Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a model

Abstract

Auxin plays key roles in a wide variety of plant activities, including embryo development, leaf formation, phototropism, fruit development and root initiation and development. Auxin/indoleacetic acid (Aux/IAA) genes, encoding short-lived nuclear proteins, are key regulators in the auxin transduction pathway. But how they work is still unknown. In order to conduct a systematic analysis of this gene family in Solanaceae species, a genome-wide search for the homologues of auxin response genes was carried out. Here, 26 and 27 non redundant AUX/IAAs were identified in tomato and potato, respectively. Using tomato as a model, a comprehensive overview of SlIAA gene family is presented, including the gene structures, phylogeny, chromosome locations, conserved motifs and ciselements in promoter sequences. A phylogenetic tree generated from alignments of the predicted protein sequences of 31 OsIAAs, 29 AtIAAs, 31 ZmIAAs, and 26 SlIAAs revealed that these IAAs were clustered into three major groups and ten subgroups. Among them, seven subgroups were present in both monocot and dicot species, which indicated that the major functional diversification within the IAA family predated the monocot/dicot divergence. In contrast, group C and some other subgroups seemed to be species-specific. Quantitative real-time PCR (qRT-PCR) analysis showed that 19 of the 26 SlIAA genes could be detected in all tomato organs/tissues, however, seven of them were specifically expressed in some of tomato tissues. The transcript abundance of 17 SlIAA genes were increased within a few hours when the seedlings were treated with exogenous IAA. However, those of other six SlIAAs were decreased. The results of stress treatments showed that most SIIAA family genes responded to at least one of the three stress treatments, however, they exhibited diverse expression levels under different abiotic stress conditions in tomato seedlings. SlIAA20, SlIAA21 and SlIAA22 were not significantly influenced by stress treatments even though at least one stress-related cis-element was identified in their promoter regions. In conclusion, our comparative analysis provides an insight into the evolution and expression patterns in various tissues and in response to auxin or stresses of the Aux/IAA family members in tomato, which will provide a very useful reference for cloning and functional analysis of each member of AUX/IAA gene family in Solanaceae crops.

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

“…Functional analysis and expression profiling of ARF, GH3 and AUX/IAA genes are helpful to reveal the mechanisms how auxin regulates plant growth and development and responses to environmental changes in a spatio-temporal specific manner. Recently, these three gene families have been widely characterized in plants such as 23 AtARFs, 19 GH3s and 29 AUX/IAAs in Arabidopsis (Remington et al 2004;Okushima et al 2005;Staswick et al 2005), 25 OsARFs, 12 OsGH3 s and 31 OsAUX/IAAs in rice (Jain et al 2006;Mukesh et al 2006;Wang et al 2007), 16 CsARFs, 10 CsGH3 s and 27 CsAUXIN/IAAs in cucumber (Wu et al 2014), 35 ZmARFs, 13 ZmGH3 s and 31 ZmAUX/IAAs in maize (Wang et al 2010;Liu et al 2011;Feng et al 2015) and 17 SlARFs, 15 SlGH3s and 26 SlAUX/IAAs in tomato (Kumar et al 2011(Kumar et al , 2012Wu et al 2012). In this study, 22 CitARFs, 11 CitGH3 s and 26 CitAUX/IAAs have been identified in citrus.…”

“…Due to their potential importance, GH3, ARF and AUX/ IAA gene families have been widely identified and characterized in great number of plant species, such as populus (Kalluri et al 2007;Yang et al 2014b), Medicaga truncatula (Shen et al 2014), soybean (Ha et al 2013), apple (Yuan et al 2013), Vitis vinifera (Wan et al 2014), Cucumis sativus (Gan et al 2013), rice (Jain et al 2006;Wang et al 2007), maize (Wang et al 2010;Liu et al 2011) and tomato (Kumar et al 2011(Kumar et al , 2012Wu et al 2012). However, no data on these gene families are available in citrus.…”

Genome-Wide Identification and Expression Profiling Analysis of the Aux/IAA Gene Family in Medicago truncatula during the Early Phase of Sinorhizobium meliloti Infection

“…The crystal structure analysis revealed that Bem1p (PB1) domain in C-terminal is the special domain for the protein-protein interaction between Aux/IAA and ARF [14]. Moreover, Aux/IAA proteins contain two nuclear localization signals (NLS), which locate Aux/IAA proteins to the nucleus [15], [16].…”

Down-regulation of SlIAA15 in tomato altered stem xylem development and production of volatile compounds in leaf exudates

“…3 In tomato, genome-wide analysis identifies 26 putative AUX/IAA genes. 4 Suppression of SlIAA3 produced auxin and ethylene-related developmental defects, such as reduced apical dominance and exaggerated hook in etiolated seedlings.…”