Derrick C. Scott
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter

◦ found in essentially all habitats
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter

◦ found in essentially all habitats

 Caulobacter thrive in low nutrient conditions and generally 

share the same phenotypic properties.
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter

◦ found in essentially all habitats

 Caulobacter thrive in low nutrient conditions and generally 

share the same phenotypic properties.

◦ Rod shaped and usually curved
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter

◦ found in essentially all habitats

 Caulobacter thrive in low nutrient conditions and generally 

share the same phenotypic properties.

◦ Rod shaped and usually curved

◦ Gram negative
 Alphaproteobacteria

◦ large and metabolically diverse group that includes the genus 

Caulobacter

◦ found in essentially all habitats

 Caulobacter thrive in low nutrient conditions and generally 

share the same phenotypic properties.

◦ Rod shaped and usually curved

◦ Gram negative

◦ Display rare dimorphic phenotype

 Wealth of information available to support cell cycle research

 Study of evolutionary biology of Caulobacters is minimal
 Despite ground breaking advances in the field of prokaryotic 

biology, there are many unanswered questions left to be 

studied that require the assembly of high quality bacterial 

genome sequences.

◦ Extensive Evolutionary Studies
 Despite ground breaking advances in the field of prokaryotic 

biology, there are many unanswered questions left to be 

studied that require the assembly of high quality bacterial 

genome sequences.

◦ Extensive Evolutionary Studies

◦ Comparison of Genomes 
 Despite ground breaking advances in the field of prokaryotic 

biology, there are many unanswered questions left to be 

studied that require the assembly of high quality bacterial 

genome sequences.

◦ Extensive Evolutionary Studies

◦ Comparison of Genomes 

◦ Proteomics
 Despite ground breaking advances in the field of prokaryotic 

biology, there are many unanswered questions left to be 

studied that require the assembly of high quality bacterial 

genome sequences.

◦ Extensive Evolutionary Studies

◦ Comparison of Genomes 

◦ Proteomics

→ Cannot be done without a high quality genome
 Despite ground breaking advances in the field of prokaryotic 

biology, there are many unanswered questions left to be 

studied that require the assembly of high quality bacterial 

genome sequences.

◦ Extensive Evolutionary Studies

◦ Comparison of Genomes 

◦ Proteomics

◦ Most genomes are in permanent draft status

◦ Traditionally has been labor intensive to sequence and finish 

assembling a genome

→ Cannot be done without a high quality genome
◦ PART 1: To find a way to quickly and reliably sequence and assemble 

a bacterial genome

◦ PART2: Use our new sequences to do evolutionary studies, genome 

comparisons, and gain insights into “genome scrambling”

◦ PART 3: Follow up with additional strains of Caulobacter using data 

from PART 1 and PART 2
Derrick C. Scott
 First Publicly Funded Human Genome Project

◦ 13 years and $3,000,000,000 (3 Billion) to complete
 First Publicly Funded Human Genome Project

◦ 13 years and $3,000,000,000 (3 Billion) to complete

 Currently in Development

◦ Less than 24 hours and $1,000 to complete
TECHNOLOGY PRICE
 Advantages and disadvantages associated with each individual 

technology 

 No one size fits all approach to a quality genome assembly.

 Researchers with no experience in bioinformatics will be attempting 

the process of genome assembly. 

◦ ME!
 These problems influenced us to compare the efficacy and accuracy 

of a panel of assembly programs that use input data derived from the 

GC-rich Caulobacter henricii
 We obtained a sample of the Caulobacter henricii bacterium 

from the American Type Culture Collection and extracted 

genomic DNA.


Adapted from Commins et al.
Adapted from Commins et al.


 Independently reached the same consensus 

build using two separate assembly algorithms.
 Positions reported of HGAP2 cut sites after 

Webcutter 2.0 analysis 
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion
 Predicted fragment sizes of HGAP2 build after 

enzymatic digestion VS Observed fragments 

after enzymatic digestion

 We found that software programs using only the MiSiq/454 

data provided accurate yet numerous contigs that did not 

result in a complete assembly. 

