A proposal for the naming of genes in Aspergillus species

The issue of naming genes can be controversial with individuals favouring either the S. cerevisiae convention or the A. nidulans convention. There are reasonable arguments for either system.

At the November 2000 meeting of the Aspergillus fumigatus genome sequencing group, held at The Institute for Genomic Research (TIGR), Rockville, MD, the issue of naming genes in A. fumigatus was discussed. The results of a Web-based questionnaire were presented and it was agreed that the majority opinion from this questionnaire should be carried. This issue has also been discussed using the aspergillus_analysis email distribution list for the three sequenced genomes (A. nidulans, A. oryzae and A. fumigatus) and during the 1st Aspergillus Meeting in Copenhagen (April 2004). The following recommendations are proposed:

1) As A. nidulans is the model species for the genus, the A. nidulans nomenclatural system (which is based on the Demerec bacterial system) should be used for all species i.e.

abcD for genes and AbcD for proteins.

2) A three letter prefix to establish which species is being referred to should be used only when it is required in order to clarify the discussion (i.e. not all the time). The proposed prefixes are:

Afu for A. fumigatus Afl for A. flavus

Ani for A. nidulans Aor for A. oryzae

Ang for A. niger

3) Superscript text can be used after the gene/protein name to refer to the yeast orthologue for clarity if required e.g.

nimXCDC2; pdmAERG11

4) A standard gene name should be assigned for experimentally characterised genes only and not on the basis of sequence similarity. The exception for this would be for an orthologous Aspergillus gene/protein that has already been characterised in another Aspergillus species.

5) The same name should be used for all Aspergillus orthologues e.g.

AfupdmA; AnipdmA

6) The use of genus or species letters in the name should be avoided e.g.

aipA for aspergillus interesting phenotype A

7) There seems to no consistency in how the number of the yeast gene/protein is transferred to the Aspergillus gene or protein and authors may prefer to use either option:

a) The yeast number can be transcribed into the corresponding letter e.g.

STE18 becomes steR

OR

b) The letter A is used for the first gene or protein to be characterised in an Aspergillus species e.g.

ABC4 becomes abcA and STE18 becomes steD

 

The following exceptions should be noted: there is an established nomenclature for allergens and a proposed nomenclature for mating type genes of filamentous ascomycetes has been published (Turgeon BG and Yoder OC Fung Genet Biol 31:1-5 2000).

Michael J. Anderson 14th May 2004.

Genomics