As a community database, AspGD does not invent gene name standards for predicted protein encoding genes on our own, but we will use and enforce guidelines developed by consensus in the community. However, we have developed a standard and systematic naming system for tRNAs which were predicted at AspGD by
tRNAScan-SE. See Format of Standard tRNA Names, below, for details.
Community guidelines for gene names, developed during discussions
around the meeting of the Aspergillus fumigatus genome
sequencing group in 2000 and the 1st International Aspergillus
Meeting in 2004, are posted
on the www.aspergillus.org.uk web site. The first name published in the scientific
literature for any given gene will be used as the standard gene name in AspGD. In addition, identifiers in use by GenBank or by the Broad Institute have been assigned as gene aliases. (Nomenclature issues related to the incorporation of the Broad Institute reannotation during preparation of Version 5 of the Aspergillus nidulans reference annotation are described in more detail in the AspGD Sequence Documentation.)
We welcome feedback
about AspGD gene name policy issues, such as:
- Should AspGD provide a Gene Name registration system, similar
to the system in place at
the Candida Genome Database?
- Would the Aspergillus research community like us to enforce guidelines for the
format of standard gene names to be used in AspGD?
- Should AspGD mediate discussions about proposed changes to
Standard Gene Names? At the Saccharomyces and Candida
Genome Databases, gene names may be changed if there is consensus
among the groups who study the gene, and the database staff serve as
facilitators during this process. AspGD would be happy to assume a
similar role for the Aspergillus community, if the community would
like us to do so.
New Systematic Names
New genes (e.g., the result of a merge between two gene models as the annotation
is refined) are assigned systematic names using the naming
conventions put in place by the original annotators. For example,
in A. nidulans, additional names of format AN#### are created,
continuing the numerical series of the existing names.
In A. oryzae, the original annotation assigns names
positionally, with a numerical series for each chromosome arm, and new
names are assigned following this convention.
Format of Standard tRNA Names
tRNA annotations were predicted by AspGD using the program tRNAscan-SE. The eukaryotic model option was used for nuclear tRNAs,
and the organeller model was used for mitochondrial tRNAs.
AspGD uses the following format for standard tRNA names: 't' + encoded amino acid [one-letter code] + (anticodon) + count.
For example, tQ(CUG)2 for the second instance of tRNA-glutamine with anticodon 'CUG'.
Mitochondrial tRNAs use the same format, but are appended by 'mt': for example, tH(GUG)4mt.
The count for mitochondrial tRNAs is continued from those of nuclear-encoded tRNAs of the same coding type.
To facilitate searching, an alias is provided with each 'U' replaced by 'T' in the anticodon.
Please note that the count suffix is arbitrary, and independent among the different species in AspGD.
It is used simply to create a unique identifier for each tRNA gene of a given species, and no special
relationship between two tRNAs with the same standard name from different species is implied.
For example, the tH(GUG)1 tRNA gene in A. nidulans and the tH(GUG)1 tRNA gene in A. fumigatus
are not necessarily expected to be more closely related to each other than to any other tH(GUG) in either genome.
A. nidulans Systematic tRNA Names
For A. nidulans, the format of systematic names is identical to that of standard names.
A. fumigatus Systematic tRNA Names
For A. fumigatus, the systematic names are generated by prefixing the standard names with 'Afu' + chromosome number. For example, the tRNA-serine with standard name tS(AGA)2, which occurs on A. fumigatus Chromosome 1, has systematic name Afu1tS(AGA)2.
A. niger Systematic tRNA Names
For A. niger, the systematic names were assigned by the genome sequencing project based on chromosome location.
A. oryzae Systematic tRNA Names
For A. oryzae, the systematic names were assigned by the
genome sequencing project based on chromosome or contig location.
New tRNAs added by AspGD are given the systematic name of the
closest upstream tRNA assigned by the sequencing project,
appended by '.1', '.2', etc. (for example, AO090002t00023.1 and AO090002t00024.1).
Format of Systematic uORF Names
Systematic names for uORFs are assigned based on the convention used
for Saccharomyces cerevisiae uORF names at
the Saccharomyces Genome Database
(SGD). The uORF names are
constructed by appending "-uORF" to the systematic name of the ORF
from which the uORF is upstream (the ORF whose translation the uORF is
expected to regulate). If an ORF has two uORFs, the name of the 2nd
uORF from the start of the ORF is given a ".2" suffix. A third uORF
would be assigned a ".3" suffix, and so forth. For
example, A. nidulans ORF AN6642 has two uORFs, which have
systematic names AN6642-uORF and AN6642-uORF.2.
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