500b_flt_counts

Mutational configurations for 500bp block

Sex-averaged linkage map of sole.

<p>Map distances are calculated using the Kosambi mapping function and shown in centimorgans. Combined SNPs are indicated with a ‘C’ at the beginning of their name.</p

Number of markers, the corresponding number of distinct contigs and map length for each linkage group of sole.

<p>Number of markers, the corresponding number of distinct contigs and map length for each linkage group of sole.</p

Syntenic relationships between sole and five other (flat)fish.

<p>The chromosomes of four model fish species, namely stickleback (S), tilapia (T), pufferfish (P) and medaka (M), were grouped in A- and B-groups according to their syntenic relationships as described in Sarropoulou et al. (2008), Kai et al. (2011) and Guyon et al. (2012) (left column). The numbers in the grid indicate the number of contigs where sequence homology was found between the sole linkage groups and the chromosomes of the four model species. For each chromosome the sole linkage group with the largest number of homologous sequences is highlighted in grey. Marked with *: the 21 linkage groups that are suggested as chromosome counterpart for sole (or at least part of it). In italics: linkage groups likely to be on the same chromosome as the linkage group marked with * to the left of it. For all 21 putative sole chromosomes (except for LG23) a homologous turbot linkage group is suggested (right column).</p

Putative SNPs discovered in genome of Cotesia vestalis

Individual paired-end reads were aligned against the artificial Cotesia vestalis reference genome obtained from the de novo genome assembly using BWA. The resulting BAM file was then used for the identification of putative SNPs using SAMTOOLS and varFilter from the samtools.pl utility. We only considered nucleotide substitutions and ignored small indels. SNPs were filtered that had a mapping quality higher than 20, a minimum read depth of 3 and a maximum read depth of 90 (3x the average read depth, a strategy to avoid orthologous SNPs, e.g. in multi copy genes

Range map for members of the Suidae.

<p>Range map for members of the Suidae.</p

Cotesia vestalis SNP information and sequences

From our list of putative SNPs across the C. vestalis genome, we selected 100 SNPs for genotyping assay development. We first selected the 200 largest scaffolds; they varied in length from 17-58Kb and contained a total of 7,878 SNPs. We then removed SNPs with a minor allele frequency (MAF) <0.2, SNPs that had another SNP within 50 bp up- or downstream, and SNPs with more than 2 alleles. The remaining SNPs were binned in MAF bins of 0.2-0.3 (1,908 SNPs), 0.3-0.4 (1,605 SNPs) and 0.4-0.5 (1,156 SNPs). Per MAF bin, SNPs were ranked by SNP quality score. We then selected the SNPs with the highest quality scores, picking 20 SNPs with a MAF between 0.2-0.3 and 40 each with a MAF between 0.3-0.4 and 0.4-0.5, all on different scaffolds. All selected SNPs had a quality score of more than 200 (based on SAMTOOLS), and an average read depth of 61. High-throughput genotyping assays based on allele-specific forward primers were developed for these 100 SNP sequences at KBioscience (now LGC Genomics, Hoddesdon, U.K.)

Positively selected sites in the three dimensional structure of TLR1/TLR2 heterodimer.

<p>Positively selected sites are colored in red. A site known to interact with bacterial lipopeptide is colored in blue. Only sites likely to affection protein function based on their location within the structure are shown.</p

Genototypes of C vestalis females at 98 SNPs

SNP genotypes of 139 Cotesia vestalis females collected in Western Taiwan at 98 polymorphic SNP

Species phylogeny of the Suidae.

<p>Shown here is a representation of the relationships among members of the Suidae used in analyses. The relationships were derived from near complete genome data of each species. The posterior probability at each node is 1.</p