10.25387/g3.10251044.v2
Chiranjibi Chhotaray
Chiranjibi
Chhotaray
Shuai Wang
Shuai
Wang
Yaoju Tan
Yaoju
Tan
Amjad Ali
Amjad
Ali
Muhammad Shehroz
Muhammad
Shehroz
Cuiting Fang
Cuiting
Fang
Yang Liu
Yang
Liu
Zhili Lu
Zhili
Lu
Xingshan Cai
Xingshan
Cai
H.M. Adnan Hameed
H.M. Adnan
Hameed
Md Mahmudul Islam
Md Mahmudul
Islam
Goverdhan Surineni
Goverdhan
Surineni
Shouyong Tan
Shouyong
Tan
Jianxiong Liu
Jianxiong
Liu
Tianyu Zhang
Tianyu
Zhang
Supplemental Material for Chhotaray et al., 2019
GSA Journals
2019
Mycobacterium abscessus
SMRT sequencing
comparative genomics
whole genome sequencing
methylation
single nucleotide variation
Genomics
Infectious Diseases
Microbial Genetics
Microbiology
2019-11-21 17:57:06
Dataset
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Chhotaray_et_al_2019/10251044
<p>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 Mab<sup>S </sup>and
Mab<sup>R</sup> whereas Figure S2 contains the COG
classification annotation statistics of Mab<sup>S </sup>and Mab<sup>R</sup>. Figure
S3 and Figure S4 contain the pan-genome and core genome phylogeny of 25
complete genome sequences of <i>M. abscessus </i>species respectively. Figure S5 contains gelelectrophoresis of plasmids extracted from <i>M. abscessus </i>clinical
strains. Figure S6 contains the maps representing the circular
visualization of insertions and deletions in Mab<sup>R</sup> (CP034191) and Mab<sup>S</sup>
(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 <i>M. abscessus</i>. 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 Mab<sup>R</sup>), (Reference vs Mab<sup>S</sup>), (Mab<sup>S
</sup>vs Mab<sup>R</sup>), respectively. Table S4 contains the
information about the drug susceptibility of <i>M. abscessus</i> isolates.<b> </b>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 <i>M. abscessus </i>clinical
strains obtained from Illumina
sequencing. Table S9 contains the raw reads statistics of two of <i>M. abscessus </i>clinical strains generated
from single molecule Real-Time (SMRT) sequencing. Table S10 contains the genome
assembly statistics of two <i>M. abscessus </i>clinical
strains obtained from single molecule Real-Time (SMRT) sequencing. File Xls S1
contains<b> </b>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 <i>M. abscessus </i>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 <i>M. abscessus </i>species. MabS.h5
and MabR.h5 contain the raw files of methylome analysis of Mab<sup>S
</sup>and MabR.h5, respectively.</p>
<p> </p>
<p> </p>