PMC

Box plot of scaffold lengths for all multi-marker scaffolds (dark gray box) and for scaffolds showing a split within or across LGs (light gray box). The split scaffolds are significantly longer than the multi-marker scaffolds in general (t = -7.70, df = 193.39, p-value = 7.00e-13).

Fraction of scaffolds that are being represented by 1-11 unique markers in the consensus map. Insert: Fraction of scaffolds that have multiple probe-markers (2-11) that are distributed over 1-3 linkage groups (inter-split scaffolds). Red dot indicate the fraction of scaffolds with multiple probe-markers which are positioned > 5cM apart on the same linkage group (intra-split scaffolds).

Sliding window analysis of neutrality statistics. Analyses were performed using 10 cM windows with 1 cM incremental steps along the consensus map linkage groups and visualized using coloring alternates between adjacent LGs. A) Number of segregating sites. Dashed horizontal line indicates the overall average of 1017. B) Pairwise nucleotide diversity (π). Dashed horizontal line indicates the overall average of 0.005. C) Tajima’s D. Dashed horizontal line indicates the overall average of -0.852. D) Linkage disequilibrium Zn scores. Dashed horizontal line indicates the overall average of 0.040.

Marker order comparison of Linkage Groups (LGs) between the Picea abies haploid consensus map presented here and the Picea glauca map from . Consensus LG I - LG XII are located on the x-axis from left to right. Pavy et al. LG 1 - LG 12 are located on the y-axis from top to bottom. Each dot represents a marker comparison from the same scaffold, where black coloration represents markers mapping to the same LG in the two species, gray coloration represents markers mapping to different LGs. Turquoise coloration represents markers located on split scaffolds, indicating an assembly error.

Marker order comparison between Linkage Groups (LGs) from the haploid consensus map presented here and the Picea abies map from . Consensus LG I - LG XII are located on the x-axis from left to right. Lind et al. LG 1 - LG 12 are located on the y-axis from top to bottom. Each dot represents a marker comparison from the same scaffold, where black coloration represents the LG where the majority of marker comparisons are mapped. Gray coloration represents markers mapping to a different LG compared to the majority of markers. Turquoise coloration represents markers located on split scaffolds, which are indicative of assembly errors.

Circos plot of the consensus map. A) Marker distribution over the 12 linkage groups (LG I-LG XII). Each black vertical line represents a marker (21,056 in total) in the map and is displayed according to the marker positions in cM. Track B-C visualizes multi marker scaffolds, where each line is a pairwise position comparison of probe-markers from the same scaffold. B) Position comparisons of probe-markers from the same scaffold that are located on the same LG. Light gray lines indicate probe-markers that are located < 5cM from each other, dark gray lines indicate probe-markers located 5-10 cM apart and red lines indicate probe-markers >10 cM apart. C) Position comparisons of probe-markers from the same scaffold that are mapping to different LGs. Orange lines indicated probe-markers from the same scaffold split over 2 LGs, while dark blue lines indicated probe-markers split over 3 LGs.