Wenxiang Zhang^1,2, Wenning Cui¹, Juan Huang³, Zhangen Lu¹, Kuijing Liang¹, Lingbao Wang^1,2, Shanshan Wei^1,2, Liran Shi¹, Huifen Li¹, Xiaoli Guo^1,2,*, Jianhui Ma^4,*

Phyton-International Journal of Experimental Botany, Vol.94, No.12, pp. 3893-3912, 2025, DOI:10.32604/phyton.2025.073736 - 29 December 2025

Abstract UDP-glycosyltransferases (UGTs) play essential roles in plant secondary metabolism and stress responses, yet their composition and functions in Sorghum bicolor, a model C4 plant, remain inadequately characterized. This study identified 196 SbUGT genes distributed across all 10 chromosomes and classified them into 16 subfamilies (A–P) through phylogenetic analysis. Among these, 61.2% were intronless, and 10 conserved motifs, including the UGT-specific PSPG box, were identified. Synteny analysis using MCScanX revealed 12 segmental duplication events and conserved syntenic relationships with other Poaceae species (rice, maize, and barley). Promoter analysis uncovered 125 distinct cis-acting elements, predominantly associated with stress and… More >

Mingxin Zhong^1,#, Yuanyuan Zhang^1,#, Xinlei Guo¹, Bainian Zhang², Chengjia Tan¹, Zhuo Xu¹, Xin Hu¹, Daren Feng³, Zhenpeng Xi⁴, Qian Wang^1,*, Hui Tian^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.10, pp. 3061-3084, 2025, DOI:10.32604/phyton.2025.070560 - 29 October 2025

Abstract Magnolia officinalis is a perennial deciduous tree that has medicinal properties. The AP2/ERF gene family has a number of roles in long-term growth and metabolism. The expression of this function varies with the growth period. In this work, based on the transcriptome data of Magnolia officinalis, the complete coding gene of Magnolia officinalis was obtained, and the corresponding protein sequence was retrieved from NCBI and compared with the model plant Arabidopsis thaliana. After screening, 75 protein sequences from the AP2/ERF gene family were identified and called MoAP2/ERF1–MoAP2/ERF75, followed by bioinformatics analysis. 75 AP2/ERF gene families were found and classified into four… More >

Abdil Hakan Eren^*

Phyton-International Journal of Experimental Botany, Vol.94, No.10, pp. 3085-3107, 2025, DOI:10.32604/phyton.2025.069506 - 29 October 2025

Abstract The FAR1-related sequence (FAR1) gene family consists of transcription factors that originated from transposases and is crucial for light signaling and stress adaptation in plants. Despite the recognized importance of FAR1 genes in model organisms, their genomic architecture, structural variability, and expression patterns in Phaseolus vulgaris have yet to be investigated. This study offers the inaugural comprehensive genome-wide identification and characterization of the FAR1 gene family in P. vulgaris. A total of 27 PvulFAR1 genes were identified, and their chromosomal distribution, gene structures, conserved domains, and phylogenetic relationships were analyzed systematically. The promoter regions of these genes were discovered… More >

Zhong Ren^1,2,3,#, Shuiming Zhang^1,#, Yuzhi Fei¹, Zhu Chen³, Yue Zhao³, Xin Meng³, Hongfei Zhao^2,*, Jie Ren^3,*

Phyton-International Journal of Experimental Botany, Vol.94, No.9, pp. 2927-2947, 2025, DOI:10.32604/phyton.2025.067310 - 30 September 2025

Abstract Acer paxii belongs to the evergreen species of Acer, but it exhibits a unique feature of reddish leaves in fall in subtropical regions. Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research, molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii. This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii. As a result, 123 ApAP2/ERFs were obtained. Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies. The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their… More >

Yuxin Zhao, Zhanxiang Tan, Yuying Li, Kaiyue Zhang, Lili Guo^*, Xiaogai Hou^*

Phyton-International Journal of Experimental Botany, Vol.94, No.4, pp. 1159-1176, 2025, DOI:10.32604/phyton.2025.063737 - 30 April 2025

Abstract Receptor-like cytoplasmic kinases (RLCKs) play a crucial role in the physiological processes of plant growth and development and stress response. To elucidate the characteristics and functions of the PBL gene family in tree peonies, the whole genome identification of PBL family members in tree peonies was conducted using a bioinformatics approach based on the published Arabidopsis thaliana PBL protein sequence. A total of 51 PoPBL members were identified, which were distributed unevenly on five chromosomes in the tree peony. PoPBL proteins were localized in the nucleus, cytoplasm, chloroplasts, and mitochondria, with most members of the same clade… More >

