Abstracts

Oral Presentation Abstracts
conformation capture techniques such as Hi-C
are used to measure long-range interactions of
DNA molecules in physical space. These tools
employ crosslinking of chromatin in intact
cells followed by intra-molecular ligation,
joining DNA fragments that were physically
nearby at the time of crosslink. Subsequent
deep sequencing of these DNA junctions generates
a genome-wide contact probability map
that allows the 3D modeling of genomic conformation
within a cell. The strong enrichment
in Hi-C signal between genetically neighboring
loci allows the scaffolding of entire chromosomes
from fragmented draft assemblies.
Hi-C signal also preserves the cellular origin
of each DNA fragment and its interacting partner,
allowing for deconvolution and assembly
of multi-chromosome genomes from a mixed
population of organisms. We have used Hi-C
to scaffold whole genomes of animals, plants,
fungi, as well as prokaryotes and archaea. We
have also been able to use this data to annotate
functional features of microbial genomes, such
as centromeres in many fungal species. Additionally,
we have applied our technology to
diverse metagenomic populations such as craft
beer, bacterial vaginosis infections, soil, and
tree endophyte samples to discover and assemble
the genomes of novel strains of known
species as well as novel prokaryotes and
eukaryotes. The high quality of Hi-C-based
assemblies allows the simultaneous closing of
numerous unculturable genomes, placement of
plasmids within host genomes, and microbial
strain deconvolution in a way not possible
with other methods. Reference: Burton JN*,
Liachko I*, Dunham MJ, Shendure J. Specieslevel
deconvolution of metagenome assemblies
with Hi-C-based contact probability maps. G3.
2014, May 22;4(7):1339-46.
n S6:3
NEXT GENERATION SEQUENCING OF
BRUCELLA MELITENSIS ISOLATES FROM
KUWAIT AND COMPARATIVE GENOME
ANALYSES
A. S. Mustafa, F. Shaheed, N. Habibi, M. W.
Khan;
Kuwait University, Jabriya, KUWAIT.
Human brucellosis is a zoonotic disease of
worldwide occurrence. In Kuwait, almost all
cases are caused by Brucella melitensis. Three
different strains (biovars) of B. melitensis have
been identified using classical techniques but
the presence of very limited variation across
strains makes it difficult to identify a particular
strain using the classical molecular methods,
e.g. PCR and Sanger sequencing. The aim of
this study was to exploit the potential of next
generation sequencing to identify the strain(s)
of B. melitensis present in Kuwait, and also
to find the extent of differences among the
isolates of the same strain by comparative
genome analyses. B. melitensis were isolated
from 15 patients suspected of human brucellosis.
The bacterial colonies from culture
plates were suspended in saline and heated at
95°C for 10 minutes. DNA released from the
bacterial cells were purified using the QIAamp
DNA Mini Kit (Qiagen). The isolated DNA
were quantitated and checked for purity using
a spectrophotometer (Epoch) and a fluorometer
(Qubit), respectively. DNA libraries were
prepared using the Nextera XT DNA Sample
Preparation Kit (Illumina) and sequenced using
the next generation sequence platform of
MiSeq (Illumina) using standard procedures.
The obtained sequence files were aligned to
the sequences of three known biovars of B.
melitensis available in the NCBI data base,
i.e. biovar 1 str. 16M, biovar 2 str. 63/9, and
biovar 3 str. Ether. The alignment and variant
calling were performed using ‘bwa mem’
and SAMtools/VCFtools, respectively. The
results showed that the genome size of all the
isolates was around 3.3 mega base pairs, and
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