When is a Hox gene not a Hox gene The importance of gene nomenclature

david e. k. ferrier gene classification is an essential precursor to evo-devo

A sensible classification of developmental control genes and an understanding of their phylogeny are essential to any endeavour of molecular evolutionary developmental biology (evo-devo) or comparative genomics, since it is crucial that the structure, expression and function of orthologous genes are being compared between taxa. This is particularly true for the homeobox genes, for which there are confusing and conflicting names and classifications that hinder our investigation and understanding of their evolution and their role in animal evo-devo (I will restrict myself here to consideration of animal homeobox genes). Since these genes are central components of most developmental processes, are important indicators of major transitions in animal genome evolution, and are often found to be targets and/or agents of the evolution of development, then we must continue to improve and coordinate our classifications of these genes as more data become available from a greater array of taxa in this age of genomics.

conventions

Animal homeobox genes can be divided, on the basis of their sequence similarities, into two major classes (ANTP and PRD) along with several minor classes (TALE, LIM, POU, ZF, cut, prox, HNF and SIX; B├╝rglin 2005, Edvardsen et al. 2005, Holland and Takahashi 2005). It is in the

Evolving Pathways: Key Themes in Evolutionary Developmental Biology, ed. Alessandro Minelli and Giuseppe Fusco. Published by Cambridge University Press. # Cambridge University Press 2008.

Table 10.1 Homeobox gene families in the ANTP-class. Human names are taken from the HUGO nomenclature website (www.gene.ucl.ac. uk/nomenclature/), with old names and synonyms given in brackets. Drosophila gene names are taken from Flybase (http://flybase.bio.indiana.edu/), along with synonyms. The 'Other animals' column provides the names of orthologues from other species that are relevant to the naming of the family. The prefix 'Amphi' denotes genes from amphioxus (Branchiostoma floridae), CapI = Capitella I (polychaete worm), Csa = Cupiennius salei (spider), Dti = Discocelis tigrina (flatworm), Gga = Gallusgallus (chicken), Odi = Oikopleura dioica (appendicularian urochordate), Nve or Nv = Nematostella vectensis (sea anemone), Nvi = Nereis virens (polychaete worm), Pdu = Platynereis dumerilii (polychaete worm), Pst = Phascolion strombus (sipunculan worm), Sko = Saccoglossus kowalevskii (hemichordate), Sp = Strongylocentrotus purpuratus (sea urchin), Tricho (and Ta of NotTa gene) = Trichoplax adhaerens (placozoan), X or Xl = Xenopus laevis (frog). Double-headed arrows demarcate groups and subclasses of gene families. Black represents the Hox and ParaHox clusters, white is the NK cluster genes (see Luke et al (2003) and Burglin

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