Intragenome variability

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Intragenome 16S rRNA gene variability

An analysis of the 230 completely sequenced bacterial genomes currently available (June 2005), reveals that a significant minority of bacteria have more than one copy of the 16S rRNA gene (Fig. 1).

Figure 1. Variation in the number of 16S rRNA genes found within currently sequenced genomes (June 2005).

Members of the Gammaproteobacteria and Firmicutes seem to be particularily prone to this phenomenon (Fig. 2), although this may well reflect the current bias towards these bacteria within the database.

Figure 2. Variation in the number of 16S rRNA genes found within currently sequenced genomes, broken down by phylum (June 2005).

Slight sequence variations are often noted between 16S rRNA genes from the same genome. In a few cases this intra-genomic variation can be surprisingly high (Fig. 3). Seven bacterial genomes have so far been recognised with intra-genomic variation between 16S rRNA gene that exceeds that normally observed between many bacterial species and even some genera (Table 1). Many of these instances appear to be the consequence of some naturally occurring recombinative event, possibly the consequence of horizontal gene transfer (Fig 4.).

Figure 3. Amount of variation recorded between intragenomic 16S rRNA genes (data from Acinas et al., 2004).

Table 1. Bacteria reported to exhibit particularly large variations between 16S rRNA gene copies.

Bacterium	Variation between 16S rRNA genes	Reference
Haloarcula marismortui (Fig. 4)	5.6%	Mylvaganam and Dennis, 1992, Denis et al., 1998, Boucher et al., 2004
Halosimplex carlsbadense	6.9%	Boucher et al., 2004
Natrinema sp. strain XA3-1	5.4%	Boucher et al., 2004
Thermobispora bispora	7.8%	Wang et al., 1997
Thermoanaerobacter tengcongensis	11.5%	Acinas et al., 2004
Thermomonospora chromogena	7.4%	Yap et al., 1999
Ochrobactrum intermedium	4.6%	Teyssier et al., 2003

Figure 4. Variation between 16S rRNA genes 1 and 2 within the genome of Haloarcula marismortui. Plot generated with a 100 base window, moving 25 bases at a time along the sequences' length. Hypervariable regions indicated.

Caution...

It is clear from the above discussion that, before diagnosing a sequence as chimeric based on its Pintail profile, consideration needs to be given to the possibility that what is being observed is in fact natural caused by some sort of recombination event, such as horizontal gene transfer.