Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/IAA and ARF Gene Families in Populus simonii

Abstract

The auxin/indole-3-acetic acid (Aux/IAA) and auxin response factor (ARF) genes are two crucial gene families in the plant auxin signaling pathway. Nonetheless, there is limited knowledge regarding the Aux/IAA and ARF gene families in Populus simonii. In this study, we first identified 33 putative PsIAAs and 35 PsARFs in the Populus simonii genome. Analysis of chromosomal location showed that the PsIAAs and PsARFs were distributed unevenly across 17 chromosomes, with the greatest abundance observed on chromosomes 2. Furthermore, based on the homology of PsIAAs and PsARFs, two phylogenetic trees were constructed, classifying 33 PsIAAs and 35 PsARFs into three subgroups each. Five pairs of PsIAA genes were identified as the outcome of tandem duplication, but no tandem repeat gene pairs were found in the PsARF family. The expression profiling of PsIAAs and PsARFs revealed that several genes exhibited upregulation in different tissues and under various stress conditions, indicating their potential key roles in plant development and stress responses. The variance in expression patterns of specific PsIAAs and PsARFs was corroborated through RT-qPCR analysis. Most importantly, we instituted that the PsIAA7 gene, functioning as a central hub, exhibits interactions with numerous Aux/IAA and ARF proteins. Furthermore, subcellular localization findings indicate that PsIAA7 functions as a protein localized within the nucleus. To conclude, the in-depth analysis provided in this study will contribute significantly to advancing our knowledge of the roles played by PsIAA and PsARF families in both the development of P. simonii tissue and its responses to stress. The insights gained will serve as a valuable asset for further inquiries into the biological functions of these gene families.

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

“…In order to identify the DOF family members within the P. simonii genome, we obtained the full DOF protein sequence of A. thaliana from the Tair database ( https://www.arabidopsis.org/ ). Moreover, we constructed a high-quality reference genome of P. simonii , featuring a contig N50 of 24 Mb ( Cai et al., 2023 ). Initially, we used the BlastP program (e-value, 1 × e −5 ) in Tbtools software (v2.080) to identify PSDOF protein sequences, employing A. thaliana DOF proteins as query sequences ( Chen et al., 2020 ).…”

“…RNA sequencing was conducted on various tissues, including terminal buds (NT), axillary buds (NB), leaves (NL), stems (NS), phloem (NP), and roots (NR) of P. simonii , to assess the expression level of PSDOF genes, more details about the plant materials and sample collection can be found in Cai et al., 2023 . Subsequently, the expression levels were graphically depicted using heat maps generated with Tbtools software.…”

Comprehensive Overview of <i>Populus</i> <i>simonii</i> Research in the Recent Years

“…Wang [43] found 10 YABBY family genes expressed under three abiotic stresses: heat, salt and osmosis in poplar (P. simonii × P. nigra). Kewei Cai [44] identified 33 potential PsIAAs and 35 PsARFs in the entire genome of P. microphylla. Among them, the PsIAA7 gene is a central hub and interacts with many Aux/ IAA and ARF proteins.…”

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

“…LcARFs in Litchi chinensis are expressed in various developmental processes, particularly during flower formation and fruit abscission [16]. Furthermore, the ARF gene family has been studied at the whole-genome level in many other plant species [7], and a large number of results have demonstrated the high diversity and abundance of ARF genes in different plant species [17][18][19][20][21]. Therefore, in-depth studies on plant ARF transcription factors contribute to a more comprehensive understanding of the growth and developmental mechanisms in plants mediated by auxin [22].…”