Abstract
The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community. This paper outlines a set of standard procedures for describing genes based on DNA, RNA, and protein sequence information that have been annotated and mapped on the sequenced genome assemblies, as well as those determined by biochemical characterization and/or phenotype characterization by way of forward genetics. With these revisions, we enhance the potential for structural, functional, and evolutionary comparisons across organisms and seek to harmonize the rice gene nomenclature system with that of other model organisms. Newly identified rice genes can now be registered on-line at http://shigen.lab.nig.ac.jp/rice/oryzabase_submission/gene_nomenclature/ .
Highlights
The biological community is moving towards a universal system for the naming of genes
Nipponbare, which was sequenced by the IRGSP (International Rice Genome Sequencing Project) [7], and by the O. sativa ssp. indica cultivar, cv. 93-11, which was sequenced by the Beijing Genomics Institute (BGI) [28]
The Nipponbare sequence has been annotated by several groups, including Rice Annotation Project (RAP) [8, 20], The Institute of Genomic Research (TIGR) [29], National Center for Biotechnology Information (NCBI)-GenBank [19], Munich Information Center for Protein Sequences (MIPS) [11], and Syngenta [6], while annotation of the O. sativa ssp. indica sequence, cv. 93-11, has been provided almost exclusively by the BGI [31]
Summary
The biological community is moving towards a universal system for the naming of genes. Genes with approved names and symbols will all be associated with a gene function or phenotype and, where possible, at the time of registration, researchers will be asked to identify a systematic locus identifier for the new gene from the RAP annotation database.
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