Ethylene biosynthesis in legumes: gene identification and expression during early symbiotic stages

The final steps of ethylene biosynthesis involve the consecutive activity of two enzymes, 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxidase (ACO). These enzymes are encoded by small gene families, which, in the case of legumes, have not been systematically characterized at the level of gene family membership or phylogenetic relationship. Moreover, the absence of consensus nomenclature complicates comparisons within the scientific literature, where authors are addressing the roles of these genes in planta. In this study, we provide a framework in which the ACS and ACO gene family members of several legume species, including the two model legumes Medicago truncatula and Lotus japonicus, were systematically annotated, named, and analysed relative to genes from other dicot and monocot model species. A combination of phylogenetic and reciprocal BLAST analyses was used to identify evolutionary relationships among genes, including the identification of orthologous relationships that can inform hypotheses about function. Given the role of ethylene as a negative regulator of the legume-rhizobium symbiosis, we queried publicly available RNA-seq expression datasets to obtain an overview of the expression profiles of these genes in the interaction between M. truncatula and its nitrogen-fixing microsymbiont. The resulting evolutionary framework, as well as structural and expression analyses, are intended to facilitate ongoing functional studies in legumes.