peccaries than in the positive control pig.…”