On 10 Jul 2012, at Tue10 Jul 09:33 , Yang Cao wrote: Dear Steven, I agree with your modifications on the nomenclature changes you mentioned here, this is more convenient for later on Drosomycin gene family named consistency. Thanks. Best regards, Yang Cao ---- On 3 Jul 2012, at Tue3 Jul 15:05 , Shuoyang Wen wrote: Dear Steven, It would be good to keep the nomenclature identical for the family from now on, your suggestion looks perfect. Many thanks! Regards, Shuoyang ---- On 3 Jul 2012, at Tue3 Jul 14:24 , ZHU wrote: Dear Dr. Steven Marygold, Overall, I agree with the nomenclature changes you mentioned here. Thanks. Best regards Shunyi Zhu ---- On 29 Jun 2012, at Fri29 Jun 17:09 , F.M. Jiggins wrote: Dear Steven, I think that the current names are actively unhelpful. There is nothing I am aware of that differs between Drs and Dro genes, nor any reason for just one of them to include 'like' in the name. Your suggestion seems extremely helpful. Frank ---- On 29 Jun 2012, at Fri29 Jun 12:37 , Steven Marygold wrote: Dear Frank, Yang Cao, Shunyi Zhu and Shuo-Yang Wen, We're reviewing the FlyBase data on the Drosomycin gene family, specifically the nomenclature of these 7 genes. It looks to me like the 'official' nomenclature FlyBase uses for these genes isn't all that helpful and implies things that aren't true. We'd like to improve things if possible. I notice that you've previously published on this gene family, so I'd like to hear your opinion (or at least an agreement to the suggestion at the end of this email!). In looking for peer-reviewed papers to help resolve this issue, the following papers from your labs appear to be the most relevant (but please let me know of any others we should consult): FBrf0190732 Jiggins and Kim, 2005, Genetics 171(4): 1847--1859 The evolution of antifungal peptides in Drosophila. (Nomenclature used: Drs, Dro1, Dro2, Dro3, Dro4, Dro5, Dro6) FBrf0193399 Yang et al., 2006, Gene 379: 26--32 Functional divergence of six isoforms of antifungal peptide Drosomycin in Drosophila melanogaster. (Nomenclature used: Drs, Drs-lC, Drs-lD, Drs-lE, Drs-lF, Drs-lG, Drs-lI) FBrf0205847 Tian et al., 2008, Molec. Immunol. 45(15): 3909--3916 Gene expression, antiparasitic activity, and functional evolution of the drosomycin family. (Nomenclature used: Drs, Dro1, Dro2, Dro3, Dro4, Dro5, Dro6) FBrf0209263 Deng et al., 2009, J. Biomed. Biotechnol. 2009: 315423 Gene expression divergence and evolutionary analysis of the drosomycin gene family in Drosophila melanogaster. (Nomenclature used: Drs, Dro1, Dro2, Dro3, Dro4, Dro5, Dro6) The current FlyBase symbol, current FlyBase full name, and FBgn ID for these genes are: Drs Drosomycin FBgn0010381 Drs-l Drosomycin-like FBgn0052274 dro2 drosomycin-2 FBgn0052279 dro3 drosomycin-3 FBgn0052283 dro4 drosomycin-4 FBgn0052282 dro5 drosomycin-5 FBgn0035434 dro6 drosomycin-6 FBgn0052268 Given *all* these genes are related, it would be useful for all these genes to have the same prefix, consistent with what we've done for other gene families in FlyBase. Furthermore, there doesn't appear to be a good reason for the current 'Drs-l'/'Drosomycin-like' gene to be the only one to include 'like' in the official name. I think it makes most sense to consistently use the 'Drs' prefix, rather than a 'dro' prefix, for these reasons: - the 'Drs' gene was the founding member, and *many* published papers have used this symbol for this gene - 'dro' could imply a relationship to a different gene in FlyBase 'Dro' (fullname 'Drosocin'), which I think is also involved in immunity but is not evolutionary related to the drosomycins - our nomenclature rules state that an initial capital letter is used for genes named for their molecular function/orthology rather than a mutant phenotype Here's a suggestion of how these gene symbols/names could be improved: Drs/Drosomycin -> <up>no change</up> Drs-l/Drosomycin-like -> Drsl1/Drosomycin-like 1 dro2/drosomycin-2 -> Drsl2/Drosomycin-like 2 dro3/drosomycin-3 -> Drsl3/Drosomycin-like 3 dro4/drosomycin-4 -> Drsl4/Drosomycin-like 4 dro5/drosomycin-5 -> Drsl5/Drosomycin-like 5 dro6/drosomycin-6 -> Drsl6/Drosomycin-like 6 Please let me know if you have an opinion so this can be taken into account before we proceed with these renames in FlyBase. Thanks, Steven -- Steven Marygold, Ph.D. FlyBase
