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Basic Local Alignment Search Tool, the most common (Altschul et al., 1990). However
BLAST is not automatically suitable for large DNA input segments such as complete
genomes. A more suitable program to align sequences in the range of megabases is Mummer,
developed at TIGR, of which version 3 is now publicly available (Kurtz et al., 2004). Further,
this method has been recently extended to include the average nucleotide identity in the
conserved core genes of a set of genomes (Deloger et al., 2009). Moreover, graphical representation
of the resulting alignment becomes an issue. Specific tools have been designed to align
genome sequences and visualize such events. The Artemis Comparison Tool (ACT) is worth
mentioning of which two versions are available: a downloadable version to be used on a local
computer (Carver et al., 2005) and a web-based version with pre-computed comparisons
between several hundred bacterial genomes. 3 BLAST results of entire bacterial chromosomes
against each other have also been used to construct phylogenetic trees (Henz et al., 2005). Blast
comparisons will be treated in Section 7 of this chapter.
5 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%. 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 over-annotated, predicting 10–15% 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). Their role in environmental bacteria is virtually
unexplored.
Although tRNA and rRNA genes are essential to life, they are sometimes missed in the
annotation of a genome, a rather embarrassing omission, or occasionally annotated on
the wrong strand (Lagesen et al., 2007). The number and location of rRNA operons in a
genome can say something about an organism. It appears that organisms with short doubling
times have larger numbers of rRNA and tRNA genes. Comparing > Figs. 2 and 3 it is
likely that G. kaustrophilus with 9 rRNA copies, nearly all located close to the origin of
replication (which boosts expression during replication as their copy number increases) can
divide more quickly than M. acetivorans which only has three copies. Some really fast-growing
bacteria can have 14 or more rRNA copies, as can be viewed from our list of genomes. 4
3 http://www.webact.org/WebACT/home
4 www.cbs.dtu.dk/services/GenomeAtlas/
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