Yuan Wang¹, Tianle Zhang¹, Xinfeng Zeng¹, Jiale Liu¹, Siyu Li¹, Siyu Yang¹, Shengnan Zhao¹, Abdullah Shah², Muhammad Saif Ullah², Guohui Qi^1,*, Peng Jia^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.12, pp. 3331-3346, 2024, DOI:10.32604/phyton.2024.059402 - 31 December 2024

Abstract LONELY GUY (LOG) is a pivotal cytokinin-activating enzyme that plays an important role in plant growth, development, and stress responses. Walnut (Juglans regia), an important woody oilseed species, has not yet undergone systematic identification of its LOG gene family. In this study, we identified 17 JrLOG genes in the walnut genome, which are unevenly distributed across 11 chromosomes. JrLOG gene expansion was primarily driven by gene duplication, along with purifying selection. Members of the JrLOG family were categorized into five groups, each exhibiting analogous gene structures, featured motifs, and conserved domains. Transcriptome and quantitative real-time PCR analyses More >

Abdil Hakan Eren^*

Phyton-International Journal of Experimental Botany, Vol.93, No.11, pp. 2883-2907, 2024, DOI:10.32604/phyton.2024.058627 - 30 November 2024

Abstract Background: Aldehyde dehydrogenase (ALDH) genes constitute an important family of supergenes that play key roles in synthesizing various biomolecules and maintaining cellular homeostasis by catalyzing the oxidation of aldehyde products. With climate change increasing the exposure of plants to abiotic stresses such as salt and drought, ALDH genes have been identified as important contributors to stress tolerance. In particular, they help to reduce stress-induced lipid peroxidation. Objectives: This study aims to identify and characterize members of the ALDH supergene family in Phaseolus vulgaris through a genome-wide bioinformatic analysis and investigate their role in response to abiotic stressors such… More >

Guanpeng Huang^1,#, Ti Wu^1,2,#, Yinjie Zheng³, Qiyun Gu², Qiaobin Chen², Shoukai Lin^2,*, Jincheng Wu^2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.11, pp. 2715-2735, 2024, DOI:10.32604/phyton.2024.056484 - 30 November 2024

Abstract Loquat (Eriobotrya japonica Lindl.), a rare fruit native to China, has a long history of cultivation in China. Low temperature is the key factor restricting loquat growth and severely affects yield. Low temperature induces the regeneration and metabolism of reduced glutathione (GSH) to alleviate stress damage via the participation of glutathione S-transferases (GSTs) in plants. In this study, 16 GSTs were identified from the loquat genome according to their protein sequence similarity with Arabidopsis GSTs. On the basis of domain characteristics and phylogenetic analysis of AtGSTs, these EjGSTs can be divided into 4 subclasses: Phi, Theta, Tau… More >

Zhenbing Qiao^1,2, Mengyun Chen^1,2, Wenjun Ma^1,2, Juan Zhao^1,2, Jiaju Zhu^1,2, Kaikai Zhu^1,2, Pengpeng Tan^1,2, Fangren Peng^1,2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.9, pp. 2349-2365, 2024, DOI:10.32604/phyton.2024.056655 - 30 September 2024

Abstract Ammonium nitrogen (NH₄⁺-N) is one of the main forms of nitrogen absorbed and utilized by plants, and mastering the regulatory mechanism of plant ammonium assimilation is a key way to improve the efficiency of plant nitrogen utilization. Glutamine synthetase (GS) and glutamate synthase (GOGAT), two key enzymes for ammonium assimilation, have rarely been studied in pecan. In this study, GS and GOGAT family members of pecan were identified and analyzed using bioinformatics methods. The results indicated that 6 GS and 4 GOGAT genes were identified. The cis-acting elements can be broadly categorized into light-responsive, hormone-responsive, and stress-responsive elements.… More >

Dongxue Su¹, Jiarui Zheng¹, Yuwei Yi¹, Shuyuan Zhang¹, Luxin Feng¹, Danzeng Quzhen², De Qiong³, Weiwei Zhang¹, Qijian Wang¹, Feng Xu^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.9, pp. 2317-2337, 2024, DOI:10.32604/phyton.2024.055350 - 30 September 2024

Abstract The multifaceted roles of MYB transcriptional regulators are pivotal in orchestrating the complex processes of secondary metabolism, stress tolerance mechanisms, and life cycle progression and development. This study extensively examined the JrMYB genes using whole genome and transcriptomic data, focusing on identifying putative MYB genes associated with fatty acid metabolism. 126 MYB genes were identified within the walnut genome, characterized by hydrophilic proteins spanning lengths ranging from 78 to 1890 base pairs. Analysis of cis-acting elements within the promoter regions of MYB genes revealed many elements linked to cell development, environmental stress, and phytohormones. Transcriptomic data was utilized… More > Graphic Abstract