Additional file 5: Figure S2. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Graphs of recombination rates across 15 of the 16 walnut physical maps. We indicate the location of synteny gap on each physical map as a thick horizontal bar. (PDF 311 kb

Additional file 1: Table S1. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Excel spreadsheet listing 1,525 SNP markers and their locations on the genetic maps of the 16 walnut chromosomes. (XLSX 106 kb

Additional file 7: Table S5. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Pairs of syntelogs and their annotations used for estimation of Ks. (DOCX 16.3 kb

Additional file 6: Table S4. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Numbers and percentages of walnut cdBES collinear with genes in the grape and poplar pseudomolecules located in SBs duplicated in the walnut genome. (DOCX 19.0 kb

Additional file 8: Table S6. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Characteristics and locations of gaps larger than 8 cM in the 16 walnut linkage groups. (DOCX 16.2 kb

Additional file 3: Table S2. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Excel spreadsheet listing all 1,031 BAC contigs including the nested BAC contigs that were removed from the physical map to generate a non-redundant physical map. (XLSX 57.6 kb

Additional file 2: Figure S1. of Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Graphical presentation of 16 walnut linkage groups. (PDF 1.09 mb

Contig assembly error identification through genome map comparison.

<p>The top line represents the <i>in silico</i> map for the original sequence assembly, the majority of which is covered by a single sequence contig. The genome map matches on the left and right sides of the contig (shown with shaded boxes). ∼3 kb of sequence was incorrectly inserted into the contig during assembly.</p

Two-color genome mapping with two enzymes.

<p>A. The DNA backbone is stained with YOYO-1 and loaded into the port of a nanochannel array chip. The DNA molecules are introduced into the region with pillars and micron-scale relaxation channels by an electric field where they unwind and linearize. Finally, they are moved into the 45 nm nanochannels, where they stretch uniformly to 85% of the length of perfectly linear B-DNA. B. Linearized BAC DNA molecules in nanochannels. The DNA molecule is stained with YOYO-1, and Nt.BspQI and Nt.BbvCI nicks are labeled with green and red dyes, respectively. C. Molecule length and nick locations are extracted from the images by custom image-analysis software. By clustering individual molecules with high similarity of green label patterns, distinct patterns are extracted (top panel). The locations of the red labels are then overlaid on the green label patterns (middle pattern). A histogram plot of the above clusters is shown in the bottom panel. The peaks represent the location of each sequence motif (GCTCTTC and CCTCAGC) along the linearized DNA molecules. D. Consensus maps for individual BAC clones are shown. Consensus maps are combined by using overlapping patterns, and the final genome map is shown at the bottom. E. The clone map from genome mapping is shown at the top and the full genome map as a grey bar with Nt.BspQI and Nt.BbvCI motif locations in green and red. Below the genome map, in blue, is the physical map from SNaPshot fingerprinting. The total length of the genome map is 2.1 Mb.</p

Deletion of incorrect contigs in genome map-guided <i>de novo</i> sequence assembly.

<p>The original assembly contained two Nt.BspQI sites and ∼8 kb of sequence that were absent from the genome map. The top image is output from gsAssembler and shows the scaffolding of contigs using paired-end reads. The green line represents the sequence coverage for each region. Paired-end reads are represented by pink (high coverage) and aqua (low coverage) carrots (□). The three contigs with red bars beneath them contain the extra sequence motifs and total sequence consistent with the predicted incorrect scaffold. They also contain weak paired-end data indicating that the contigs are misplaced. The bottom line shows the sequence assembly after deletion of the three contigs with red bars.</p