An Anecdote from a Symbiote

Benjamin Voight
Aug 28, 2017 · 6 min read

Note: This post was contributed jointly along with Humberto Julio Debat.

It is absolutely true that story below is about a Spider Genome and novel Spider Viruses. It is also a story about Research Symbiosis.

The Golden Orb-Weaver, N. clavipes. Photo: Paul Babb.

[Voice of B. Voight] Success at my job as a researcher relies crucially on the availability of large amount of data in the public domain. The Lion’s Share of scientific inferences that I made over my career thus far derive heavily from the efforts others have undertaken to place their work and data in public spaces. Put another way: I would like to think I’ve been a respectable Research Parasite.

Recently, I was able to turn the tables for once, turning from Research Parasite to Research Host. For those that know me and the sorts of science I think about, you might wonder how on earth did I ever involve myself in generating a draft, de novo genome assembly of the Orb-Weaving Spider, Nephila clavipes, the first assembled genome of its kind.

Our cover at Nature Genetics. Incroyable!

It’s a whimsical story: “Fortune favors the prepared mind”, winks Louis Pasteur. Creating a completely new genome to me is potentially a qualifying check-boxes for “Bioinformatician”. Years back, I felt it absurd that the community lacked a draft genome of any species of spider, and thought that it would be something I/we could do, as I was just about to start my own independent lab. The Parasite becomes the Host.

Building new genomes is one of those things that one simply cannot keep behind a gate, restrict or condition access to. Could you imagine the outcry and scientific stagnation if the first human genome sequence was restricted or gated to access? Quelle horreur. Anything less than unfettered access is not even in the conversation. Know that genome assembly, annotation, and analysis is a boat load of work to do well. Years of work — my post-doc (Paul Babb) was the main driver, essentially solo, in the trenches.

Ben Voight (left) and Paul Babb (right) pouring over some spider silk genomic sequences. Mind the cubicle art!

This tug-of-war: Community Benefit vs. “Payback” to Data Generators is a discussion that is ongoing. We obviously need better ways to recognize data generators. I do wish this discussion was more resolved than it is — which is to say that Data Generators demonstrate continued resolve in placing their works in the domain for use.

So it was with some glee that I was able to take an admittedly very small step to encourage Research Parasitism. This occurred even before our publication was in print: we had been working to post the data at NCBI/GenBank (for those that know that horror, we graciously accept your condolences). Also note: identifying novel spider viruses was not even close to “on our radar”.

***

[Voice of H. J. Debat] I have never seen a Golden Orb Weaver spider before — except by photograph. I have also never met Dr. Voight (Ben), personally.

I am a researcher in Plant Pathology at an institute of agricultural technology, located 400 miles west from Buenos Aires. That’s ca. 5,000 miles from Ben’s lab. This is the kind of story where the dots get connected only in the context of chance, and a shift in research practices.

Humberto pays homage to a photo of N. clavipes. Source of Photo: http://bit.ly/wiki-nephila-cc

Some years ago, I was working on generating a transcriptome of one of the most representative species of plants in Argentina, the Ilex paraguariensis tree. We use their leaves to generate an infusion rich in caffeine and antioxidants, called mate. It is such a widespread and pervasive beverage that around 98% of our population drinks it!

My training was in classic cytogenetics and basic plant virology, so that was my first encounter with High-Throughput Sequencing data. Some time ago, I noticed a sequence corresponding to a new species of latent Endornavirus, the first reported virus to be associated with mate. This sparked my interest and since then, I have been taking advantage of available RNA sequencing data to search for new viruses. I’ve found plenty, and generated many ongoing collaborations as a result.

I stumbled onto the N. clavipes data just by chance. I was scanning data at the shotgun sequencing archive (TSA) at NCBI for plant infecting Tospoviridae, and I noticed a divergent hit in the recently posted N. clavipes RNA transcriptomic assembly and seemed to correspond to a Bunyavirales-like virus. These data were literally fresh off the presses, having been released only two days previously.

I went ahead with a much more detailed analysis, which resulted in the first ten virus species associated to N. clavipes and the Nephilidae family of spiders. This may come as a surprise: even with more than 35,000 species of spider, there exist only a handful of associated viruses. Paraphrasing a quote from Louis Pasteur: “One can only see what he wants to see”. I guess nobody thought to look for them!

I reached out to Ben to share these findings. He immediately encouraged me to independently communicate this. As you can see in my email response below, I was admittedly a little bit reticent:

Dear Dr. Voight
Thank you for your kind reply.
When I wrote you i was just hoping to encourage you to follow up on this topic, which i find very interesting and understudied (if the info was new).
Nevertheless, if you are ok with it, I could arrange a brief MS to just highlight these minor findings, only if you consider sharing authorship. I have read somewhere an editorial about “Research Parasites” and i definitely don’t want to be framed as one :)

To which, he responded:

I fully embrace “Research Parasite” as a good thing, rather than that icky, pejorative meaning from that NEJM editorial.

We made the data, and shared it specifically so that enterprising people like yourself could pick it up and work with it.

You should take full credit for your own efforts, and again, I applaud the effort. A citation is all that we require (that was, in fact, our only contribution).

Continue your good works! And keep your eyes out for our next spider genome, hopefully coming soon.

Best, -BV

I posted a preprint of that work at bioRxiv, which is (as of this writing) in a second round of peer review, hopefully to be published soon. Thus, this is how — by expanding the associated holobiome of a great spider, which was only possible in the context of a transparent sharing policy — that I became a Research Parasite.

***

The moral of the story — if there is any at all — is for the community to heed two “Calls-to-Banner”. Research Parasites: Come from out the woodworks! Be not shy nor unwilling to ask for data. You should expect nothing less than full access! Research Hosts: Release your great works! Relinquish your grip from around your data. For the impact of your great works is judged not exclusively on what you produced and the initial science you attempted, but how much the work and data is ultimately utilized by others!

And: Louis Pasteur is a readily quotable person.

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