Plant Genome I Conference
Town & Country Conference Center, San Diego, CA, November, 1992.
PG-I: 71pg1
TOWARDS A COMMON NOMENCLATURE FOR SEQUENCED PLANT GENES
Ellen M. Reardon and Carl A. Price, ISPMB Commission on Plant
Gene Nomenclature, Waksman Institute, Rutgers University,
Piscataway, NJ 0-8855-0759, USA.
In 1991 the ISPMB formed a Commission on Plant Gene
Nomenclature with the objective of establishing a common
nomenclature for sequenced genes across the plant kingdom. The
project was initiated when it was realized that, in contrast to
the well-ordered nomenclature of chloroplast and mitochondrial
genes, plant nuclear genes were becoming a Tower of Babel. Names
of genes often provide no clue to their gene products, their
function within a specific plant, or their relationship to
similar genes in other plants. Genes encoding phytochrome, for
example, have been named PhtaP, PhyA, AP3, and Phy3). Additional
sources of confusion have been the incorporation of the name of
the plant into the name of the gene (e.g., PVPK for "Phaseolus
vulgaris protein kinase), and naming the gene after the plasmid
from which its cDNA was isolated (e.g., pTOM13).
The Commission has formulated a general plan for the
nomenclature, and is organizing groups of experts to develop
specific recommendations for various groups of genes. The
nomenclature will consist of two, closely parallel systems:
mnemonic designations, such as Adh1 and RbcS, and numerical
designations, patterned after the EC numbers of the IUB.
The Commission plans to organize a Plant Gene Registry to
serve as a clearing house for naming newly sequed plant genes.
A resource of this Registry will be Mendel, a database relating
plant-wide gene designations to the occurrence of genes in
specific plants, their products, and details of their expression,
together with cross references to sequence databases and to
plant-specific genetic databases.
As a precursor to Mendel and as an aid to the work of the
Commission, we have generated,a database named PGCDB, containing
information on 3700 plant nuclear sequences collated from the
EMBL Library and GeneBank. We shall demonstrate PGCDB at Plant
Genome I.
PGCDB provides some perspectives on the present state of
plant molecular biology: (i)In the first 2100 entries we found
381 distinct gene products. That number will change as
conservation among genes is examined more carefully, but it can
be compared with the 30,000 genes expected to occur in genomes of
individual plants. (ii) Among the 390 different plant species
represented, only 44 have more than 10 entries. Zea mays,
Arabidopsis thaliana, and Oryza sativa lead the way with 352,
318, and 220, respectively; 258 score from 1 to 10; and l62
plants are singletons. (iii) 1700 now sequences were reported
between December 1991 and June 1992. Although the diversity of
plants and gene products represented is still manageable, the
clock is ticking.
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