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Porcelli, D., Marygold, S.J. (2014.9.16). Systematic nomenclature for OXPHOS nuclear genes of D. melanogaster. 
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The nuclear genes encoding mitochondrial proteins involved in oxidative phosphorylation (OXPHOS) in D. melanogaster have been identified in several publications from the group of Corrado Caggese (notably FBrf0184015, FBrf0204833 and FBrf0226220), but a systematic nomenclature for these genes has not been incorporated into FlyBase to date (as of the FB2014_05 release).
We have used these publications to produce a comprehensive list of D. melanogaster nuclear OXPHOS genes and establish a systematic nomenclature for use in FlyBase.
Our aims were:
- give each gene an informative symbol and name in FlyBase
- symbols and names should reflect usage in the Drosophila literature and wider OXPHOS community
- use a common prefix for genes encoding components of each respiratory complex
- within each complex, refer to genes named for their molecular function in a standardized way (ie. don't use a mixture of symbols based on orthology and based on weight)
- retain gene symbols/names based on mutant phenotype where these have precedence and/or have been widely used in the literature (adding the standard nomenclature as synonyms)
- distinguish between gene duplicates/triplicates in an obvious and meaningful way - i.e. use a 'L'/'like' suffix
See the associated file for the full list of OXPHOS nuclear genes and their nomenclature.
- genes in blue were identified in FBrf0184015 as less-conserved duplicates/triplicates of a primary OXPHOS gene
- in the 'New FlyBase nomenclature column', bold type indicates that a gene symbol/name is new; of these, black type indicates genes that previously had no meaningful symbol/name in FlyBase, while red type indicates genes that did have a meaningful symbol/name but these are being changed here to be consistent with the standardized nomenclature.
Related Publication(s)
Research paper

MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion.
Sardiello et al., 2003, Nucleic Acids Res. 31(1): 322--324 [FBrf0156028]

Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.
Tripoli et al., 2005, Genome Biol. 6(2): R11 [FBrf0184015]

The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.
D'Elia et al., 2006, Mitochondrion 6(5): 252--257 [FBrf0192813]

The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates.
Porcelli et al., 2007, BMC Evol. Biol. 7: 215 [FBrf0204833]


MitoDrome: D. melanogaster OXPHOS genes.
Caggese et al., 2006, MitoDrome: D. melanogaster OXPHOS genes. [FBrf0226220]

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File date: 2014.9.16 ; File size: 54784 ; File format: xls ; File name: OXPHOS_genes.xls
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