Retraction Watch

Tracking retractions as a window into the scientific process

Researchers retract a paper when they realize they had sequenced the wrong snail’s genome

with 6 comments

Researchers in China thought they had sequenced the genomes of two snails that help transmit diseases to other species — an important first step to stopping the spread. But their hopes were soon dashed after they realized they had misidentified one of the snails.

The researchers published their findings earlier this year in the journal Parasites & Vectors. In the paper, the authors stressed that understanding the genetic makeup of these molluscs is important because many “freshwater snails are intermediate hosts for flatworm parasites and transmit infectious diseases” to humans and other animals. They also acknowledged that identifying snail species from their appearance alone can be tricky.

Indeed, not long after the study was published, a reader raised concerns that the authors had misidentified one of the snails. After re-examining their data, the authors realized their mistake: They had not used a genome database software program, called Basic Local Alignment Search Tool (BLAST), which compares biological sequences against known ones and finds regions of similarity. If they had, the authors may have discovered they had sequenced the wrong species.

Here’s the retraction notice for “The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications,” published in January 2017:

The authors are retracting this article [1]. A reader recently raised questions related to the identification of one of the snail species whose complete mitochondrial (mt) genomes have been characterised in our article, because the gene order and mt genome sequence of the sample of Radix swinhoei (family Lymnaeidae) strongly resemble those of Physella acuta (family Physidae) (GenBank JQ390525.1 and JQ390526.1) published by Nolan et al. [2].

The initial morphology-based identification of the snail as “Radix swinhoei” was not tested with BLAST searches and as a result we did not realise that we had characterised the mitochondrial genome of a different species. Upon re-examination of our data, we suggest that the sample “Radix swinhoei” does in fact represent a species of Physella (referred to as Physella sp.). Because of this misidentification and the fact that the phylogenetic analysis did not include members of the family Physidae, the conclusions drawn from the “Radix swinhoei” sample in our article are incorrect.

All authors agree with this retraction.

We contacted the paper’s corresponding author, Yinchan Hu, based at the Chinese Academy of Fishery Sciences in the Ministry of Agriculture in Guangzhou, as well as the first author, Xidong Mu, and second-to-last author, Hongmei Song, both based at the same institution. We will update the post if we hear back.  

Hat tip: Rolf Degen

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Comments
  • Marco August 7, 2017 at 12:48 pm

    Shouldn’t this one be tagged “doing the right thing”?

  • Steven Salzberg August 7, 2017 at 8:11 pm

    I’m afraid you have two major scientific errors in your article about this retraction. First of all, BLAST is a software program, something commonly known as a sequence alignment tool, that aligns DNA or protein sequences to one another. It is most definitely not the name of “a genome database.” One uses BLAST to search genome databases, but one can use it to search many different databases – as I have done myself, thousands of times.
    What the researchers failed to do was to search the GenBank database (that is, indeed, a database). They should have done that, and the BLAST program is the best tool to use.
    Your second major scientific error is in the title of this Retraction Watch notice, where you write that “they had sequenced the wrong snail’s genome.” This is just wrong. Snails have quite large genomes, and the paper in question did not sequence any such thing. Rather, they sequenced the MITOCHONDRIAL genomes of two snails, which are about 14,000 base pairs of DNA in length. These are tiny compared to the full genome, which for snails varies widely but will usually be 100’s of millions of bases, up to a billion bases. Thus the mitochondrial genome is much, much less than 1% of the animal’s genome.
    To be accurate, you should change the title of this notice to “the wrong snail’s mitochondrial genome” or “the wrong snail’s mitochondrion.” Or you could be vague and just write “the wrong snail.”

    • Eduardo G P Fox August 8, 2017 at 1:19 am

      “they sequenced the MITOCHONDRIAL genomes of two snails” — Technically I’d say they did sequence the genomes as stated below from their (rather superficial) methods description:
      ” Total genomic DNA was isolated from each species(…)”
      It is common practice to just extract and sequence everything and “fish out” the putative mitochondrial sequences for assembly.
      So in practice they did sequence the whole genome but did not assemble/analyse it, which is finally the hardest part.

      • Steven Salzberg August 8, 2017 at 9:49 am

        Eduardo, you’re correct in that they did isolate total genomic DNA, so the headline is not terrible, but it’s misleading. The error about BLAST is a real howler, though, and that was the main thing I wanted to get the Retraction Watch people to fix. (N.B.: I’ve sequenced and assembled dozens of whole genomes and also mitochondrial genomes in my lab over the years.)

    • Alison McCook August 8, 2017 at 11:54 am

      Fixed, thanks!

  • David Campbell August 8, 2017 at 12:01 pm

    If you have a Radix and hold the coiled end of the snail up, the opening is on the right. If you have a Physella and hold the coiled end of the snail up, the opening is on the left. The anatomy differs, too, but coiling direction should be easy. Identifying the correct species within Radix or Physella is a problem.

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