Gene Nomenclature Proposal for the Oomycete community
From the Oomycete nomenclature committee (Chair Howard Judelson) with input from
discussion at the Oomycete Molecular Genetics Workshop in Wageningen
With the arrival of genome sequences of Phytophthora sojae P. ramorum, P. infestans, P.
capsici, and Hyaloperonospora parasitica, as well as EST resources for several other
oomycetes, a vast plethora of genes have suddenly become available to the community.
This has generated a need to standardize the naming of oomycete genes in order to
maximize the value of comparative genomics approaches. Following discussion at the
2005 Workshop in Asilomar a committee was established to develop a detailed proposal
to the community, consisting of Paul Morris (Bowling Green State University; P. sojae
researcher), Howard Judelson (University of California, Riverside; P. infestans
researcher) and Jim Beynon (Warwick University, UK; Hyaloperonospora parasitica
researcher).
The committee presented its recommendation at the 2006 meeting in Wageningen and
received input from the attendees. The principal recommendations, including
modifications based on the discussion, are as follows:
1. The overall philosophy behind the guidelines are to maintain as much flexibility as
possible, while creating sufficient order to maximize the value of comparative genomics.
2. General naming guidelines.
a) Genes would be described by 3 to 7 characters (beginning with a letter), followed
optionally by a numeral to indicate a series of functionally related genes. The first letter
would be uppercase, capitalization of other letters to be at the option of the namer. e,g,
ABC1, AbcG1, ParA1, Avr1b1. Hyphens should only be used where essential for clarity,
e.g. Avr4-1 and Avr4-2 (rather than Avr41 and Avr42) if needed to distinguish two
different genes conferring avirulence against R4 – but just Avr4 if there is only one such
gene. Alternatively Avr(R4)1 and Avr(R4)2 could be used.
b) Alleles would be designated by superscripts. e.g. Atr1Ndor Avr488069. Dominance and
recessiveness would be optionally indicated where appropriate by superscripts as in E.
coli by + (wild-type, dominant), – (loss-of-function recessive) and –d (dominant
negative), e.g. Ade1-.
c) Functional names are encouraged rather than whimsical ones.
d) Gene models predicted electronically from genome sequences would not be given gene
names until the models had been curated manually and/or experimental evidence had
been obtained to verify the existence of the gene. Gene models would be identified by a
GeneID maintained at the organization that created the sequence.
e) Gene names, but not the final numeral(s), would be italicized, e.g. Avr1b1. Protein
gene products would take the name of the gene, but be non-italicized. Prefixes or suffixes
of “p” would not be used.
f) Duplications of gene names would be avoided by use of a name list maintained at the
community web site. Peer reviewed publication will not be required to establish a gene
name.
3. A 2 to 5 letter prefix indicating genus and species should be used in contexts where
there may be confusion, e.g. PiELL1, PsELL1
Because many oomycete species share similar initial letters, e.g. Phytophthora infestans,
Phytophthora inflata, Pythium insidiosum, in some cases is may be necessary to have up
to 5 or 6 letters in the prefix. On the other hand, long prefixes were considered clumsy
and to be avoided if possible.
Two suggestions were made to solve this problem:
(i)
Prefixes would be assigned to species on a first come first served basis, as
recorded on the community web site. This would enable the most
commonly studied (and hence written about) species to have the simplest
prefixes.
(ii)
Prefixes would be created ad hoc for each paper/presentation/report to
distinguish only those species being discussed. e.g. Pi could be used for
Phytophthora inflata if P. infestans was not discussed.
4. Names already in the literature could be changed to the standard format at the
discretion of the publishing investigator.
5. Once nomenclature guidelines are adopted, journals the frequently published reports of
oomycete genes e.g. MPMI, Phytopath., FGB, Curr Genet would be notified so that they
can encourage authors to follow the guidelines.