Abstract
BackgroundComparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls.ResultsWe have generated ~3.84 million shotgun sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis.The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human.ConclusionThe addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.
Highlights
Comparative whole genome analysis of Mammalia can benefit from the addition of more species
More species are needed, and an artiodactyl like pig is an obvious choice for the following reasons. 1), By comparing rodents and human, it is not possible to determine whether observable differences, e.g. difference in isochore structure, are mainly due to changes in the rodent or primate lineage since their divergence; 2) Rodents have only a subset of the biological functions important to humans
By including pig additional functions will be covered; 3) Even though rodents, artiodactyls and primates diverged at approximately the same time [6,7], molecular evolution has been faster in the rodent branch, the pig is expected to be closer in sequence to human than mouse is
Summary
Comparative whole genome analysis of Mammalia can benefit from the addition of more species. By including pig additional functions will be covered; 3) Even though rodents, artiodactyls and primates diverged at approximately the same time [6,7], molecular evolution has been faster in the rodent branch, the pig is expected to be closer in sequence to human than mouse is. The importance of these points is generally appreciated and comparative genomics sequencing initiatives focusing on restricted regions of the genomes have recently provided much insight [e.g. The importance of these points is generally appreciated and comparative genomics sequencing initiatives focusing on restricted regions of the genomes have recently provided much insight [e.g. [1,2]]
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