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Another Neat Article in PLoS ONE

Molecular markers are becoming more and more popular for species identification — a practice known as DNA barcoding. Researchers sequence a region of the genome from an organism of interest and search that sequence against a DNA database using BLAST. Such an analysis is contingent on a comprehensive database containing sequences from representatives of many diverse taxa.

We do not possess such a database for fungal species. Researchers have estimated that less than 5% of all fungal species have been identified, which means the chances are good that you may be the first person to sequence anything — let alone a common molecular marker — from a fungal species you are interested in identifying. Adding to the problem, a paper in PLoS ONE reports that approximately 20% of fungal sequences are misidentified (either containing incorrect or insufficient information) at the species level in the International Nucleotide Sequence Database.

The authors report that less that 1% of all fungal species have sequences from the internal transcribed spacer (ITS) of the ribosomal genes — a common molecular marker — deposited in the database. The issue of incorrect or insufficient information seems trivial compared to that of lack of information. Whereas the goal of a database of cytochrome c oxidase I (COI) genes (a locus in the mitochondrial genome) from all animal species in 15-20 years may be feasible, it’s unlike that fungi — a taxon far more evolutionarily diverse that animals — will be there anytime soon.

Comments

  1. #1 Nicholas Crawford
    December 25, 2006

    I really enjoy reading your blog. However, before you get too excited about barcoding may I direct your attention to the following article:

    Meier, Rudolf; Shiyang, Kwong; Vaidya, Gaurav; Ng, Peter. 2006. DNA Barcoding and Taxonomy in Diptera: A Tale of High Intraspecific Variability and Low Identification Success. Systematic Biology. 55; 5, 715-728.

    The point being that barcoding does not always work very well. COI is certainly an appropriate marker for some taxa, but homoplasy is often a complicating factor. Particularly with ancient lineages.

  2. #2 RPM
    December 25, 2006

    I thought this post reflected a tentative feeling towards the potential of DNA barcoding. Excitement wasn’t what I was going for.

  3. #3 Nicholas Crawford
    December 25, 2006

    Cool. I have bit of a knee jerk negative reaction when it comes to COI. I hope I did not come across as too obnoxious.