Sequence reads stringently filtered for quality were first assembled using SSAKE [ 50] to constitute a reference draft sequence.
Less stringently filtered reads were subsequently mapped onto the reference draft using MAQ [ 51], allowing the detection of SNPs.
The assembled sequences were aligned into corresponding scaffolds based on the reference draft genome sequence of Tanjil by Short Oligonucleotide Alignment Program (SOAP 2.20) [ 72].
As it was the simpler and less computationally intensive of our two best assembly strategies, we chose the postprocessed SPAdes assembly for our reference draft assembly.
To identify homologs, we performed sequence alignment searches using tBlastx of the flanking sequence for each of our mapped markers (cDNA contigs for new markers and ESTs for markers from Pritchard et al. [ 15]) against each reference draft genome assembly, with a threshold of E-value ≤ 10-3 and the default settings.
KM has contributed to the conception, design, intellectual analysis, acquisition of references, draft writing, and revision of the manuscript.
NMG carried out the survey of the literature, created the taxonomy, analyzed the references, drafted the manuscript, and identified th open issues and future challenges.
SM, HI, and AA have equally contributed to the conception, design, acquisition, and interpretations of references; drafting the manuscript and revising it critically for intellectual content; and have given final approval of the version to be published.
C-JW participated in the study with primary responsibility in conception and design drafting, overview the entire study, and data collection and analysis, literature review, reference search, draft writing and critically revised the manuscript and read proof of the final manuscript.
A comparison of the number of LCBs between reference and draft to the number between other genomes expected to show similar levels of rearrangement can provide an estimate of this effect.
Using the C3-41 chromosome as the reference, the draft genome sequences of 2297, LP1-G, SSII-1, NRS1693 and Bacillus sp. NRRL B-14905 were compared and mapped with BRIG (version 0.95) [ 41] and GBrowse (version 2.49) [ 42, 43], with the complete genomes of B. anthracis strain Ames, B. cereus strain AH187, B. thuringiensis strain BMB171, and B. subtilis strain 168 as outgroups.
