ASSIGNMENT OF GENOMICS

NAME OF THE GROUP

1.
ABERU DABA
2.
GENET TSEGA

ID.NO.

BDU0901121PR
BDU0901135PR
SUBMMITED TO Dr. BIZUAYEHU

BACTERIAL GENOME
ATLAS BACMAP
INTRODUCTION

Introduction
A genome can be more than one DNA molecule.
Approximately 10% of the bacterial genomes
sequenced so far have more than one chromosome.
By definition a genome includes all chromosomes (and
plasmids) that constitute an organisms total DNA.
Chromosomes are essential, single-copy,
independently replicating DNA molecules present in
each member of
the species. Some species contain plasmids; these are
frequently strain-specific and sometimes (incorrectly, in
our opinion) omitted from a genome sequence.

Contd

The largest bacterial genome sequenced is that of

Solibacter usitatus(strain Ellin 6076), a soil bacterium
belonging to the Acidobacteria. It consists of a single
chromosome of 9.97 mega basepairs (Mbp).

The smallest bacterial genome known is that of

Carsonella ruddii (PV), an endosymbiont of a plant
sap-feeding insect with a mere 159,662 bp.

Genome size is a rough indicator of biological

adaptive potential so it is no surprise that soil
bacteria have bigger genomes, as they have to adapt
to environmental variation, whereas the protective
niche of an endosymbiont allows for small genome.

Visualization of Genomic
Data: The Genome Atlas

Genome atlases are circular plots of chromosomes

or plasmids (a linear version is available when
applicable) on which general properties of the DNA
molecule are plotted as colors.
Genome atlases are available from our web server
for many of the currently sequence bacterial
genomes.
2

CONTD

Figure 1 shows a Genome Atlas for the

chromosome of Geobacillus kaustophilus strain
HTA426 (a thermophilic Firmicute that also contains
a plasmid of 4.8 kb).
This isolate was obtained from a deep sea sediment
of the Mariana Trench in the Pacific Ocean (Takami
et al., 2004a, b).
Its genome is 3.5 Mbp long and contains 52.1%
GC. G. kaustophilus.

Contd

A Genome Atlas maps four different aspects of the

chromosomal DNA sequence in various lanes in a
standard manner:
DNA structural features are represented in the
three outer lanes, all coding sequences are
indicated in the next lane, two kinds of repeats are
mapped in the next two lanes, and base
composition properties are plotted in the two
innermost lanes (Jensen et al., 1999). The scale in
the center corresponds with the sequence
numbering in GenBank.

contd
The DNA structural features of the three outermost
circles
are based on the physical chemical properties of the
DNA helix. The annotated genes are given
in blue for protein-coding genes oriented clockwise, and
red for genes on the other strand
(counterclockwise). The tRNA and rRNA genes have
their own color. The clockwise strand
corresponds with the sequence stored in GenBank
(genes on the other strand are annotated as
complement in there).

 A Genome atlas combines a number of features in

one single figure that summarizes a very long and
detailed story about a chromosome or plasmid.

Comparing the Coding Fraction of

Genomes

The typical coding density for a bacterial genome is

about 90%, ranging from 95%
for Pelagibacter ubique (an alpha-proteal marine
bacterium that counts to the most numerous bacteria
in the world) (Giovannoni et al., 2005) to around 75%
for M. acetivorans.

Intracellular bacteria can have a coding density as

low as 50%.

CONTD
This means the majority of bacterial DNA codes for
genes, which mostly are not spliced so that introns
are absent (with very few exceptions).
However, not every open reading frame is a gene,
and it appears that many bacterial genomes are overannotated, predicting 1015% more genes than are
real (Skovgaard et al.,2001).
These over-annotated genes are frequently short
open reading frames.

In addition, genes can be missed in the annotation.

A frequent mistake is that genes are annotated on
the wrong strand, which can happen if the reading
frame is open in either direction.
The intergenic regions separating genes regulate
transcription,and in intracellular bacteria frequently
contain pseudogenes or repeats.

Genes not coding for proteins include tRNA and rRNA

genes, and some parts of intergenic regions can be
transcribed into stable RNA that are transcribed but
do not code for proteins.
E. coli contains several hundred small non-coding
RNA genes (ncRNA) (Chen et al., 2002) that can act
as regulators (Gottesman, 2005).

THANK YOU!!!