A small tale from a BLAST

Dear students, we performed a simple “de novo assembly” using the gDNA reads longer than 100bp. This gave us 5Mbs of assembly spread across 27222 contigs (N50=190).

We BLASTed one of the largest contigs (~2kb) against “nr” and found: 

BLAST output

Apparently the whole query is covered by two sequences (#1 and #3) from a beetle (D. ponderosae)! The second match, however, is more consistent with our expectation: a sequence from Acinetobacter, that we already found to be quite abundant in our samples.

If you inspect the second hit you’ll notice that it refers to a natural plasmid (pAV2) related to Acinetobacter sexual activity 🙂 Could this be a hint of bacteria having sex into a beetle, as we did in the Sixties? It happens, when sequencing a genome, to sequence also contaminating species…

And indeed, in the Dendroctonus ponderosae genome paper:

Examination of the assembly identified a fraction of sequences from a
gammaproteobacteria most similar to Acinetobacter. The microbial community
associated with Dendroctonus spp. is known to be diverse, and Acinetobacter spp.
have previously been shown to associate with bark beetles [Keeling et al, 2013]

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