Abstract
Understanding the functional basis of auxin homeostasis requires knowledge about auxin biosynthesis, auxin transport and auxin catabolism genes, which is not always directly available despite the recent whole-genome sequencing of many plant species. Through sequence homology searches and phylogenetic analyses on a selection of 11 plant species with high-quality genome annotation, we identified the putative gene homologs involved in auxin biosynthesis, auxin catabolism and auxin transport pathways in carnation (Dianthus caryophyllus L.). To deepen our knowledge of the regulatory events underlying auxin-mediated adventitious root formation in carnation stem cuttings, we used RNA-sequencing data to confirm the expression profiles of some auxin homeostasis genes during the rooting of two carnation cultivars with different rooting behaviors. We also confirmed the presence of several auxin-related metabolites in the stem cutting tissues. Our findings offer a comprehensive overview of auxin homeostasis genes in carnation and provide a solid foundation for further experiments investigating the role of auxin homeostasis in the regulation of adventitious root formation in carnation.
Highlights
In many plant species, the vegetative propagation of elite lines depends on the rooting ability of stem cuttings, a process affected by complex interactions between nutrients and phytohormone levels, in which auxin plays an essential role [1, 2]
Identification of genes involved in auxin biosynthesis in carnation stem cuttings In this work, orthologous genes coding putative auxin biosynthetic, transport and catabolic proteins in the carnation genome were identified with previously published annotated genomes and transcriptome sequences [6, 30] by the following methods: i) identification of the reciprocal best-hits (RBH) between carnation and Arabidopsis protein sequences, ii) construction of maximum-likelihood trees built with homologous protein sequences of selected plant species, and iii) analysis of gene expression profiles from previous RNA-seq experiments
Trp is converted to indole-3-pyruvic acid (IPyA) by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) and TRYPTOPHAN AMINOTRANSFERASE RELATED (TAR) enzymes, and the YUCCA (YUC) family of flavin monooxygenases converts IPyA to Indole-3-acetic acid (IAA) [34,35,36]
Summary
The vegetative propagation of elite lines depends on the rooting ability of stem cuttings, a process affected by complex interactions between nutrients and phytohormone levels, in which auxin plays an essential role [1, 2]. Auxin homeostasis genes in carnation number of molecular, histological and physiological markers to initiate the genetic dissection of adventitious root formation in this species [6, 7]. The conversion of Trp to IAA occurs via different pathways named after its downstream intermediate, namely, the indole3-acetaldoxime (IAOx), indole-3-pyruvic acid (IPyA) and indol-3-acetamide (IAM) pathways [9, 11]. The endogenous IAOx pathway has only been identified in some Brassicaceae species [12] indicating that this pathway is not common in plants and is absent in carnation
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