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Genome Sequencing Study Uncovers Phylogeny for Meningococcal Bacteria Species

By Andrea Anderson

NEW YORK (GenomeWeb News) – By sequencing more than a dozen new bacterial genomes, researchers from Italy, the US, and UK have gained phylogenetic insights for the bacterial species Neisseria meningitidis — including information about how components of a bacterial "immune system" contribute to its phylogeny.

"Now we have a very clear picture of what the population structure of this species looks like," Duccio Medini, a researcher with Novartis Vaccines and Diagnostics in Siena, Italy, and senior author of a study on his and his colleagues work, told GenomeWeb Daily News. "And we have a theoretic framework that will allow us now, with much faster sequencing technologies, to clarify this picture at the whole-species level."

The group sequenced the genomes of 15 N. meningitidis strains and analyzed these alongside the genomes of five previously sequenced strains. In the process, they found three distinct phylogenetic clades, along with nearly two-dozen restriction modification systems that correspond to this phylogeny and appear to influence the extent to which different strains can swap DNA. The findings appeared online last night in the Proceedings of the National Academy of Sciences.

"If two strains with a different repertoire of restriction modification systems try to exchange DNA, the efficiency of the horizontal gene exchange during the homologous recombination event is reduced, because the DNA that is coming into the cell is not methylated where it needs to be methylated to be recognized as self-DNA," Medini said, "so it gets cut by the restriction modification machinery of the recipient cell."

Restriction modification systems methylate DNA at specific sequence signatures, he explained, and cut sequences with these motifs that are not methylated. This contributes to bacterial immunity by helping discern between self-DNA and that of foreign invaders. But the new findings are consistent with the notion that the same mechanism can have consequences for genetic flux within N. meningitidis as well.

The researchers used a combination of Sanger and Roche 454 sequencing to sequence the genomes of 14 serogroup B N. meningitidis strains and a single strain from serogroup X. The team then incorporated publicly available genome data for five more N. meningitidis strains for their subsequent analyses.

Based on the patterns detected in the 20 genomes, the team estimated that the core N. meningitidis genome is comprised of around 1,630 genes. This may be a slight over-estimate, Medini noted, since it includes some genes that likely fall into the species' pan-genome.

The pan-genome, meanwhile, is still growing and expected to hit around 2,500 genes if 100 N. meningitidis genomes were to be sequenced, the researchers reported.

"There is a significant genome flux — genetic flux — in and out of the species," Medini said.

Even so, he added, the overall pan-genome size is not dramatically larger than the core genome, mainly because there are relatively few strain-specific genes. Instead, the team found that many genes in the pan-genome are shared between groups of strains.

Their analyses also offered a much more refined view of relationships between N. meningitidis strains. Although it was possible to identify dozens of so-called clonal complexes in the past using multi-locus sequence typing, Medini noted, MLST data alone could not define phylogenetic relationships between these strains.

Using whole-genome data, though, the team found that the 20 N. meningitidis strains tested, which represent 10 clonal complexes, make up at least three phylogenetic clades.

Consistent with past research hinting at a role for restriction modification systems in N. meningitidis genetic diversity, the researchers found 22 restriction modification systems that coincided with these phylogenetic clades.

Together, these results help explain how a bacterial species that uses extensive homologous recombination also maintains a broader phylogenetic structure, Medini noted.

"Some recombination will always happen," he said, explaining that relatively small bits of DNA are swapped between strains with restriction modification systems that don't jive. "On the other hand, if two strains having the same restriction modification repertoire exchange DNA, this will happen at a very high frequency with a very high efficiency."

Those involved in the study say the results might have implications beyond the N. meningitidis species as well. "These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations," they wrote, "and they could provide an evolutionary framework for the population biology of a number of other bacterial species that show contradictory population structure and dynamics."

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