A Few Classics on #Genomics and the Origin of “Shotgun DNA Sequencing”

I was on Spring Break recently, and I’m not entirely sure how I ended up doing this, but on the last day of my vacation I spent several hours chasing down and reading classical papers in #genomics and #bioinformatics. In some cases, these were papers I remembered from when I was back in grad’ school, but for others they were new to me – and thoroughly enjoyable to read. One of the main questions I was asking myself was “Who coined the phrase ‘shotgun sequencing’?” I then started digging.

I was fairly certain this had to of been someone involved with the human genome project, if not Venter himself.

But it turns out I was way off and totally wrong.

As far as I can tell – the first time “shotgun sequencing” appeared in the literature (referring specifically to a fragment library for DNA sequencing) was in 1980 (!!) by Joachim Messing in NAR. Shortly thereafter (also in NAR) Stephen Anderson used the same language in a single author NAR paper – presumably borrowing the phrase from the Messing paper which had been published a few short months beforehand. (For the record, there’s an earlier paper by Staden that refers to “shotgun cloning”, but this is not quite right[1]) In any case, if you’re reading this and I’m wrong – please leave a comment and point me to an earlier reference!

The first paragraph of the Messing 1980 paper includes this gem…

“Since currently used methods for DNA sequencing (1,2) are relatively time-consuming, a rapid sequencing system is presented involving a shotgun approach.”

– Messing, Crea, and Seeburg (1980)

There are a couple really cool things about this – one being that Stephan Anderson was working on sequencing the entire human mitochondrial genome with Frederick Sanger and others at the same time, and soon after this Messing paper was published, Anderson published their results in a landmark paper in Nature in April 1981. Interestingly, the phrase “shotgun DNA sequencing” wasn’t used in this Nature paper – and I believe didn’t enter into the lexicon of early genomics until Anderson’s single author NAR paper which was submitted in May of 1981 (and published in October that year). In this paper he repeats Joachim Messing’s phrase “shotgun DNA sequencing” and (I think) that sealed the deal.

After that – the phrase pops up all over the published literature.

Of interest and particular note: Anderson was first author in the 1981 paper on the human mitochondrial genome in what looks like an all-star cast of genomics superstars (Sanger, Staden, Young, etc.). References / citations below.

The Messing 1980 paper opened up a rabbit hole of awesome classical papers for me to read, but no matter how deep I dug I couldn’t find an earlier reference to “shotgun sequencing” as it related to fragment libraries than. I know this is probably a silly thing to be chasing down – but the end result was about four hours of deep reading and wonderment at what the early days of genomics must have been like.

Below are the rest of these “classic papers” I read end to end that day (many more were in my queue) – enjoy!

Anderson, Stephen. “Shotgun DNA Sequencing Using Cloned DNase I-Generated Fragments.Nucleic Acids Research 9, no. 13 (1981): 3015–27. 

Anderson, S., A. T. Bankier, B. G. Barrell, M. H. de Bruijn, A. R. Coulson, J. Drouin, I. C. Eperon, et al. “Sequence and Organization of the Human Mitochondrial Genome.” Nature 290, no. 5806 (April 9, 1981): 457–65.

Gardner, Richard C., Alan J. Howarth, Peter Hahn, Marianne Brown-Luedi, Robert J. Shepherd, and Joachim Messing. “The Complete Nucleotide Sequence of an Infectious Clone of Cauliflower Mosaic Virus by M13mp7 Shotgun Sequencing.” Nucleic Acids Research 9, no. 12 (1981): 2871–88. https://doi.org/10.1093/nar/9.12.2871.

Gingeras, T.R., J.P. Milazzo, D. Sciaky, and R.J. Roberts. “Computer Programs for the Assembly of DNA Sequences.” Nucleic Acids Research 7, no. 2 (1979): 529–43. https://doi.org/10.1093/nar/7.2.529.

Korn, L. J., C. L. Queen, and M. N. Wegman. “Computer Analysis of Nucleic Acid Regulatory Sequences.” Proceedings of the National Academy of Sciences 74, no. 10 (October 1, 1977): 4401–5. https://doi.org/10.1073/pnas.74.10.4401.

Messing, Joachim, Roberto Crea, and Peter H. Seeburg. “A System for Shotgun DNA Sequencing.” Nucleic Acids Research 9, no. 2 (1981): 309–21. https://doi.org/10.1093/nar/9.2.309.

Sanger, F., A.R. Coulson, B.G. Barrell, A.J.H. Smith, and B.A. Roe. “Cloning in Single-Stranded Bacteriophage as an Aid to Rapid DNA Sequencing.” Journal of Molecular Biology 143, no. 2 (October 1980): 161–78. https://doi.org/10.1016/0022-2836(80)90196-5.

Venter, J. C., H. O. Smith, and L. Hood. “A New Strategy for Genome Sequencing.” Nature 381, no. 6581 (May 30, 1996): 364–66. https://doi.org/10.1038/381364a0.

[1] A slightly earlier paper by (1979) from R.Staden on the infamous “Staden Package” of bioinformatics software reads “The whole of the DNA to be sequenced is shotgunned into a suitable vector and cloned.” which is perhaps very close, but I still think Anderson may have been the first to write “shotgun DNA sequencing”. Staden, R. “A Strategy of DNA Sequencing Employing Computer Programs.” Nucleic Acids Research 6, no. 7 (1979): 2601–10. https://doi.org/10.1093/nar/6.7.2601.

[2] A less important but still cool thing here was the discovery that this was the same Stephan Anderson that sits on the faculty at Rutgers University’s Center for Advanced Biotechnology and Medicine, which is where I started my graduate work in 1999 before following my PI (and the rest of Dinman’s lab) to University of Maryland. I wish I had been as interested in genomics back then as I am now, or I would have definitely made time to talk with Anderson about his work when I had the chance…