Pig genome

Dr Denis Larkin

The genome sequence of pigs has been completed and annotated for the first time by an international team of scientists that includes researchers at Aberystwyth University.

The research by the International Swine Genome Sequencing Consortium has been led by researchers at the University of Illinois, Wageningen University and the University of Edinburgh.

Dr Denis Larkin, a Lecturer in Animal Genomics at Aberystwyth University’s Institute of Biological, Environmental and Rural Sciences (IBERS), led the Pig Chromosome Evolution Analysis Group within the Consortium.

Dr Larkin is one of the primary authors of the paper, Analyses of pig genomes provide insight into porcine demography and evolution, which is published in the journal Nature on Thursday 15 November 2012.

This is the first time that differences between the pig genome and the genomes of other mammals have been revealed and analysed in detail at whole genome level.

The researchers found that pigs have around 22,000 protein-coding genes and their genome has a recent expansion of genes responsible for their perception of smell. In addition, they report findings on pig demography, adaptive and chromosome evolution.

“Pig chromosomes were significantly rearranged after pigs and humans split from a common ancestor about 90 million years ago”, said Dr Larkin.

Under Larkin’s supervision, Aberystwyth University graduate student Jitendra Narayan aligned pig chromosomes to the sequences of nine other mammals, including mice, dogs, horses and cattle.

He detected over 100 evolutionary rearrangements that distinguish pig chromosomes. “It is amazing to see ancient rearrangements in the DNA of contemporary species. A whole evolutionary history of an organism can be read from its DNA”, says Jitendra.

Larkin and colleagues from the University of Illinois, University of California and the University of Kent, performed a detailed analysis of genome rearrangements in the pig chromosomes.

“Some chromosomal changes can be traced to the artiodactyl common ancestor of pigs and cattle that existed around 65 million years ago,” argues Larking. “These changes are not randomly distributed in chromosomes but often affect gene networks related to the adaptation of species to new environments.”

Larkin’s group has found that genes involved in taste perception are heavily affected by chromosome rearrangements in the pig genome. Pigs have fewer taste genes than humans and mice, but in addition, the remaining genes have been reshuffled in pig chromosomes.

“This may well be the reason why pigs can eat food not suitable for humans. Pigs were domesticated and became an important agricultural species because they could transform food which was not suitable for humans into meat, a rich source of protein. Humans and pigs do not compete for food. Now it is clear that this feature is encoded in pig genes and chromosome structure”, Larkin says.

The researchers found that parts of pig chromosomes had broken during the evolutionary process and recombined in a way that is different to other genomes.

Scientists link this process to the presence of repetitive sequences or ‘mobile elements’ that can move and insert themselves into different regions of chromosomes in multiple copies.

“Mobile elements make some chromosome intervals unstable and fragile, causing them to break and join with other chromosomes during the evolutionary process”, says Larkin. “We first found this when we looked into the cattle genome back in 2009.”

“By comparing two artiodactyl genomes, those of pigs and cattle, we were able to see that very specific mobile elements were involved in shaping the chromosomes of their common ancestor, and those elements which later shaped the chromosomes of pigs and cattle.”

Analysis of the pig genome shows how much about the lineage-specific biology and evolutionary history can be learned from a nearly compete genome sequence of a species.

Since the publication of the human genome sequences in 2001, genomes of at least 12 mammalian species have been sequenced and assembled at chromosome level.

“Every new genome provides important insights into the species-specific biology and evolution. However, a totally new level of knowledge can be achieved when the genomes of different species are cross-compared,” adds Larkin.

“For example, multiple genomes need to be analysed to understand how evolution and adaptation works. The origin of organs (like the rumen) that make some groups of animals more suitable for domestication and agriculture than others could be revealed from multispecies multi-genome comparisons.”

Dr Larkin is involved in the analysis of the data generated by the 10,000 genomes project (G10K). G10K aims to assemble DNA sequences representing the genomes of 10,000 vertebrate species. Dr Larkin hopes that this will provide enough data to answer these and other fundamental biological questions.

AU38012

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