Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: From algae to angiosperms

Abstract

Introduction: The Indeterminate Domain (IDD) proteins are a plant specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, however the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail. Methods: In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes. Key results: We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, however all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns. Conclusions: IDD were present in the last common ancestor of Streptophyta. On land, IDD duplicated extensively originating ten lineages. Later, IDD were recruited by angiosperms where they diversified greatly in number; C-terminal and expression patterns accompanying important aspects of plant body evolution.This study provides a solid framework of the orthology relations of green land plant IDD transcription factors, thus increasing the accuracy of ortholog identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.