The rate and molecular spectrum of spontaneous mutations in the GC-rich multi-chromosome genome of
Burkholderia cenocepacia
Marcus M. Dillon, Way Sung, Michael Lynch, and Vaughn S. Cooper
Supporting Information
Daily Generations
26.4
26.2
26.0
25.8
25.6
25.4
25.2
25.0
24.8
0
50
100
150
200
250
Total Days of Mutation Accumulation
Figure S1 Estimates of the number of generations each line experienced per day, measured monthly over the course
of the MA experiment.
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Figure S2 Frequency distributions of the number of base substitutions (A) and indels (B) identified per line. Neither
2 = 1.81, p = 0.99; indels: 2 = 0.48, p = 0.92).
distribution differs significantly from a Poisson distribution
.
M. M. Dillon et al.
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18
Count of Identified Indels
16
14
12
10
8
6
4
2
0
0
0.2
0.4
0.6
0.8
Read Frequency of Shared Putative
Insertion-Deletion Mutations
1.0
Figure S3 Distribution of the full-coverage read frequencies leading to the identification of each insertion-deletion
mutation (indel) in this study. Full-coverage read frequency is the number of reads with >25 bases on each side of the
indel mutation that supported the call, divided by the total reads with >25 bases on each side of the indel.
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Number of Insertion-Deletion Mutations
30
25
20
15
10
5
0
0
5
10
15
20
Number of Lines Identifying Each
Insertion-Deletion Mutation
25
Figure S4 Distribution of the number of MA lines that identified each insertion-deletion mutation (location, size, and
motif) called in this study.
M. M. Dillon et al.
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A
OriC
OriC
OriC
Chr1
3.48 Mb
Chr2
3.00 Mb
Chr3
1.06 Mb
C
7
0.07
0.06
6
Evolutionary Rate (dN)
Normalized Expression
B
5
4
3
2
1
0.05
0.04
0.03
0.02
0.01
0
0
Chr 1
Chr 2
Chr 3
Chr 1
Chr 2
Chr 3
Figure S5 Chromosome size and expression (derived from RNAseq as described in (GOUT et al. 2013)) decline from
chromosome 1 (chr1) to chromosome 3 (chr3) (A,B), while evolutionary rate is lowest on chr1 and highest on chr3 (C)
(MORROW and COOPER 2012).
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M. M. Dillon et al.
Base Substitution Mutation Rate Per
Effective Genome Per Generation (x10 -4)
10 3
10 2
10 1
Bc
10 0
10 0
10 1
10 2
10 3
10 4
Effective Population Size (x10
10 5
4)
Figure S6 Relationship between base substitution mutation rate per effective genome size per generation and
effective population size (NE) in five multicellular eukaryotes (red), seven unicellular eukaryotes (black), and eight
prokaryotes (blue; B. cenocepacia – green) (SUNG et al. 2012). The log-linear regression is highly significant (r2=0.85,
p<0.0001, df=19).
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Conditional Relative Substitution Rate
1.4
atpD
lepA
trpB
1.2
gltB
phaC
gyrB
recA
1.0
0.8
0.6
0.4
0.2
0.0
A:T>G:C
G:C>A:T
A:T>T:A
G:C>T:A
Transitions
A:T>C:G
G:C>C:G
Transversions
Figure S7 Relative conditional substitution rates at seven B. cenocepacia loci (atpD, gltB, gyrB, lepA, phaC, recA, and
trpB). Relative conditional substitution rates are estimated by assuming that the most common nucleotide at each
site is ancestral and any deviation from that nucleotide is caused by a single mutation. Substitution rates were
calibrated to the nucleotide content at polymorphic sites for each gene, whereby only covered sites capable of
producing a given substitution are used in the denominator of each calculation.
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Ratio of Coding to Non-Coding
Substitutions
1.0
0.8
0.6
0.4
0.2
0
C
:A
:A
:G
:G
A:T
G:
>T :C>T T>C C>C
>
>
T
C
:
T
:
:
:
A
G
A
A:
G
G
Transitions
Transversions
Figure S8 The ratio of coding (Black) to non-coding (Grey) substitutions for each B. cenocepacia substitution type.
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File S1
SupplementaryTableS1andS2
File S1 is available for download as a .xls at
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References
GOUT J.-F., KELLEY THOMAS W., SMITH Z., OKAMOTO K., LYNCH M., 2013 Large-scale detection of in vivo transcription errors.
Proc. Natl. Acad. Sci. U. S. A. 110: 18584–9.
MORROW J. D., COOPER V. S., 2012 Evolutionary effects of translocations in bacterial genomes. Genome Biol. Evol. 4:
1256–1262.
RASMUSSEN T., JENSEN R. B., SKOVGAARD O., 2007 The two chromosomes of Vibrio cholerae are initiated at different time
points in the cell cycle. Embo J. 26: 3124–3131.
SUNG W., ACKERMAN M. S., MILLER S. F., DOAK T. G., LYNCH M., 2012 Drift-barrier hypothesis and mutation-rate
evolution. Proc. Natl. Acad. Sci. U. S. A. 109: 18488–18492.
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