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Title: A standard nomenclature for gene designation in the Rosaceae

Author
item JUNG, SOOK - Washington State University
item Bassett, Carole
item BIELENBERG, DOUGLAS - Clemson University
item CHENG, CHUN-HUAI - Washington State University
item DARDICK, CHRISTOPHER - Chris
item MAIN, DOREEN - Washington State University
item MEISEL, LEE - Universidad De Chile
item Slovin, Janet
item TROGGIO, MICHAELA - Agricultural Institute Of San Michele (IASMA)
item SCHAFFER, ROBERT - University Of Auckland

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/8/2015
Publication Date: 9/26/2015
Publication URL: http://handle.nal.usda.gov/10113/62317
Citation: Jung, S., Bassett, C.L., Bielenberg, D.G., Cheng, C., Dardick, C.D., Main, D., Meisel, L., Slovin, J.P., Troggio, M., Schaffer, R.J. 2015. A standard nomenclature for gene designation in the Rosaceae. Tree Genetics and Genomes. 11:108.

Interpretive Summary: Plants grouped into the Rosaceae family include many important fruit and nut crops, such as apples, peaches, almonds, strawberries and raspberries, as well as plants prized for their ornamental qualities, such as cherries, roses, and crabapples. Modern technology has made it possible and economical to sequence the genomes of several of these Rosaceae plants, allowing scientists to identify their genes and study the functions of these genes. A committee was formed to develop a standardized gene naming system, which is described in this manuscript. The standardized nomenclature allows scientists across laboratories to be sure of the identity of any gene being studied, and facilitates identifying genes in common among the various plants. This makes it possible for information about a gene in one member of the family to become useful for studying this gene in a related plant.

Technical Abstract: The plant family Rosaceae is comprised of a highly diverse group of plants, with a wide range of ornamental and agricultural uses throughout the world. Comparative genomic analyses between rosaceous species are increasingly being used to assign putative function. With the wealth of new data there is a need to standardize nomenclature to ensure uniformity and clarity across research groups. The Rosaceae Gene Name Standardization Committee was formed to develop a naming guideline for genes in Rosaceae family members. This manuscript details the issues involved with naming genes and proposes a common nomenclature system. The Genome Database for Rosaceae (GDR) (www.rosaceae.org) has developed a gene database that will support user-submitted gene names and annotations in addition to the predicted genes from whole genome sequences. GDR also hosts user-curated lists of gene class symbols. To facilitate standardization of gene names and avoid misinterpretation, the committee recommends that the GDR serve as the database of record for the names of Rosaceae genes, and that gene names, gene class symbols, and gene annotation be registered in GDR prior to publication in peer reviewed journals.