Science Advances

Supplementary Materials

The PDF file includes:

  • Supplementary Materials and Methods
  • Fig. S1. Cumulative contig coverage (Mb) as a function of contig length for different PacBio/Illumina assembly strategies.
  • Fig. S2. Read span coverage as a function of read span size bins for Hi-C data summed over two Hi-C libraries.
  • Fig. S3. Mummer dot plot for chromosome 3 assemblies.
  • Fig. S4. Hi-C scaffolding results in chromosome-sized scaffolds that are considerably longer than the raw contigs.
  • Fig. S5. A comparison of a P. maniculatus linkage map (orange) and the P. leucopus genome (blue).
  • Fig. S6. The Hi-C contact map for the region near the putative chromosome 16 and 21 fusion.
  • Fig. S7. Rat syntenic groups associated with the chromosome 16 and 21 fusion.
  • Fig. S8. P. leucopus synteny with rat.
  • Fig. S9. P. leucopus synteny with rat with P. leucopus chromosomes reordered to reflect the scaffold numbers produced by 3d-dna.
  • Fig. S10. DEGs between tissues.
  • Fig. S11. SNPs and INDELs identified by aligning Illumina reads from the reference individual back to the assembly.
  • Fig. S12. Selected tracks from the Santa Cruz Browser genomehub interface for IL-6.
  • Table S1. Chromosome-sized scaffold lengths and names.
  • Table S2. Summary of the RepeatMasker analysis of the P. leucopus genome.
  • Table S3. Summary of gene predictions.
  • Table S4. Samples used in the tissue RNA-seq experiment.
  • Table S5. Gene Ontology categories showing change between tissues.
  • Legends for tables S6 and S7
  • Table S8. R2 as a function of distance for chromosome 10 SNPs.
  • Table S9. Resources.
  • References (3373)

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Other Supplementary Material for this manuscript includes the following:

  • Table S6 (.csv format). DEGs in the blood following infection with B. burgdorferi.
  • Table S7 (.csv format). DEGs in the skin following infection with B. burgdorferi.

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