The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs

Abstract

It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.

African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments

“…These have laid foundations for the preliminary understanding on their phylogeny, behavior, and adaptation. With the accumulation of genomic data in recent years for the family Suidae ( Groenen et al 2012 ; Frantz et al 2013 , 2016 ; Groenen 2016 ; Liu et al 2019 , 2022 ; Warr et al 2020 ; Garcia-Erill et al 2022 ), this provides a baseline that will underpin further studies on the potential molecular mechanisms of the evolution and phenotypic adaptations of the African suids with genomic approaches.…”

Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States

“…Thus, artificial selection resulted in a severe decrease of the brain–body ratio in several domestic pig breeds compared to wild boar (Kruska, 1970; Maselli et al., 2014). Multiple olfaction GO terms were enriched, including ‘Sensory perception of smell’ (GO:0007608, 33 genes), hinting at the olfactory receptor family known to play an important role in rapid pig evolution (Liu et al., 2022; Maga et al., 2015). Our results are in line with previous research among Italian feral pigs that describes olfactory traits reverting to predomestication phenotypes (Petrelli et al., 2022).…”

Inference of ancestral alleles in the pig reference genome

“…We first used reference sequences of six suids for genome alignment: the domestic Duroc (Sscrofa11.1) and Diannan small‐ear pig, the European wild boar (also belonging to S. scrofa ), Visayan warty pig ( Sus cebifrons ), and the African common warthog and red river hog (Chen et al, 2022; Liu et al, 2022; Warr et al, 2020; Xie et al, 2022). Cattle (Rosen et al, 2020) and horse (Kalbfleisch et al, 2018) served as outgroups (Appendix S1).…”