Genome-Wide Identification and Expression Analysis of the PIN Auxin Transporter Gene Family in Zanthoxylum armatum DC

Abstract

PIN-formed (PIN) proteins are important auxin carriers that participate in the polar distribution of auxin in plants. In this study, 16 ZaPIN genes were identified from the whole genome of Zanthoxylum armatum DC. The physicochemical properties and structure of PIN proteins were determined, and the gene sequences and promoter regions were analyzed to identify cis-acting elements and conserved motifs. The transcript profiles of ZaPIN genes in different tissues and in response to auxin and gibberellin treatments were also analyzed. A phylogenetic analysis separated the 16 ZaPIN genes into four groups. The ZaPIN genes showed the closest evolutionary relationship to those of Citrus sinensis and the most distant evolutionary relationship to those of Oryza sativa. A cis-element analysis revealed a large number of cis elements in ZaPIN promoter regions related to plant hormones, plant growth and development, and stress stimuli, suggesting that ZaPINs have a wide range of biological activities. Additionally, gene expression profiling revealed that ZaPINs had different expression patterns in nine tissues. Further qRT-PCR analyses revealed that most ZaPINs were upregulated by auxin and gibberellin in young leaves. Our results provide useful information for further structural and functional analyses of the ZaPIN gene family in Z. armatum.

Genome Identification and Expression Profiling of the PIN-Formed Gene Family in Phoebe bournei under Abiotic Stresses

“…Furthermore, the secondary structure prediction of these proteins demonstrated that all PbPINs are composed of α-helices, extended chains, β-sheets, and random coils. The αhelices and random coils represent the major secondary structural elements of the PbPINs, consistent with observations in bamboo pepper [33]. Tertiary structure prediction indicated a high similarity in 3D structure among proteins from different categories, except for PbPIN7, PbPIN9, and PbPIN12.…”

“…Analysis of the physicochemical properties of these proteins revealed that, with the exception of PbPIN9, the theoretical isoelectric points (pI) of the remaining 12 PIN gene family members were all above seven. The analysis of physical and chemical properties showed that most of the PbPIN genes were alkaline amino acids, and each member contained the conserved domain Men_Trans (PF03547) in P. bournei, with consistent results in other plant species such as bamboo pepper [33] and soybean [40]. Moreover, PbPIN7, PbPIN9, and PbPIN12 exhibited relatively shorter amino acid sequences, likely contributing to structural, functional, and property distinctions.…”

“…Sixteen ZaPIN genes have been identified in the entire genome of Zanthoxylum armatum. In young leaves, most of the ZaPINs exhibited up-regulation following stimulation with exogenous auxin and gibberellin [33]. In 2020, a total of 15 PpPINs were identified in Prunus persica.…”

“…In L. chinense, 11 LcPIN genes have been identified, with experimental data suggesting that LcPIN5 and LcPIN8 may play a crucial role in auxin transport in L. chinense stems and leaves under abiotic stresses [45]. Recent studies have indicated the presence of 16 ZaPINs in Z. armatum and 12 VvPINs in V. vinifera, and through stress experiments, it was observed that a majority of these genes responded to hormone stimulation or abiotic stresses in both species [33,46]. Accumulating evidence suggests that PIN genes, as a core part of signal transduction, play a key role in plant coordination and adaptation to multifarious abiotic stresses (Figure 1B).…”

Identification and Expression Analysis of the Ethylene Response Factor Gene Family in Tea Plant (Camellia sinensis)

“…The expression levels (FPKM) of eight different tissues of tea plant (roots, mature leaves, stems, flowers, young leaves, old leaves, terminal buds, and fruits) and the expression levels of tea plant under cold stress were downloaded from the tea plant database (http://tpdb.shengxin.ren/ accessed on 4 September 2022) [40]. The expression levels (FPKM) were calculated with log2 (FPKM + 1) [55] and visualized with TBtools software version 0.665 [41].…”