Davidson Genomics Student Course Page

Mike Waters's
Genomics Web Page

This web page was produced as an assignment for an undergraduate course at Davidson College.

Opinion
The authors the paper The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution provided evidence to support the hypothesis that L. bulgaricus is actively specializing its genome to subsist in milk and yogurt.
The evidence the authors used to support this hypothesis included a large number of fragmented genes and pathways: 270 psuedogenes, lack of certain carbohydrate metabolic pathways, an inability to produce unsaturated fatty acids (strain would not grow unless provided with unsaturated fatty acid found in milk Tween 80), and lack of stress response pathways to protect against oxidative stress and low pH.
The authors also cited a high ratio of GC content at codon position 3 to the GC content of the organism as an indication of rapid evolution toward higher GC content (codon position 3 mutates faster than positions 1 and 2). L. bulgaricus also has a much higher GC content then the other members of its family (acidophilus complex). The authors hypothesize that this is suggestive of divergent evolution that is possibly a result of specialization to a particular environment.
A more comprehensive summary of the paper and figures can be found in the paper summary and figure summaries below.

I think the authors made a convincing case for the reductive evolution of L. bulgaricus.
The data in Figures 1 and 3 clearly depict L. bulgaricus as a standout in markers of reductive evolution.
One of issues that I think should have been addressed was the nature of the comparison parameters of figures 1 and 3. Figure 1 claimed to compare L. bulgaricus to 232 eubacterial genomes.
I would like to know how the number 232 was chosen and why each of the 232 were chosen.
I think the paper would have been stronger if the authors could have compared the reductive evolution to a consensus reduced genome and listed similarities instead of inferring processes that could mark the reduction of a genome.
That being said the arguments made for genome reduction were logical and convincing (rRNA and tRNA to genome size, fragmented pathways and genes etc.)

A summary (bullet points) of The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution can be found here

Figures and Tables

Table 1 (see paper for visual)
Depicts characteristics of the L bulgaricus ATCC11842 genome.
They found the genome to contain 1,864,998 base pairs.
The overall GC content was 49.7%.
The GC content for coding regions was 51.6%.
The GC content of coding sequences at codon position 3 (evolves more rapidly) was 65.0%.
The number of coding sequences was 1562 which makes up 73% of the genome.
598 of the coding sequences have an unknown function.
270 pseudogenes are present along with 9 rrn operons, and 95 tRNA genes.

Figure 1

Figure 1.
The GC content of 232 eubacterial genomes and the GC content of codon position 3 for each genome is plotted. L. bulgaricus is circled.
L. bulgaricus ratio of GC content in the GC3 position to its GC content of its genome is noticeably high.

Figure 2

Figure 2. is a graphical description of the L. bulgaricus genome
Each circle represents the entire L. bulgaricus genome.
Circle 1. Red lines mark pseudogenes on positive strand, blue lines mark pseudogenes on negative strand.
Circle 2. Insertion Sequence (IS) elements (transposases and ISL4 related hypothetical genes). Gray= elements with four or fewer copies, Red (ISL7 >5 copies), Purple (ISL4> 5 copies), Blue (ISL5> 5 copies), Green (ISL4-5> copies).
Circle 3. Coding sequences (CDS), Red=positive strand, Blue= negative strand.
Circle 4. rRNA genes (red), tRNA genes (green)
Circle 5. GC (window size 2000) less than -0.1(cyan), more than +0.1 (red)
Circle 6. AT (window size 500) from <.3 (cyan) to >0.7 (red)
Circle 7. Position on the genome

Figure 3

Figure 3.
Plots the number of rRNA and tRNA genes as a function of genome size
Chart A shows the number of 16S rRNA genes and genome size in 54 firmicutes genomes. L. bulgaricus genome is circled.
Chart B shows the number of tRNA genes an genome size in 54 firmicutes genomes. L. bulgaricus genome is circled.
The ratio of rRNA and tRNA genes to genome size is very high in L. bulgaricus compared to the rest of the firmicutes genomes.
L. bulgaricus appears to have approximately as many 16S rRNA genes as an organism with a 3.5-4.5 Mb genome (it has a 1.8 Mb genome.
Also L. bulgaricus appears to have approximately as many tRNA genes as an organism with 3.5-5.5 Mb genome (it has a 1.8 Mb genome).
The high ratio of rRNA and tRNA genes to genome size suggests a rapid decrease in genome size.

Figure 4

Figure 4.
Synteny between L. bulgaricus and L. acidophilus genomes.
Colors of dots indicate BLAST score ratios.
There is high sequence similiarity from appx. .1 Mb- .2Mb, .4 Mb-.7 Mb, 1.1 Mb- 1.3 Mb, 1.6 Mb-1.8 Mb.

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