Additional file 1: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

Figure S1. Contamination check with Blobtools. Circles represent scaffolds, while their colors represent different Phyla. All putative contaminating scaffolds are false-positive and have H. glycines origins. The one outlier represents the mitochondrial scaffold, which was misassembled and collapsed to appropriate size. Table S1. Rates of read alignment to the genome for PacBio reads, RNA-seq, and Trinity transcripts. Table S2. Busco genes found in Complete, Single-copy, Duplicated, Fragmented, and Missing categories for assembled genomes in the Tylenchida. Figure S2. Globodera rostchiensis synteny. 439 syntenic regions were identified between G. rostochiensis and H. glycines. Green contigs are H. glycines, while blue contigs are G. rostochiensis. Figure S3. Globodera pallida synteny. 341 syntenic regions were identified between G. pallida and H. glycines. Green contigs are H. glycines, while blue contigs are G. pallida. Figure S4. Globodera ellingtonae synteny. 362 syntenic regions were identified between G. ellingtonae and H. glycines. Green contigs are H. glycines, while blue contigs are G. ellingtonae. Figure S5. Meloidogyne hapla synteny. 112 syntenic regions were identified between M. hapla and H. glycines. Green contigs are H. glycines, while blue contigs are M. hapla. Figure S6. Meloidogyne incognita synteny. 15 syntenic regions were identified between M. incognita and H. glycines. Green contigs are H. glycines, while blue contigs are M. incognita. Figure S7. Repeatmodeler contig alignments overlapping effector alignments in the genome. Three separate examples, with the top track representing final gene models, middle representing Repeatmodeler/Repeatmasker contig alignments, and the lower track representing known effector alignments. Figure S8. Motif analysis of effector sequences. The 80 known effector proteins were subjected to a MEME analysis, and motifs identified in 61 effector proteins implemented with FIMO to find effector candidates in the genome. Table S3. H. glycines genes previously shown to be acquired by horizontal gene transfer in closely related plant-parasitic nematodes. Figure S9. Network of interrelated tandemly duplicated genes. Connections indicate protein similarity, while the text represents the BLAST hits to NR for the three most highly connected nodes in each subnetwork (hexagons). Table S4. Repeatmodeler/Repeatmasker repeats identified in the H. glycines genome. Figure S10. Colocalized transposons, tandem duplications, and effectors. A. JBrowse display of scaffold_345, showing four tracks: Gene annotations, DNA transposons, 80 known effector alignments, and tandem duplications. The large transposon colocalizes with five tandem duplications, four of the 80 known effectors, and four genes annotated as effectors. B. A highly similar transposon on scaffold_97 with the same effector types present within and tandem duplications nearby. Figure S11. Principal components analysis of SNPs from 15 populations of H. glycines nematodes. Colors represent Hg-type, the capability to reproduce to a certain threshold on seven soybean cultivars. The labels by each circle represent the names of each population. Figure S12. Alternative splicing changes in isoforms for all genes in the genome. All isoforms containing an ORF in the transcriptome were analyzed for three biological groups, and all pairwise comparisons were considered to show the changes in transcript structures caused by alternative splicing. AS isoform structures are characterized by three types of annotations: intron retention, NMD (nonmediated decay), and effect on ORF. Figure S13. Alternative splicing changes in isoforms for all effectors in the genome. Effector isoforms containing an ORF in the transcriptome were analyzed for three biological groups, and all pairwise comparisons were considered to show the changes in transcript structures caused by alternative splicing. AS isoform structures are characterized by three types of annotations: intron retention, NMD (nonmediated decay), and effect on ORF. (DOCX 6288 kb