Additional file 1 of High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing
Creators: name: Urban, John M.
name: Foulk, Michael S.
name: Bliss, Jacob E.
name: Coleman, C. Michelle
name: Lu, Nanyan
name: Mazloom, Reza
name: Brown, Susan J.
name: Spradling, Allan C.
name: Gerbi, Susan A.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1 : Supplemental Figure S1: Comparing evaluations of short read assemblies to long read assemblies. Supplemental Figure S2: Assembly ranking correlation matrices. Supplemental Figure S3: Filtering out non-Arthropod, contaminating reads using Taxonomy- annotated GC plots. Supplemental Figure S4: Length Distributions for Illumina Scaffolds, PacBio Reads and MinION Molecules. Supplemental Figure S5: Percent identity of MinION reads compared to a PacBio-only assembly. Supplemental Figure S6: Evaluations across Quiver polishing rounds. Supplemental Figure S7: Blended assemblies with both PacBio and MinION data tended to receive better ranks than PacBio-alone assemblies. Supplemental Figure S8: Metrics comparing assemblies after scaffolding. Supplemental Figure S9: Aligning chosen and discarded scaffolds from each assembler (Canu and Falcon). Supplemental Figure S10: BlobTools analysis of the Canu scaffolds. Supplemental Figure S11: BlobTools analysis and anchoring Falcon scaffolds. Supplemental Figure S12: The single locus that contains the full-length Escribá insert. Supplemental Figure S13: Pairwise comparisons of final Canu and Falcon scaffolds. Supplemental Figure S14: Pairwise comparisons of final Canu and Falcon annotations. Supplemental Figure S15: Dosage compensation of X-linked genes in Sciara coprophila. Supplemental Figure S16: Distribution of DNA modifications across Sciara genome (PacBio analysis). Supplemental Figure S17: Position weighted 7-mer motifs learned from different filtering and different subsets of the genome sequence (PacBio analysis). Supplemental Figure S18: MEME motifs in the PacBio and MinION analyses. Supplemental Figure S19: MinION signal distributions for 6mers defined by motifs learned in the PacBio analysis and negative controls. Supplemental Figure S20: The GCG trimer is depleted in the genome and transcriptome compared to expectation. Supplemental Figure S21: Distribution of distances between adjacent DNA modifications (PacBio analysis) on the same strand shows enrichment of short distances, a 10 bp periodicity, and a spike of enrichment at mono-nucleosome lengths of ~ 175 bp. Supplemental Figure S22: Distribution of distances between adjacent DNA modifications (PacBio analysis) on either strand also shows enrichment of short distances, a 10 bp periodicity, and a spike of enrichment at mono-nucleosome lengths of ~ 175 bp for 6mA and 5mC. Supplemental Table S1 A-E: Expected genome and chromosome sizes. Supplemental Table S2: RNA-seq samples spanning both sexes and 4 life cycle stages. Supplemental Table S3: Short read assembly size statistics. Supplemental Table S4: Long read assembly size statistics. Supplemental Table S5: Pairwise comparisons of size statistics of hybrid scaffolds from pair of Canu or Falcon assemblies. Supplemental Table S6: Size statistics of Canu C3.2 across the work flow. Supplemental Table S7: Size statistics of Falcon F9 across the work flow. Supplementary Table 8 A-C: Gap size statistics. Supplemental Table S9: Bacterial contig statistics in each assembly. Supplemental Table S10: Sciara (Bradysia) coprophila repeat family classes from RepeatModeler. Supplemental Table S11: Sub-classification of classified Repeat Families found in Sciara coprophila genome with RepeatModeler. Supplemental Table S12 A-B: Repeat Masking on Canu. Supplemental Table S13 A-B: Repeat Masking on Falcon. Supplemental Table S14: Transcriptome Evaluations. Supplemental Table S15 A-B: Maker Annotation Transcript Evaluations on Canu and Falcon. Supplemental Table S16: Additional characterization and comparisons of the final annotations of Canu and Falcon assemblies. Supplemental Table S17 A-C: Putative Sciara homologs for proteins involved in reading, writing, and erasing DNA methylation marks for adenine and cytosine. Supplemental Table S18 A-F: DNA modification percentages in male embryonic genomic DNA. Supplemental Table S19: Which dimers are observed with modifications more often than expected?. Supplemental Table S20: Which trimers are observed with modifications more often than expected?. Supplemental Table S21 A-F: Binomial tests for enrichment or depletion of DNA modifications in various genomic features. The Supplement also contains detailed experimental and bioinformatic methods sections, as well as software versions and supplemental references.