Supplemental Material for Chhotaray et al., 2019

Supplementary sheet 1 contains details of Illumina sequencing library
preparations and Bioinformatics analysis of sequencing
data. Figure S1 contains the KEGG Classification annotation statistics of MabS and
MabR whereas Figure S2 contains the COG
classification annotation statistics of MabS and MabR. Figure
S3 and Figure S4 contain the pan-genome and core genome phylogeny of 25
complete genome sequences of M. abscessus species respectively. Figure S5 contains gelelectrophoresis of plasmids extracted from M. abscessus clinical
strains. Figure S6 contains the maps representing the circular
visualization of insertions and deletions in MabR (CP034191) and MabS
(CP034181). Table S1 contains the annotations and related data for linear
plasmid pMabS_GZ002 gene. Table S2 contains the information
about the variation in methylation sites in the genes of interest between two
clinical strains of M. abscessus. Table
S3.1, Table S3.2, and Table S3.2, contain the information about the gene content in the inserted and deleted regions (Reference vs MabR), (Reference vs MabS), (MabS
vs MabR), respectively. Table S4 contains the
information about the drug susceptibility of M. abscessus isolates. Table
S5 contains statistics of PF data generated by Illumina sequencing. Table S6 contains the
statistics of clean data after quality control. Table
S7 contains the proportion of statistics of the
clean data compared to PF data after quality control. Table S8 contains
the genome alignment
statistics of two M. abscessus clinical
strains obtained from Illumina
sequencing. Table S9 contains the raw reads statistics of two of M. abscessus clinical strains generated
from single molecule Real-Time (SMRT) sequencing. Table S10 contains the genome
assembly statistics of two M. abscessus clinical
strains obtained from single molecule Real-Time (SMRT) sequencing. File Xls S1
contains result of structural variation
analysis. File Xls S2 contains the information about the identified SNVs, each
motif’s methylation site, methylation score, type of methylation, and all locations of discovered motifs in strains, motif
information of pMabS_GZ002 plasmid, identified methyltransferase in both
strains. File Xls S3 contains the statistics of the 25 available
complete genomes of M. abscessus used
for pan-genome analysis. File Xls S4 contains the statistics number of
accessory genes, unique genes as well as exclusively absent genes determined
among the M. abscessus species. MabS.h5
and MabR.h5 contain the raw files of methylome analysis of MabS
and MabR.h5, respectively.