nomenclature

chlamy at ACPUB.DUKE.EDU chlamy at ACPUB.DUKE.EDU
Wed Jun 1 14:34:26 EST 1994


A forwarded message from Carl Price:

I stick my oar in the waters of genetic nomenclature with considerable
trepidation: I am not a geneticist and I do not work with Chlamydomonas.
Nonetheless, the Commission on Plant Gene Nomenclature (CPGN), mentioned
earlier in these discussions by Mike Gray and Lib Harris, has been
concerned
with developing a common nomenclature for SEQUENCED plant genes, and it may
be
helpful to share some ideas that have been developed within the CPGN.

The CPGN adopted earlier recommendations for genes of chloroplast and
mitochondrial genomes; today, under the auspices of the CPGN, Rick Hallick
continues to run the chloroplast group, and David Lonsdale the
mitochondrial
group. The common designations for genes of these organellar genomes have
become accepted throughout the plant community. Some interesting problems
are
developing as extensive sequences are reported from plastid genomes of
chromophytic algae, which contain genes that in green algae, Euglena, and
higher plants are the exclusive province of nuclear genomes. We can expect
to
see more instances of extra-nuclear locations for traditionally nuclear
genes
as the sequences of organelle genomes and of nucleomorph DNA are unraveled.

The focus of your current discussions is designations for genetic loci as
distinct from those for sequenced DNA. I should like to draw your attention
to
ambiguities in designations for nuclear loci containing members of
multigene
families. 

Traditionally, two distinct loci with similar mutant phenotypes might be
designated Pqr1 and Pqr2. Pqr1 and Pqr2 might encode enzymes that catalyze
sequential steps in the same biosynthetic pathway but are structurally
unrelated to one another. If two loci are found to encode the SAME product,
there are similarly designated Stu1 and Stu2. The gene products of Stu1 and
Stu2, in contrast to those of Pqr1 and Pqr2, may be identical or differ by
only
a few residues. 

The problem, then, is that mnemonic designations of the type XyzN perform
two
very different functions: to designate gene loci whose mutant phenotype are
similar and to designate gene loci whose gene products are similar.

In the nomenclature developed by the CPGN, genes that encode substantially
similar products bear the same plant-wide designation. Members of multigene
families within a species are distinguished by a separate field, which we
call
MEMBER NUMBER. 

Let me cite an example in Chlamydomonas:  The plant-wide mnemonics for
genes
encoding alpha-, beta-, and gamma-tubulins are TubA, TubB, and TubC,
respectively. Chlamy has at least two TubA genes and at least two TubB
genes.
One TubA gene is represented by accession numbers K01805, M11447, and
M25916 ;
a second TubA  is represented by accession numbers K01806, K01807, M11448,
and
M25917. In the CPGN nomenclature, the two genes are represented as:

     Plant-wide mnemonic     Member number

          TubA                     1
          TubA                     2

The two genes can also be represented as TubA;1 and TubA;2.

We would not dream of telling the Chlamydomonas community (nor the maize or
Arabidopsis communities) how they should designate their genetic loci. If,
however, you are thinking of a renovation of your nomenclature, you may
wish to
consider a distinctive mechanism for the identification of loci that encode
members of multigene families.

The CPGN has published its detailed recommendations in a Supplement to the
June
issue of the Plant Molecular Biology Reporter. The Supplement should reach
subscribers in early July. While the supply lasts, we shall be pleased to
mail
copies of the Supplement; send requests to price at mbcl.rutgers.edu.

Carl Price
Chairman, CPGN







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