Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals

Abstract

Abstract:The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.

Genome‐wide identification and expression analysis reveal the potential function of ethylene responsive factor gene family in response to Botrytis cinerea infection and ovule development in grapes (Vitis vinifera L.)

“…The Ka/Ks ratios of tandem or segmental duplicated gene pairs were calculated using the MYN method in the Ka/Ks Calculator 2.0 program (Wu et al . ).…”

Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals

“…The Aux/IAA proteins contain four key domains (Paul et al ; Wu et al ; Luo et al ); domain I recruits TPL/TPR co‐repressors to enhance repression of ARF target genes, domain II facilitates interaction with the TIR1/AFB proteins (Worley et al ; Ramos et al ; Lee et al ), and domains III and IV facilitate interaction with ARF activator proteins and dimerization between Aux/IAA proteins (Ulmasov et al ; Guilfoyle et al ). These domains are sometimes absent, depending on the gene and species (Luo et al ).…”

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

“…There were 29 Aux/IAA family members in Arabidopsis, but not all genes were induced by auxin [67]. Many Aux/IAA genes have also been identi ed in other plants, such as, Eucalyptus grandis [68], Solanum Lycopersicon [69], Cucumis sativus [70], Populus trichocarpa [71], Zea mays [72] and Oryza sativa [73][74]. SAUR genes were consisted of a large multigene family, played crucial roles in regulating plant growth and development [75,76].…”