Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that several Aux/IAA and ARF subgroups have differentially expanded or contracted between the two dicotyledonous plants. Activator ARF genes were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression.The present study examines the extent of conservation and divergence in the structure and evolution of Populus Aux/IAA and ARF gene families with respect to Arabidopsis and rice. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.Aux/IAAs are auxin response genes that code for nuclear localized proteins [1]. Aux/IAA proteins generally have four characteristic domains; an N-terminal repression domain, an adjacent domain involved in protein stability, and two C-terminal domains (CTD), III and IV, through which Aux/IAA proteins form homo- and heterodimers with Aux/IAA or ARF proteins [2]. Most ARF proteins contain an N-terminal B3-like DNA binding domain that includes an ARF family-specific domain, a variable middle region that confers activator or repressor activity, and domains III and IV that are also found in Aux/IAA [3]. ARF proteins are capable, irrespective of auxin status, of binding to auxin responsive cis-elements (AuxRE; TGTCTC) present upstream to the coding sequence of auxin responsive genes [4,5]. Aux/IAA proteins bind to the DNA-bound ARF partner proteins via domains III and IV and repress ARF activity. In the auxin activated status, Aux/IAA proteins are ubiquitinated via interactions with the auxin-modified SCFTIR1compl