Highlights of our annotation: heavy metal resistance, lateral gene transfer, genomic islands, mega plasmids!

This was the last day of annotation for our students, where they had to write up their results. Next week, oral presentations of the results. In the meantime, I asked each group of 2 or 3 students for some highlights of their annotation efforts. Please keep in mind that this is all preliminary.

Some highlights from our annotation of the Neochlamydia genome:

We clarified which amino acids could be synthesized. The striking results is that very few amino acids can be synthesized: this intracellular bacteria lives inside amoeba, and is very dependent on synthesis or transport by the amoeba.


Presence / absence of amino acid synthesis pathways: Green: present; red: absent; yellow: maybe present. Temporary figure, results still being updated.

A comparison of type III secretion among Chlamydiae showed that the structural proteins are very well conserved. On the other hand, CopB and CopC are less conserved. Despite low sequence conservation, CopB can be identified by conserved synteny. But CopD appears absent from not only our Neochlamydia, but from most Chlamydiae, whereas it is reported in complex with CopB in Yersinia and Salmonella. Three new genes were identified while studying this system, inserted in the conserved syntenic region: a transposase, a heat shock protein, and a potential secreted effector.

T3SS figure

Conservation of type III secretation system among several bacteria

While looking for prophages in vain, we found a super cool 55 kb genomic island, bordered by magnificient direct repeats (34 bp). Integrase, recombinase, and multiple antibiotic resistance genes, how cool can it be? (The students were quite excited by this find.)

Some highlights from our annotation of the Ralstonia genome:

Replicons I and II (3.5 and 1.5 Mb) follow the GC skew pattern of a real chromosome, whereas replicon III (0.5 Mb) doesn’t have a clear pattern. tRNA genes only on replicon I, with a initiation of replication DNA-dependent, whereas II and III have a plasmid type Rep system.

Chromosome III probably corresponds to the mega plasmid pHG1 of Ralstonia eutropha. In general, many similarities of our strain with R. eutropha. E.g., also has genes for lithoautotrophic growth.


R. eutropha pHG1 on top, our Ralstonia chromosome III on bottom. Generated using Artemis.

Looking for transporters, found heavy metal transport in both bacteria, more in Ralstonia, as expected from its isolation. Two copies of mercury resistance cluster on chromosome III, which suggests lateral transfer of the whole system with the plasmid. Surprisingly (for us), four copies of the operon for Cobalt-zinc-cadmium resistance (genes CzcA-B-C), which from phylogeny seem to come from three operon duplications shared by other species, and one lateral gene transfer.

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1 Response to Highlights of our annotation: heavy metal resistance, lateral gene transfer, genomic islands, mega plasmids!

  1. Heidi Gumpert says:


    It’s a really nice blog and accompaniment for your course. How did you make the Type II secretion system gene order comparison figure? I looked up the paper it ended up in, but it didn’t explicitly say what software or R package was used. I would be super appreciative if you could let me know the name of software/package ^_^

    Thanks and great work!

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