Table 1 Swine Genome Sequencing Consortium genome sequence analysis groups
From: Pig genome sequence - analysis and publication strategy
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. |