 The HGAP 2.0 assembler generated an accurate and 

complete de novo genome assembly of Caulobacter henricii 

using Pacific Biosciences RS II data. 

 So did the Celera 8.0 assembler by error correcting the 

PacBio RS II long reads with Illumina short reads (PBcR).
Derrick C. Scott and Bert Ely

Department of Biological Sciences, 

University of South Carolina, Columbia, SC, USA
 Caulobacter sp. K31

◦ Novel Caulobacter which was isolated from a research station in Finland.

 C. crescentus NA1000

◦ Laboratory strain derived from C. crescentus CB15 C. crescentus NA1000

 C. segnis strain TK0059

◦ Genome published in 2011

 C. henricii CB4

◦ Newly Sequenced for this Study

 Brevundimonas subvibrioides strain CB81

◦ Genome published in 2010

 Brevundimonas DS20 

◦ Newly Sequenced for this Study


NA1000 C. segnis CB4 K31 B. sub B. DS20

NA1000 100%

C. segnis 99% 100%

CB4 98% 98% 100%

K31 97% 97% 99% 100%

B. sub 93% 94% 93% 93% 100%

B. DS20 94% 95% 94% 93% 97% 100%

A comparison of 16S rRNA nucleotide sequences among the species included in this study 

(percent identity).
 16s region is relatively short

 Bacterial species often have multiple copies

 Most 16s in databanks are truncated

 16s tree sometimes not congruent with actual gene-gene homology
NA1000 C. segnis CB4 K31 B. sub B. DS20

NA1000 100%

C. segnis 88% 100%

CB4 82% 82% 100%

K31 83% 81% 84% 100%

B. sub 73% 75% 76% 73% 100%

B. DS20 75% 73% 76% 75% 79% 100%

A comparison of dcw cluster nucleotide sequences among the species included in this 

study (percent identity). 26 gene operon.
NA1000 C. segnis CB4 K31 B. sub B. DS20

NA1000 100%

C. segnis 96% 100%

CB4 90% 91% 100%

K31 90% 90% 93% 100%

B. sub 79% 79% 79% 80% 100%

B. DS20 80% 80% 80% 80% 86% 100%

A comparison of ribosomal protein operon nucleotide sequences among the species 

included in this study (percent identity). 28 gene operon.
NA1000 C. segnis CB4 K31 B. sub B. DS20

NA1000 100% N/A N/A

C. segnis 83% 100% N/A N/A

CB4 90% 84% 100% N/A N/A

K31 87% 87% 75% 100% N/A N/A

B. sub N/A N/A N/A N/A N/A N/A

B. DS20 N/A N/A N/A N/A N/A N/A

A comparison of conserved phage region nucleotide sequences among the species 

included in this study (percent identity). 20 gene operon.
 The nucleotide sequence differs by as much 

17% in pairwise 

 No significant identity in Brevundimonads

 Upon closer inspection, we found that there 

was significant amino acid identity among 

the genes in this region in all six genomes. 
 Caulobacter phage regions

◦ Codon usage bias for CTG (Leucine), GGG (Glycine), 

GCG (Alanine), and CGG (Arginine) 

 Brevundimonas phage region

◦ Bias towards CTC(Leucine), CGC (Glycine), GCC 

(Alanine), and CGC(Arginine)

 We were also able to locate an inversion event in the 

Brevundimonads that was absent in the Caulobacters. 

 Only found codon bias in phage region
MAUVE alignment of CB4 (top) and K31 

(bottom).
MAUVE alignment of CB4 (top) and K31 

(bottom).

MAUVE alignment of C. segnis TK0059 

(top) and CB4 (bottom)
 Previous studies have shown that Caulobacters exhibit an 

extremely high rate of genome rearrangement when compared to 

similarly related bacteria. 

 We found no correlation between relatedness and genome 

scrambling

 Scrambling did not disrupt the conservation of the essential 

genome

 More studies are needed to determine exactly what is responsible 

for the organized chaos that is genome scrambling in 

Caulobacters.