Large read mapping of TN10 cDNA sequences to the HgSLP-1 genomic sequence.

<p>The Y-axis shows depth of mapped cDNA coverage (99% identical with 99%overlap of each read) and the X-axis indicates the base position along the <i>HgSLP-1</i> gene. The numbers mark the exons of <i>HgSLP-1</i>.</p

Protein gel blot of HgSNARE-like protein (HgSLP-1) and soybean α-SNAP protein expressed in <i>E</i>. <i>coli</i>. Proteins in lanes 1–5 were detected using an antibody that binds to HgSLP-1.

<p>Proteins in lanes 6–9 were detected using an antibody that binds to soybean α-SNAP. Lanes 1 and 6 contain purified protein from <i>E</i>. <i>coli</i> co-expressing full size HgSLP-1 and soybean α-SNAP. Lane 2, 3, 7, and 8 contain independent replicates of proteins purified from <i>E</i>. <i>coli</i> co-expressing HgSLP-1 missing its signal peptide and soybean α-SNAP. Lanes 4 and 9 contain purified protein from <i>E</i>. <i>coli</i> that only expresses full sized HgSLP-1. Lane 5 contains total protein from <i>E</i>. <i>coli</i> that only expresses full sized HgSLP-1. Protein sizes are shown in kDa.</p

SCN genetic linkage groups containing SCN SNPs linked to virulence.

<p>The left column has the map distance in centimorgans and the right column shows the SNP number. The SCN SNPs that show an allelic imbalance when grown on resistant and susceptible soybean plants are shown in red.</p

Immunolocalization of HgSNARE-like protein-1 (HgSLP-1).

<p>Panels A—D are 40 x light field images matched with corresponding epiflorescent images of sections of SCN in soybean roots stained using HgSLP-1 antibodies. Arrows point to the basal cell of a subventral esophageal gland in A, the median bulb and esophageal lumen in B and the stylet in C. Panel D shows negative control sections lacking HgSLP-1 antibody staining in the nematode. Arrows in D point to the basal cell of an esophageal gland and the stylet. Panel D is a composite of two sequential sections from the same nematode. For all light field images, 20 micron scale bars are shown.</p

Quantitative PCR of <i>P</i>. <i>dendritiformis</i>-like gene (<i>HgSLP-1)</i> genomic copy number relative to <i>HgFAR-1</i> in inbred SCN strains, TN10, TN20 OP25, OP20 and OP50.

<p>Quantitative PCR of <i>P</i>. <i>dendritiformis</i>-like gene (<i>HgSLP-1)</i> genomic copy number relative to <i>HgFAR-1</i> in inbred SCN strains, TN10, TN20 OP25, OP20 and OP50.</p

Multiple sequence alignment of the HgSLP-1 SNARE domain to related t-SNARE proteins.

<p>The **marks the zero layer residue (red) critical for membrane fusion and * indicates conserved hydrophobic residues (green) in the flanking heptad repeat domains. The following sequences are in the alignment: 1). Locus: 2NPS_B; protein name: chain B; crystal structure of the early endosomal SNARE complex; accession: 2NPS_B; organism: <i>Rattus norvegicus</i> (Norway rat). 2). Locus: HgSLP; protein name: <i>Heterodera glycines</i> SNARE-like protein 1; accession: KM575849; organism: <i>Heterodera glycines</i> (soybean cyst nematode). 3). Locus: SYP24_ARATH, protein name: putative syntaxin-24; accession: Q9C615; organism: <i>Arabidopsis thaliana</i> (thale cress). 4. Locus: Q9SML5_CAPAN; protein name: syntaxin t-SNARE; accession: Q9SML5; organism: <i>Capsicum annuum</i> (peppers). 5). Locus: Q8S4W4_PORYE; protein name: Syntaxin PM. Accession: Q8S4W4; organism: <u><i>Pyropia yezoensis</i></u> (marine red alga). 6). Locus: SYP72_ARATH; protein name: Syntaxin-72; accession: Q94KK6; organism: <i>A</i>. <i>thaliana</i>. 7). Locus: BET1L_RAT; protein name: golgi SNARE 15 kDa; accession: O35152; organism: <i>R</i>. <i>norvegicus</i>. 8). Locus: SNP30_ARATH; putative SNAP25 homologous protein SNAP30; accession: Q9LMG8; organism: <i>A</i>. <i>thaliana</i>. 9). Locus: O44419_STRPU; Protein name: Synaptosomal-associated protein 25; accession: O44419; organism: <i>Strongylocentrotus purpuratus</i> (purple sea urchin). 10). Locus: O01389_HIRME; protein name: SNAP-25 homolog; accession: O01389; organism: <i>Hirudo medicinalis</i> (medicinal leech).</p

Alignment of paired SOLiD DNA sequencing reads from SCN inbred strain TN20 to the scaffold 385 reference sequence derived from TN10 genomic sequence.

<p>The Y-axis shows depth of coverage and the X-axis indicates the base position along the scaffold. The <i>P</i>. <i>dendritiformis</i>-like gene (<i>HgSLP-1</i>) spans bases 17816 to 21445.</p

Synteny between <i>Glycine latifolia</i> linkage groups and <i>G. max</i> chromosomes.

<p>Sequences containing mapped <i>G. latifolia</i> SNPs were aligned to the <i>G. max</i> genome sequence. <i>Glycine latifolia</i> linkage groups (top) and physical maps for each <i>G. max</i> chromosome (bottom) are displayed as linear arrays. Vertical and diagonal lines connect genetic and physical locations of SNP markers between the two species.</p

Comparison of F₂, F₅ and merged linkage maps for GBS SNP markers for <i>Glycine latifolia</i> linkage groups 1 and 20.

<p>Orders of SNP markers were very similar between the F₂ and F₅ populations. In some cases, markers that segregated in the F₂ population co-localized in the F₅ population, which may have resulted from errors in calling heterozygous loci in the F₂ population. While linkage group 1 showed a high level of collinearity with <i>G. max</i> chromosome 1, linkage group 20 had regions of collinearity with multiple <i>G. max</i> chromosomes. Even so, there was good agreement in marker order between the F₂ and F₅ populations for linkage group 20. Markers were named for the <i>G. max</i> chromosome and the nucleotide position on the chromosome (×10⁻⁶) to which the SNP-containing sequences aligned. Markers that did not align to a <i>G. max</i> chromosome were named for the <i>G. latifolia</i> scaffold containing the SNP.</p

Comparison of synteny of individual <i>Glycine latifolia</i> linkage groups 7, 10 and 20 with <i>G. max</i> and <i>Phaseolus vulgaris</i> chromosomes.

<p><i>Glycine latifolia</i> linkage groups (A & B) and <i>G. max</i> chromosomes (C) are placed at the top of each circle with colored lines connecting positions of <i>G. latifolia</i> SNP markers (A & B) or <i>G.max</i> gene model (C) sequences to positions in <i>G. max</i> (Gm01 – Gm20) or <i>P. vulgaris</i> (PV01 – PV11) chromosomes, represented by gray boxes. <i>Glycine latifolia</i> linkage groups 7 and 20 appeared to have larger syntenic blocks with single <i>P. vulgaris</i> chromosomes than <i>G. max</i> chromosomes. Both <i>G. latifolia</i> linkage groups 10 and 20 showed large blocks of synteny with <i>P. vulgaris</i> chromosome 7, as did <i>G. max</i> chromosome 10. Synteny maps were constructed using MizBee <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099427#pone.0099427-Meyer2" target="_blank">[42]</a>.</p