The analysis of pig genomes provides insights into porcine demography and evolution. Domestic pigs have been shaped by humans over the past 10,000 years. This study presents the genome sequence of a female domestic Duroc pig (Sus scrofa) and compares it with genomes of wild and domestic pigs from Europe and Asia. Wild pigs originated in Southeast Asia and spread across Eurasia. The results show a deep phylogenetic split between European and Asian wild boars about 1 million years ago, with genes involved in RNA processing and regulation under selective sweep. Genes related to immune response and olfaction show fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides a valuable resource for improving this important livestock species and extends the potential of the pig as a biomedical model.
The domestic pig is a eutherian mammal and a member of the Cetartiodactyla order, which last shared a common ancestor with humans about 79-97 million years ago. Molecular genetic evidence indicates that Sus scrofa emerged in Southeast Asia during the early Pliocene. Pigs were domesticated in multiple locations across Eurasia about 10,000 years ago. A high-quality draft pig genome sequence was developed by the Swine Genome Sequencing Consortium. The assembly (Sscrofa10.2) comprises 2.60 gigabases assigned to chromosomes with 212 megabases in unplaced scaffolds.
Genome annotation revealed 95 novel repeat families, including LINEs, SINEs, satellites, and LTRs. The relative content of repetitive elements is lower than in other mammalian genomes. The main repetitive element groups are LINE1 and glutamic acid transfer RNA (tRNA Glu)-derived SINEs or PRE (porcine repetitive element). The expansion of PRE is specific to the porcine lineage. Phylogenetic analysis of LINE1 and PRE indicates that only a single lineage of each is currently active.
Annotation of genes, transcripts, and predictions of orthologues and paralogues was performed using the Ensembl analysis pipeline. Further annotation for non-protein-coding RNAs (ncRNAs) was undertaken with another analysis pipeline. The evolution of the porcine genome is discussed, including the evolution of genes and gene families. The study identified 9,000 as 1:1 orthologues within six mammals, revealing similar evolutionary rates in pigs and other mammals. The observed dN/dS ratio indicates an intermediate level of purifying selection pressure in the pig. Genes showing increased dN/dS ratios were analyzed using DAVID to examine whether these rapidly evolving genes were enriched for specific biological processes.
Immune genes are known to be actively evolving in mammals. The study examined a subset of 15The analysis of pig genomes provides insights into porcine demography and evolution. Domestic pigs have been shaped by humans over the past 10,000 years. This study presents the genome sequence of a female domestic Duroc pig (Sus scrofa) and compares it with genomes of wild and domestic pigs from Europe and Asia. Wild pigs originated in Southeast Asia and spread across Eurasia. The results show a deep phylogenetic split between European and Asian wild boars about 1 million years ago, with genes involved in RNA processing and regulation under selective sweep. Genes related to immune response and olfaction show fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides a valuable resource for improving this important livestock species and extends the potential of the pig as a biomedical model.
The domestic pig is a eutherian mammal and a member of the Cetartiodactyla order, which last shared a common ancestor with humans about 79-97 million years ago. Molecular genetic evidence indicates that Sus scrofa emerged in Southeast Asia during the early Pliocene. Pigs were domesticated in multiple locations across Eurasia about 10,000 years ago. A high-quality draft pig genome sequence was developed by the Swine Genome Sequencing Consortium. The assembly (Sscrofa10.2) comprises 2.60 gigabases assigned to chromosomes with 212 megabases in unplaced scaffolds.
Genome annotation revealed 95 novel repeat families, including LINEs, SINEs, satellites, and LTRs. The relative content of repetitive elements is lower than in other mammalian genomes. The main repetitive element groups are LINE1 and glutamic acid transfer RNA (tRNA Glu)-derived SINEs or PRE (porcine repetitive element). The expansion of PRE is specific to the porcine lineage. Phylogenetic analysis of LINE1 and PRE indicates that only a single lineage of each is currently active.
Annotation of genes, transcripts, and predictions of orthologues and paralogues was performed using the Ensembl analysis pipeline. Further annotation for non-protein-coding RNAs (ncRNAs) was undertaken with another analysis pipeline. The evolution of the porcine genome is discussed, including the evolution of genes and gene families. The study identified 9,000 as 1:1 orthologues within six mammals, revealing similar evolutionary rates in pigs and other mammals. The observed dN/dS ratio indicates an intermediate level of purifying selection pressure in the pig. Genes showing increased dN/dS ratios were analyzed using DAVID to examine whether these rapidly evolving genes were enriched for specific biological processes.
Immune genes are known to be actively evolving in mammals. The study examined a subset of 15