Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains

Chidiebere Akusobi, Sanjeevani Choudhery, Bouchra S. Benghomari, Ian D. Wolf, Shreya Singhvi, Thomas R. Ioerger, Eric J. Rubin

Supplemental Tables

• Supplemental Table S1: M. abscessus clinical isolates and characteristics.
• Supplemental Table S2: Genome sequencing statistics.
• Supplemental Table S3: Pangenome analysis by Ptolemy (clustering of genes across isolates, i.e. panorfs).
• Supplemental Table S4: Summary of TnSeq data for Mab clinical isolates.
• Supplemental Table S5: Correlation of transposon insertion counts between replicate libraries.
• Supplemental Table S6: Essential genes among mutual orthologs between M. abscessus ATCC 19977 and M. tuberculosis H37Rv.
• Supplemental Table S7: Calls of essential genes by HMM in each Mab strain.
• Supplemental Table S8: Analysis of conditionally-essential genes in each strain compared to ATCC 19977 using the resampling method.
• Supplemental Table S9: ANOVA analysis - genes exhibiting variability of fitness (insertion counts) across Mab clinical isolates.
• Supplemental Table S10: PCA analysis - top 20 genes that separate subspecies.
• Supplemental Table S11: PCA analysis - top 20 genes that contribute to variation in Cluster 1 (T35, T37, T50 and T5).
• Supplemental Table S12: Correlation analysis - pairs of genes with siginificant correlation of insertion counts across the 21 isolates.
• Supplemental Table S13: Network analysis using Cytoscape - clustering of genes into communities.

Raw Genome Assemblies using Abyss

• Genomes were assembled de-novo using Abyss, producing multiple contigs.
• Contigs were sorted by size, dropping those smalled than 1kb. (header lines begin with contig numbers)
• Annotations were produced by RAST.
  • *RAST_ORFs.txt files are effectively .gff format
  • ORF ids are assigened uniquely within and between strains as "peg" ids)

Scaffolded Genome Assemblies

• Full-length genomes were generated by Blasting contigs to M. abscessus ATCC 19977 and concatenating them in syntenic order.
• *.mabs_mod.prot_table files contain annotations based on the ATCC 19977 with conventional ORF ids (like MAB_0001), with adjusted ORF coordinates.
• The format of prot_tables is simple tab-separated text files:
  • Col1=description, Col2=start, Col3=end, Col4=strand, Col8=gene name, Col9=ORF id
• Some ORFs might have been dropped if either terminus was deleted.