Additional file 1: Figures S1 – S4 and Tables S1, S2, S4, S5. of Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

Supplemental figures and tables on CNV calling and eQTL mapping. (DOCX 1151 kb

Additional file 2: Table S3. of Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

Quantitative genotypes for all 15,183 inferred CNV regions (CNVRs). chr represents the chromosome on which the CNVR is located, while start and end indicate the coordinates of the first respectively last CGH probe contained in the CNVR. length_kb is the estimated CNVR length in kilobases. CNV_detection_status indicates whether a CNVR contains only deletions (del), duplications (dup) or both (cnv) and eqtl_mapping indicates whether a given CNVR was detected in at least two individuals and was therefore used for cis-eQTL mapping (1) or not (0). The columns thereafter are the quantitative genotypes defined as an individual’s median log2-ratio of all CGH probes within a given CNVR. (XLSX 5415 kb

Evolution of two distinct phylogenetic lineages of the emerging human pathogen -6

<p><b>Copyright information:</b></p><p>Taken from "Evolution of two distinct phylogenetic lineages of the emerging human pathogen "</p><p>http://www.biomedcentral.com/1471-2148/7/177</p><p>BMC Evolutionary Biology 2007;7():177-177.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2098775.</p><p></p>h dot representing one patient isolate as defined in materials and methods. The five InDel haplotypes are encircled

Evolution of two distinct phylogenetic lineages of the emerging human pathogen -1

<p><b>Copyright information:</b></p><p>Taken from "Evolution of two distinct phylogenetic lineages of the emerging human pathogen "</p><p>http://www.biomedcentral.com/1471-2148/7/177</p><p>BMC Evolutionary Biology 2007;7():177-177.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2098775.</p><p></p>h dot representing one patient isolate as defined in materials and methods. The five InDel haplotypes are encircled

Evolution of two distinct phylogenetic lineages of the emerging human pathogen -2

<p><b>Copyright information:</b></p><p>Taken from "Evolution of two distinct phylogenetic lineages of the emerging human pathogen "</p><p>http://www.biomedcentral.com/1471-2148/7/177</p><p>BMC Evolutionary Biology 2007;7():177-177.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2098775.</p><p></p> Tool software release 5) over at least 30 kb: M on top, Agy99 at the bottom, and of either haplotype, the Asian (RD2 and RD5) or the South American (RD9 and RD10) in the middle. Regions of sequence conformity are shown in parallel light grey plains, inverted DNA segments are depicted in dark grey and inverted surfaces, and white areas represent non-homologous regions like deletions and insertions. Some sequence displacements are visualized as grey areas displaying across the panels. Cut-off value for inclusion of sequence identity was 100 bp. The principal genetic backbone of the Asian and South American haplotypes (both members of the ancestral lineage) is identical for each alignment shown, but – as a matter of how the RDs were found – the particular excluded haplotypes reveal deletions in the respective RDs. Although showing the same genetic backbone as in the marginal parts, the Mexican strains disclose large deletions over their respective RDs and are therefore not included in this computational analysis. The sequence regions were retrieved by scanning the contigs by PCR, and by cloning and sequencing of critical segments

Evolution of two distinct phylogenetic lineages of the emerging human pathogen -5

<p><b>Copyright information:</b></p><p>Taken from "Evolution of two distinct phylogenetic lineages of the emerging human pathogen "</p><p>http://www.biomedcentral.com/1471-2148/7/177</p><p>BMC Evolutionary Biology 2007;7():177-177.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2098775.</p><p></p

Evolution of two distinct phylogenetic lineages of the emerging human pathogen -4

<p><b>Copyright information:</b></p><p>Taken from "Evolution of two distinct phylogenetic lineages of the emerging human pathogen "</p><p>http://www.biomedcentral.com/1471-2148/7/177</p><p>BMC Evolutionary Biology 2007;7():177-177.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2098775.</p><p></p>Note that both the progenitor and the MRCA are hypothetical strains. Features differentiating clusters or strains are dedicated to the branches between the nodes. RDs indicated here are all differentiated by features that are also shown in Fig. 4, whereas more RDs bear supporting features between the nodes (Table 1). The lengths of the internodes do not reflect time or genetic distance

Additional file 2: Table S2. of Functional analysis and transcriptional output of the GĂśttingen minipig genome

Contig assembly statistics. Roche-454 reads that were not incorporated into the minipig genome were assembled de-novo with Roche-Newbler software. (DOCX 13 kb

Additional file 7: Figure S3. of Functional analysis and transcriptional output of the GĂśttingen minipig genome

Schematic description of the in silico workflow for selection of Sus scrofa specific lncRNAs. * 16 genomes: cow, horse, dog, human, orang utan, chimpanzee, cynomolgus monkey, rhesus monkey, marmoset, rabbit, guinea pig, hamster, mouse, rat, opossum, chicken. See text for more detailed description. (JPEG 854 kb