Molecular Taxonomy

Barcodes for Identification of Strains, Isolates and Individual Specimens

Mark Blaxter et al, Edingburgh, U.K.

Here in Edinburgh, we are sequencing DNA segments from individual nematodes as part of a program to develop a "molecular barcode" for taxon identification (see http://www.nematodes.org/). While some of our sequences come from cultured isolates, and thus can be tagged with a standard culture identifier (as proposed by Dave Bird and Don Riddle in Journal of Nematology 1994 26:138: eg. ED1234), we realise that there is no current accepted similar convention for naming sequences or other data from individual nematode specimens.

For individual nematodes, we also collect data pertaining to site of collection and date of collection. In addition, for many specimens we also record digital images that may permit identification by morphological criteria. We are concerned that the release of sequences derived from such specimens may result in data that is difficult for other researchers to interpret.

We propose here a coding protocol for sequences generated from single specimens of nematodes. These specimens may be identified (to various levels of accuracy) or not, but a "strain" code is not relevant, as there is no "strain". It is still important to have a registered code that represents:

• a specimen for which a photograph or set of photographs (analogue or digital) is available
• a specimen for which a fixed slide is available (of the head and tail, for example)
• a specimen for which diagnosis authorship information is available (who identified it as what)
• a specimen for which collection details are available.

The importance is, as with strain designators, that specimen designation should not change even if taxonomic ID does. The specimen ID would be attached to any database submission of the sequence, but can also be used before submission, with confidence. It also allows for multiple submissions per specimen (if someone sequences the D2-D3 LSU and the SSU from a specimen for example).

As cultured strain codes have the format "lab alphabetic code - numeral", we suggest that individual noncultured nematode sequences (and other data) are designated with a "numeral - lab alphabetic code". Thus an individual nematode sequence from our Edinburgh project could have the code "4321ED". We would also attach this code to any digital image or isolation data associated with the nematode.

1. Each participating laboratory should set up a registry of such sequences and specimens, including a web page giving a digest of the information (and possibly access to the digitised photographs)
2. The code follows that adopted for strains, but in reverse: ie the lab alphabetic designator FOLLOWS the specimen number, eg 123PDL

We propose that this protocol is followed by other molecular tag projects.

Two letter laboratory designations can be obtained in consultation with Prof. J. Hodgkin (Oxford <jah@bioch.ox.ac.uk>) as proposed by Bird and Riddle.

MOLECULAR BARCODING AND SOIL NEMATODE DIVERSITY

An eighteen-month, NERC-funded post is available for a postdoctoral research assistant to join an ongoing project using molecular methods to understand soil nematode diversity. The project is part of a major initiative linking biodiversity with soil processes.

Tasks:

1. Performing PCR and DNA sequencing on individual nematodes and nematode DNA samples
2. Building a sequence and diversity database for soil nematodes
3. Performing analyses of the database to examine patterns and processes in soil nematode diversity, population structure and dynamics