Additional file 1 of Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies
Creators: name: Orellana, Luis H.
name: Krüger, Karen
name: Sidhu, Chandni
name: Amann, Rudolf
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Average coverage and sequence diversity for SR and LR metagenomic samples. a. The estimated abundance-weighted average community coverage as determined in Nonpareil for each SR and LR metagenomic sample. For LR metagenomes, we first selected ~250 bp fragments from each LR and then used them to generate a model. Coverage was predicted from generated models and the original sequencing effort b. Sequence diversity (total diversity; Nd) as defined in Nonpareil. Figure S2. Read overlapping between short- and long-read metagenomic samples. The bars show the mapping of SR on LR for each time point. The dark shades indicate the mapped fractions, and the light shades show unmapped SR and LR. Figure S3. Assembly statistics for contigs generated using short- and long-read metagenomic samples. a. N statistics for contigs generated using SR and LR metagenomic samples. b. Distribution of sequencing depth (x-axis) for contigs generated using SR and LR metagenomic samples. Figure S4. Distribution of predicted protein lengths using different gene prediction tools vs. best hit match in UniProt TrEMBL. a Only predicted proteins &gt;= 100 amino acids were used for all comparisons. The boxplots show the quotients between the length of predicted proteins using FragGeneScan (FGS), MetaGenemark, and Prodigal and the best match in UniProt TrEMBL for the unassembled long-reads of the 2020-03-10 sample. b. Distribution of predicted protein lengths from contigs vs. best match in UniProt TrEMBL for the 2020.03.10 LR sample. Figure S5. Statistics for pairs of MAGs recovered from SR and LR metagenomes. a. Difference between the number of predicted genes in MAG pairs recovered in SR and LR metagenomic samples. The boxplot in the lower right corner summarizes the comparison of predicted genes for MAG pairs. b. GC content for pairs of SR and LR MAGs colored according to their class taxonomic affiliation. The right side of the plot shows histograms for the distribution of GC content values of MAGs belonging to Bacteroidia and Gammaproteobacteria class levels. The thick black line depicts the median value of the distribution. c,d. Relative abundance for all MAGs recovered (c) and pairs of 99% ANI MAGs (d). Colors represent the taxonomic affiliation of MAGs according to GTDB-tk. Figure S6. Relationship between relative abundances of MAG pairs in SR and LR metagenomes for each time point. Figure S7. Comparison of the breadth of the coverage vs. sequencing depth for cross-mapping of reads. The figures summarize the mapping of (a) short-reads on long-read derived MAGs and (b) long-reads on short-read MAGs. Uniquely detected species are colored according to the inferred taxonomy. The rest of the points represent MAG species detected in both technologies. The dotted purple line represents the expected breadth of coverage for a given level of sequencing depth, according to Lander and Waterman (1998). The letters indicate the novelty taxonomic level for each of the MAGs (p=phylum, c=class, o=order, f=family, g=genus, and the species level is omitted for clarity).