Volume 21, Issue 3, Pages 834-844 (October 2017) Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus  Christian Rödelsperger, Jan M. Meyer, Neel Prabh, Christa Lanz, Felix Bemm, Ralf J. Sommer  Cell Reports  Volume 21, Issue 3, Pages 834-844 (October 2017) DOI: 10.1016/j.celrep.2017.09.077 Copyright © 2017 The Author(s) Terms and Conditions

Cell Reports 2017 21, 834-844DOI: (10.1016/j.celrep.2017.09.077) Copyright © 2017 The Author(s) Terms and Conditions

Figure 1 Genetic Linkage along P. pacificus Chromosomes A new genetic linkage map based on RNA-seq data from a cross between the P. pacificus reference strain PS312 and the wild isolate RSB001 from La Réunion Island. The linkage map was used to order and orient contigs along the six P. pacificus chromosomes. The x axis on the plot shows the physical position of ∼6,000 SNP markers along the chromosome and their corresponding genetic position on the y axis. Isolated, discontinuous signals are most likely due to genotyping errors or structural variations in the RSB001 strain. The light blue boxes in the background mark the contig boundaries. Cell Reports 2017 21, 834-844DOI: (10.1016/j.celrep.2017.09.077) Copyright © 2017 The Author(s) Terms and Conditions

Figure 2 Phylogenetic Relationships between Different P. pacificus Isolates Whole-genome resequencing data for 323 strains (Rödelsperger et al., 2014; McGaughran et al., 2016) was mapped to the new P. pacificus assembly. The tree shows a neighbor-joining tree based on ∼600,000 concatenated variable sites that could be genotyped in all strains. Individual subtrees define specific P. pacificus clades that roughly differ in 1% of their genomic sequences. All internal nodes have a bootstrap support of 100/100. Two extremely divergent strains of P. pacificus (RS5279 and JU723) have been used to root the tree, since previous genome-wide analysis including the sister species P. exspectatus has demonstrated that these two strains fall outside all known clades of P. pacificus (Baskaran and Rödelsperger, 2015). Cell Reports 2017 21, 834-844DOI: (10.1016/j.celrep.2017.09.077) Copyright © 2017 The Author(s) Terms and Conditions

Figure 3 Genome Architecture of P. pacificus The figure shows the six P. pacificus chromosomes arranged in a circular manner with the inner tracks displaying GC content, repeat content, gene density, and diversity at variable positions in two deeply sampled P. pacificus populations as calculated in non-overlapping 100-kb windows. The arms of all autosomes show higher levels of diversity and lower gene density, which is consistent with the previously observed negative correlation between gene density and diversity (Rödelsperger et al., 2014), suggesting background selection as a major factor shaping diversity in the P. pacificus genome. Cell Reports 2017 21, 834-844DOI: (10.1016/j.celrep.2017.09.077) Copyright © 2017 The Author(s) Terms and Conditions

Figure 4 Macrosynteny between P. pacificus and C. elegans (A) Positions of predicted one-to-one orthologs of C. elegans genes on the P. pacificus chromosomes were used to calculate the fraction of genes per 500-kb window that is orthologous to a given chromosome in C. elegans. The consistent coloring of chromosomes indicates strong conservation of macrosynteny between both species. P. pacificus chromosome I contains one part that is homologous to C. elegans chromosome V and another part that corresponds to C. elegans chromosome X. This indicates an ancient translocation between autosomes and sex chromosomes. (B) Conserved X chromosome genes as well as genes that have been subject to the aforementioned translocation are dispersed across the C. elegans X chromosome. (C) Comparison of macrosynteny with the remotely related nematode B. xylophilus identifies the same breakpoint region as in P. pacificus (a number of conserved C. elegans orthologs is shown to highlight the degree of macrosynteny). (D) Schematic phylogeny of nematodes used in this study (Holterman et al., 2006; Susoy et al., 2016). Comparative genomic and resequencing coverage analysis (Figure S1) indicates that the configuration in P. pacificus and B. xylophilus represents the ancestral configuration and that the translocation to the X chromosome has occurred along the branch leading to the ancestor of the Caenorhabditis as well as the strongylid (e.g., A. ceylanicum) lineage. Cell Reports 2017 21, 834-844DOI: (10.1016/j.celrep.2017.09.077) Copyright © 2017 The Author(s) Terms and Conditions