Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses

Abstract

16Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth 17 and development. Previous studies focusing genes from limited number of species were unable to uncover the 18 evolutionary trajectory of this family. Here, more than 3,500 ARFs collected from plant genomes and transcriptomes 19 covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin 20 and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-21 group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply 22 conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting 23 distinct groups. Recurrent duplication events, such as those that occurred in seed plant, angiosperms, core eudicots and 24 grasses contributed the expansion of ARF genes which facilitated functional diversification. Ancestral transposition 25 activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network 26 analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may 27 have accelerated the functional diversification process of paralogues. Our study provides insights into the evolution of 28 ARFs which will enhance our current understandings for this important transcription factor family. 29 30

Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes

“…AUXIN RESPONSE FACTORs (ARFs), of which we found one in locus 7_14.52, are transcription factors mediating auxin-induced gene expression (Die et al 2018 ; Gao et al 2019 ; Gomes and Scortecci 2021 ). One effect of auxin is its stimulation of cell elongation through transcriptional changes leading to increased cell wall acidification and extensibility, allowing for cell elongation (Arsuffi and Braybrook, 2018 ; Majda and Robert 2018 ; Wang et al 2020b ).…”

Auxin and its role in plant development: structure, signalling, regulation and response mechanisms

“…Therefore, all auxin transport proteins are stable through an auxin concentration gradient. These are regulated by means of gene expression and the subcellular localization of the carrier proteins in response to the perception of environmental signals (Leyser, 2018;Gao et al, 2019;Sun et al, 2019).…”

“…Auxin concentrations control the expression of several genes through interaction with the ubiquitin complex (regulatory particles), with transcription factors capable of activating or repressing gene expression, including auxin response factor (ARF) and AUX/IAA repressors (Gao et al, 2019). In this molecular mechanism of action, members of the F-box TIR1/ AFB family of proteins act as auxin receptors (Leyser, 2018;Zhang et al, 2019).…”

“…The repressor proteins are composed of four highly conserved domains, including domain I, which contains an LxLxL motif (where 'L' designates leucine, 'x' corresponds to other amino acids) with amphiphilic repression at its N-terminus (Fig. 4) (Gao et al, 2019). This is essential for the recruitment of the TOPLESS (TPL)/TPL-RELATED transcriptional co-repressor, which has the ability to block the action of ARFs on target gene transcripts (Choi et al, 2018).…”

Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

“…To visualize patterns of an entire syntenic relationship from multigene families across multiple genomes, a microsynteny network analysis was recently proposed. This approach allows a rapid analysis and visualization of synteny relationships and obtains new knowledge from it about the evolutionary history of a target gene family [ 43 , 45 , 46 , 49 ]. In this study, a phylogenomic analysis was carried out on 854 proteins from the NRT2 family and 299 proteins from the NRT3 family across 132 plant ( Sensu lato ) genomes.…”