Table 1.

Swine Genome Sequencing Consortium genome sequence analysis groups

Analysis group	Lead contact	Notes
Assembly	Alan Archibald alan.archibald@roslin.ed.ac.uk	The target for the next assembly is to incorporate all the available sequence data for Duroc 2-14, including BAC clones sequences, WGS Sanger and next-generation short sequence reads. Contig and scaffold order and orientation will be tested against other genome maps and in particular the high resolution radiation hybrid maps.
Structural variation, segmental duplication, copy number variation	Christian Bendixen christian.bendixen@agrsci.dk	The reference genome sequence will be analysed for evidence of segmental duplications. Comparative Genomic Hybridisation data, paired-end and mate-pair re-sequence data from other pigs will be used to identify smtructural and copy number variation.
Repetitive DNA, transposable elements Speciation, wild and related suids and selection	Geoff Faulkner geoff.faulkner@roslin.ed.ac.uk Lawrence Schook schook@uiuc.edu	Retroviruses and related repetitive sequences in Sus scrofa and related species will be characterized. Sequence and 60 K SNP genotype data from wild boar and related species will be explored to address the origins of domestic pigs. Comparative sequence analyses of domesticated and wild boar genome sequences is expected to reveal signatures of artificial and natural selection.
Evolution	Leif Andersson Leif.andersson@imbim.uu.se	Natural and artificial selection will have shaped the pig genome sequence. Comparison of the pig genome sequence with the sequences of other mammals is expected to reveal genes that are evolving more rapidly in the pig and artiodactyl lineages.
Comparative genomics	Martien Groenen Martien.groenen@wur.nl	Genome rearrangements and conserved synteny compared to other suids and other mammals.
Imprinting	Ole Madsen Ole.madsen@wur.nl	RNA-seq data from a range of tissues from Duroc 2-14 or her clones will be analysed to identify genes that show differential allelic expression and potentially imprinted genes.
SNP	Martien Groenen martien.groenen@wur.nl	Re-sequence data and the WGS sequence data from Duroc 2-14 will be examined for putative SNPs and small indels, including those for which Duroc 2-14 is heterozygous.
ncRNA	Jan Gorodkin gorodkin@genome.ku.dk	The genome sequence will be explored for putative ncRNA sequences and microRNA encoding loci.
Gene builds	Steve Searle Searle@sanger.ac.uk	The Ensembl automated pipeline will be used to establish a Gene Build for the pig genome that will be compared with builds generated by other systems including NCBI.
Protein interactions	Soren Brunak brunak@cbs.dtu.dk	Development of a proteome will be initiated.
Immune genes	Chris Tuggle cktuggle@iastate.edu	The immune gene analysis group will manually annotate pig genes predicted/known to have roles in the immune system. The repertoire of pig immune genes will be examined for evidence of pig-lineage specific features.
Reproduction	Max Rothschild mfrothsc@iastate.edu	The reproduction gene analysis group will manually annotate pig genes predicted/known to have roles in reproductive functions and seek to identify pig-lineage specific features.
Obesity	Max Rothschild mfrothsc@iastate.edu	The obesity gene analysis group will manually annotate pig genes predicted/known to have roles in obesity and seek to identify pig-lineage specific features
Olfaction, neuropeptide and prohormone	Sandra Rodriguez-Zas rodrgzzs@illinois.edu	Approximately 5% of the genes in the Sscrofa9 Gene Build are predicted to have olfactory functions. These genes will be manually annotated and examined for pig-specific characteristics. In addition, the neuropeptide and prohormone gene families will be annotated.
Manual annotation	Jim Reecy jreecy@iastate.edu	The pig research community is engaged in efforts to manually Annotate genes identified/predicted by the Ensembl analysis pipeline. The otterlace system will be used to enable this community annotation activity.
Biomedical Models	Lawrence Schook schook@illinois.edu	The use of genomic information to enhance the utilization of the pig in xenotransplantation and as a model for cardiovascular, cancer and obesity will be addressed. How genomic information supports the further development of transgenic pigs for creating essential animal models will also be discussed.